From 7441f1dbd77b09f6170858795bc7deea6280b972 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 28 Jul 2017 17:47:19 +0200 Subject: [PATCH 001/162] build: Make Guile-Git a hard requirement. * configure.ac: Error out when (git) is missing. * doc/guix.texi (Requirements): Mention Guile-Git. * Makefile.am (MODULES): Add guix/git.scm unconditionally. --- Makefile.am | 8 +------- configure.ac | 10 ++++++---- doc/guix.texi | 4 ++++ 3 files changed, 11 insertions(+), 11 deletions(-) diff --git a/Makefile.am b/Makefile.am index 5888bc0266..0a7e375c29 100644 --- a/Makefile.am +++ b/Makefile.am @@ -66,6 +66,7 @@ MODULES = \ guix/gnu-maintenance.scm \ guix/upstream.scm \ guix/licenses.scm \ + guix/git.scm \ guix/graph.scm \ guix/cache.scm \ guix/cve.scm \ @@ -207,13 +208,6 @@ MODULES += \ endif HAVE_GUILE_SSH -if HAVE_GUILE_GIT - -MODULES += \ - guix/git.scm - -endif HAVE_GUILE_GIT - if BUILD_DAEMON_OFFLOAD MODULES += \ diff --git a/configure.ac b/configure.ac index 2b75c900cc..9ad7598f8b 100644 --- a/configure.ac +++ b/configure.ac @@ -100,14 +100,16 @@ if test "x$have_gnutls" != "xyes"; then AC_MSG_ERROR([The Guile bindings of GnuTLS are missing; please install them.]) fi +dnl Check for Guile-Git. +GUILE_MODULE_AVAILABLE([have_guile_git], [(git)]) +if test "x$have_guile_git" != "xyes"; then + AC_MSG_ERROR([Guile-Git is missing; please install it.]) +fi + dnl Guile-JSON is used in various places. GUILE_MODULE_AVAILABLE([have_guile_json], [(json)]) AM_CONDITIONAL([HAVE_GUILE_JSON], [test "x$have_guile_json" = "xyes"]) -dnl Check for Guile-Git. -GUILE_MODULE_AVAILABLE([have_guile_git], [(git)]) -AM_CONDITIONAL([HAVE_GUILE_GIT], [test "x$have_guile_git" = "xyes"]) - dnl Make sure we have a full-fledged Guile. GUIX_ASSERT_GUILE_FEATURES([regex posix socket net-db threads]) diff --git a/doc/guix.texi b/doc/guix.texi index 6b4b19d0cf..7957565e85 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -580,6 +580,10 @@ later, including 2.2.x; @uref{http://gnutls.org/, GnuTLS}, specifically its Guile bindings (@pxref{Guile Preparations, how to install the GnuTLS bindings for Guile,, gnutls-guile, GnuTLS-Guile}); +@item +@c FIXME: Specify a version number once a release has been made. +@uref{https://gitlab.com/guile-git/guile-git, Guile-Git}, from August +2017 or later; @item @url{http://www.gnu.org/software/make/, GNU Make}. @end itemize From 59a16275189f55ddd692b0ea5b415c706fa1fd69 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 28 Jul 2017 17:38:19 +0200 Subject: [PATCH 002/162] pull: Fetch source code from Git. * guix/scripts/pull.scm (%snapshot-url, with-environment-variable) (with-PATH): Remove. (ensure-guile-git!): New procedure. (%repository-url): New variable. (%default-options): Add 'repository-url' and 'ref'. (show-help, %options): Add '--commit' and '--url'. (temporary-directory, first-directory, interned-then-deleted) (unpack): Remove. (build-from-source): Rename 'tarball' to 'source'. Remove call to 'unpack'. (build-and-install): Rename 'tarball' to 'source'. (honor-lets-encrypt-certificates!, report-git-error): New procedures. (with-git-error-handling): New macro. (guix-pull)[fetch-tarball]: Remove. Wrap body in 'with-git-error-handling'. Rewrite to use 'latest-repository-commit'. * build-aux/build-self.scm (build): Print an error message and exit when GUILE-GIT is #f. * doc/guix.texi (Invoking guix pull): Mention Git. Document '--commit' and '--branch'. --- build-aux/build-self.scm | 17 +++ doc/guix.texi | 25 ++--- guix/scripts/pull.scm | 237 +++++++++++++++++++++------------------ 3 files changed, 153 insertions(+), 126 deletions(-) diff --git a/build-aux/build-self.scm b/build-aux/build-self.scm index 8fb9af23ca..4933e02712 100644 --- a/build-aux/build-self.scm +++ b/build-aux/build-self.scm @@ -224,6 +224,23 @@ files." (current-error-port) (%make-void-port "w"))))) + (unless guile-git + ;; XXX: Guix before February 2017 lacks a 'guile-git' package altogether. + ;; If we try to upgrade anyway, the logic in (guix scripts pull) will not + ;; build (guix git), which will leave us with an unusable 'guix pull'. To + ;; avoid that, fail early. + (format (current-error-port) + "\ +Your installation is too old and lacks a '~a' package. +Please upgrade to an intermediate version first, for instance with: + + guix pull --url=https://git.savannah.gnu.org/cgit/guix.git/snapshot/v0.13.0.tar.gz +\n" + (match (effective-version) + ("2.0" "guile2.0-git") + (_ "guile-git"))) + (exit 1)) + (mlet %store-monad ((guile (guile-for-build))) (gexp->derivation "guix-latest" builder #:modules '((guix build pull) diff --git a/doc/guix.texi b/doc/guix.texi index 7957565e85..0ea677387b 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -2477,7 +2477,8 @@ Packages are installed or upgraded to the latest version available in the distribution currently available on your local machine. To update that distribution, along with the Guix tools, you must run @command{guix pull}: the command downloads the latest Guix source code and package -descriptions, and deploys it. +descriptions, and deploys it. Source code is downloaded from a +@uref{https://git-scm.com, Git} repository. On completion, @command{guix package} will use packages and package versions from this just-retrieved copy of Guix. Not only that, but all @@ -2503,24 +2504,18 @@ but it supports the following options: Produce verbose output, writing build logs to the standard error output. @item --url=@var{url} -Download the source tarball of Guix from @var{url}. +Download Guix from the Git repository at @var{url}. -By default, the tarball is taken from its canonical address at +By default, the source is taken from its canonical Git repository at @code{gnu.org}, for the stable branch of Guix. -With some Git servers, this can be used to deploy any version of Guix. -For example, to download and deploy version 0.12.0 of Guix from the -canonical Git repo: +@item --commit=@var{commit} +Deploy @var{commit}, a valid Git commit ID represented as a hexadecimal +string. -@example -guix pull --url=https://git.savannah.gnu.org/cgit/guix.git/snapshot/v0.12.0.tar.gz -@end example - -It can also be used to deploy arbitrary Git revisions: - -@example -guix pull --url=https://git.savannah.gnu.org/cgit/guix.git/snapshot/74d862e8a.tar.gz -@end example +@item --branch=@var{branch} +Deploy the tip of @var{branch}, the name of a Git branch available on +the repository at @var{url}. @item --bootstrap Use the bootstrap Guile to build the latest Guix. This option is only diff --git a/guix/scripts/pull.scm b/guix/scripts/pull.scm index 58b87d4df4..e3b07e08b1 100644 --- a/guix/scripts/pull.scm +++ b/guix/scripts/pull.scm @@ -41,6 +41,7 @@ #:use-module (gnu packages compression) #:use-module (gnu packages gnupg) #:use-module (srfi srfi-1) + #:use-module (srfi srfi-11) #:use-module (srfi srfi-34) #:use-module (srfi srfi-35) #:use-module (srfi srfi-37) @@ -48,23 +49,39 @@ #:use-module (ice-9 match) #:export (guix-pull)) -(define %snapshot-url - ;; "http://hydra.gnu.org/job/guix/master/tarball/latest/download" - "https://git.savannah.gnu.org/cgit/guix.git/snapshot/master.tar.gz" - ) +(module-autoload! (resolve-module '(guix scripts pull)) + '(git) '(git-error? set-tls-certificate-locations!) + '(guix git) '(latest-repository-commit)) -(define-syntax-rule (with-environment-variable variable value body ...) - (let ((original (getenv variable))) - (dynamic-wind - (lambda () - (setenv variable value)) - (lambda () - body ...) - (lambda () - (setenv variable original))))) +(define (ensure-guile-git!) + ;; Previously Guile-Git was not a prerequisite. Thus, someone running 'guix + ;; pull' on an old installation may be lacking Guile-Git. To address this, + ;; we autoload things that depend on Guile-Git and check in the entry point + ;; whether Guile-Git is available. + ;; + ;; TODO: Remove this hack when Guile-Git is widespread or enforced. -(define-syntax-rule (with-PATH value body ...) - (with-environment-variable "PATH" value body ...)) + (unless (false-if-exception (resolve-interface '(git))) + (leave (G_ "Guile-Git is missing but it is now required by 'guix pull'. +Install it by running: + + guix package -i ~a + export GUILE_LOAD_PATH=$HOME/.guix-profile/share/guile/site/~a:$GUILE_LOAD_PATH + export GUILE_LOAD_COMPILED_PATH=$HOME/.guix-profile/lib/guile/~a/site-ccache:$GUILE_LOAD_COMPILED_PATH +\n") + (match (effective-version) + ("2.0" "guile2.0-git") + (_ "guile-git")) + (effective-version) + (effective-version))) + + ;; XXX: For unclear reasons this is needed for + ;; 'set-tls-certificate-locations!'. + (module-use! (resolve-module '(guix scripts pull)) + (resolve-interface '(git)))) + +(define %repository-url + "https://git.savannah.gnu.org/git/guix.git") ;;; @@ -73,7 +90,8 @@ (define %default-options ;; Alist of default option values. - `((tarball-url . ,%snapshot-url) + `((repository-url . ,%repository-url) + (ref . (branch . "origin/master")) (system . ,(%current-system)) (substitutes? . #t) (graft? . #t) @@ -86,7 +104,11 @@ Download and deploy the latest version of Guix.\n")) (display (G_ " --verbose produce verbose output")) (display (G_ " - --url=URL download the Guix tarball from URL")) + --url=URL download from the Git repository at URL")) + (display (G_ " + --commit=COMMIT download the specified COMMIT")) + (display (G_ " + --branch=BRANCH download the tip of the specified BRANCH")) (display (G_ " --bootstrap use the bootstrap Guile to build the new Guix")) (newline) @@ -105,8 +127,15 @@ Download and deploy the latest version of Guix.\n")) (alist-cons 'verbose? #t result))) (option '("url") #t #f (lambda (opt name arg result) - (alist-cons 'tarball-url arg - (alist-delete 'tarball-url result)))) + (alist-cons 'repository-url arg + (alist-delete 'repository-url result)))) + (option '("commit") #t #f + (lambda (opt name arg result) + (alist-cons 'ref `(commit . ,arg) result))) + (option '("branch") #t #f + (lambda (opt name arg result) + (alist-cons 'ref `(branch . ,(string-append "origin/" arg)) + result))) (option '(#\n "dry-run") #f #f (lambda (opt name arg result) (alist-cons 'dry-run? #t (alist-cons 'graft? #f result)))) @@ -129,81 +158,28 @@ Download and deploy the latest version of Guix.\n")) (define indirect-root-added (store-lift add-indirect-root)) -(define (temporary-directory) - "Make a temporary directory and return its name." - (let ((name (tmpnam))) - (mkdir name) - (chmod name #o700) - name)) - -(define (first-directory directory) - "Return a the name of the first file found under DIRECTORY." - (match (scandir directory - (lambda (name) - (and (not (member name '("." ".."))) - (file-is-directory? name)))) - ((directory) - directory) - (x - (raise (condition - (&message - (message "tarball did not produce a single source directory"))))))) - -(define (interned-then-deleted directory name) - "Add DIRECTORY to the store under NAME, and delete it. Return the resulting -store file name." - (mlet %store-monad ((result (interned-file directory name - #:recursive? #t))) - (delete-file-recursively directory) - (return result))) - -(define (unpack tarball) - "Return the name of the directory where TARBALL has been unpacked." - (mlet* %store-monad ((format -> (lift format %store-monad)) - (tar (package->derivation tar)) - (gzip (package->derivation gzip))) - (mbegin %store-monad - (what-to-build (list tar gzip)) - (built-derivations (list tar gzip)) - (format #t (G_ "unpacking '~a'...~%") tarball) - - (let ((source (temporary-directory))) - (with-directory-excursion source - (with-PATH (string-append (derivation->output-path gzip) "/bin") - (unless (zero? (system* (string-append (derivation->output-path tar) - "/bin/tar") - "xf" tarball)) - (raise (condition - (&message (message "failed to unpack source code")))))) - - (interned-then-deleted (string-append source "/" - (first-directory source)) - "guix-source")))))) - (define %self-build-file ;; The file containing code to build Guix. This serves the same purpose as ;; a makefile, and, similarly, is intended to always keep this name. "build-aux/build-self.scm") -(define* (build-from-source tarball #:key verbose?) - "Return a derivation to build Guix from TARBALL, using the self-build script +(define* (build-from-source source #:key verbose?) + "Return a derivation to build Guix from SOURCE, using the self-build script contained therein." ;; Running the self-build script makes it easier to update the build ;; procedure: the self-build script of the Guix-to-be-installed contains the ;; right dependencies, build procedure, etc., which the Guix-in-use may not ;; be know. - (mlet* %store-monad ((source (unpack tarball)) - (script -> (string-append source "/" - %self-build-file)) - (build -> (primitive-load script))) + (let* ((script (string-append source "/" %self-build-file)) + (build (primitive-load script))) ;; BUILD must be a monadic procedure of at least one argument: the source ;; tree. (build source #:verbose? verbose?))) -(define* (build-and-install tarball config-dir +(define* (build-and-install source config-dir #:key verbose?) - "Build the tool from TARBALL, and install it in CONFIG-DIR." - (mlet* %store-monad ((source (build-from-source tarball + "Build the tool from SOURCE, and install it in CONFIG-DIR." + (mlet* %store-monad ((source (build-from-source source #:verbose? verbose?)) (source-dir -> (derivation->output-path source)) (to-do? (what-to-build (list source))) @@ -227,44 +203,83 @@ contained therein." (return #t)))) (leave (G_ "failed to update Guix, check the build log~%"))))) +(define (honor-lets-encrypt-certificates! store) + "Tell Guile-Git to use the Let's Encrypt certificates." + (let* ((drv (package-derivation store le-certs)) + (certs (string-append (derivation->output-path drv) + "/etc/ssl/certs"))) + (build-derivations store (list drv)) + + ;; In the past Guile-Git would not provide this procedure. + (if (module-defined? (resolve-interface '(git)) + 'set-tls-certificate-locations!) + (set-tls-certificate-locations! certs) + (begin + ;; In this case we end up using whichever certificates OpenSSL + ;; chooses to use: $SSL_CERT_FILE, $SSL_CERT_DIR, or /etc/ssl/certs. + (warning (G_ "cannot enforce use of the Let's Encrypt \ +certificates~%")) + (warning (G_ "please upgrade Guile-Git~%")))))) + +(define (report-git-error error) + "Report the given Guile-Git error." + ;; Prior to Guile-Git commit b6b2760c2fd6dfaa5c0fedb43eeaff06166b3134, + ;; errors would be represented by integers. + (match error + ((? integer? error) ;old Guile-Git + (leave (G_ "Git error ~a~%") error)) + ((? git-error? error) ;new Guile-Git + (leave (G_ "Git error: ~a~%") (git-error-message error))))) + +(define-syntax-rule (with-git-error-handling body ...) + (catch 'git-error + (lambda () + body ...) + (lambda (key err) + (report-git-error err)))) + (define (guix-pull . args) (define (use-le-certs? url) (string-prefix? "https://git.savannah.gnu.org/" url)) - (define (fetch-tarball store url) - (download-to-store store url "guix-latest.tar.gz")) - (with-error-handling - (let* ((opts (parse-command-line args %options - (list %default-options))) - (url (assoc-ref opts 'tarball-url))) - (unless (assoc-ref opts 'dry-run?) ;XXX: not very useful - (with-store store - (set-build-options-from-command-line store opts) - (let ((tarball - (if (use-le-certs? url) - (let* ((drv (package-derivation store le-certs)) - (certs (string-append (derivation->output-path drv) - "/etc/ssl/certs"))) - (build-derivations store (list drv)) - (parameterize ((%x509-certificate-directory certs)) - (fetch-tarball store url))) - (fetch-tarball store url)))) - (unless tarball - (leave (G_ "failed to download up-to-date source, exiting\n"))) - (parameterize ((%guile-for-build - (package-derivation store - (if (assoc-ref opts 'bootstrap?) - %bootstrap-guile - (canonical-package guile-2.0))))) - (run-with-store store - (build-and-install tarball (config-directory) - #:verbose? (assoc-ref opts 'verbose?)))))))))) + (with-git-error-handling + (let* ((opts (parse-command-line args %options + (list %default-options))) + (url (assoc-ref opts 'repository-url)) + (ref (assoc-ref opts 'ref)) + (cache (string-append (cache-directory) "/pull"))) + (ensure-guile-git!) -;; Local Variables: -;; eval: (put 'with-PATH 'scheme-indent-function 1) -;; eval: (put 'with-temporary-directory 'scheme-indent-function 1) -;; End: + (unless (assoc-ref opts 'dry-run?) ;XXX: not very useful + (with-store store + (set-build-options-from-command-line store opts) + + ;; For reproducibility, always refer to the LE certificates when we + ;; know we're talking to Savannah. + (when (use-le-certs? url) + (honor-lets-encrypt-certificates! store)) + + (format (current-error-port) + (G_ "Updating from Git repository at '~a'...~%") + url) + + (let-values (((checkout commit) + (latest-repository-commit store url + #:ref ref + #:cache-directory cache))) + + (format (current-error-port) + (G_ "Building from Git commit ~a...~%") + commit) + (parameterize ((%guile-for-build + (package-derivation store + (if (assoc-ref opts 'bootstrap?) + %bootstrap-guile + (canonical-package guile-2.0))))) + (run-with-store store + (build-and-install checkout (config-directory) + #:verbose? (assoc-ref opts 'verbose?))))))))))) ;;; pull.scm ends here From 3085b50200a49429d51b043c742bf053f37d1491 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 28 Jul 2017 17:58:18 +0200 Subject: [PATCH 003/162] pull: Use the commit ID as the version string. * guix/scripts/pull.scm (build-from-source): Add #:commit parameter. Pass it to BUILD. (build-and-install): Add #:commit and pass it to 'build-from-source'. (guix-pull): Pass #:commit to 'build-and-install'. --- guix/scripts/pull.scm | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/guix/scripts/pull.scm b/guix/scripts/pull.scm index e3b07e08b1..02cec999a3 100644 --- a/guix/scripts/pull.scm +++ b/guix/scripts/pull.scm @@ -163,9 +163,10 @@ Download and deploy the latest version of Guix.\n")) ;; a makefile, and, similarly, is intended to always keep this name. "build-aux/build-self.scm") -(define* (build-from-source source #:key verbose?) +(define* (build-from-source source + #:key verbose? commit) "Return a derivation to build Guix from SOURCE, using the self-build script -contained therein." +contained therein. Use COMMIT as the version string." ;; Running the self-build script makes it easier to update the build ;; procedure: the self-build script of the Guix-to-be-installed contains the ;; right dependencies, build procedure, etc., which the Guix-in-use may not @@ -174,12 +175,13 @@ contained therein." (build (primitive-load script))) ;; BUILD must be a monadic procedure of at least one argument: the source ;; tree. - (build source #:verbose? verbose?))) + (build source #:verbose? verbose? #:version commit))) (define* (build-and-install source config-dir - #:key verbose?) + #:key verbose? commit) "Build the tool from SOURCE, and install it in CONFIG-DIR." (mlet* %store-monad ((source (build-from-source source + #:commit commit #:verbose? verbose?)) (source-dir -> (derivation->output-path source)) (to-do? (what-to-build (list source))) @@ -280,6 +282,7 @@ certificates~%")) (canonical-package guile-2.0))))) (run-with-store store (build-and-install checkout (config-directory) + #:commit commit #:verbose? (assoc-ref opts 'verbose?))))))))))) ;;; pull.scm ends here From c53fc481440ff9d4cf23e8da3abc0759faca337a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Tue, 1 Aug 2017 23:38:07 +0200 Subject: [PATCH 004/162] pull: Honor '--no-grafts'. * guix/scripts/pull.scm (guix-pull): Parameterize %GRAFT? as a function of OPTS. --- guix/scripts/pull.scm | 54 +++++++++++++++++++++++-------------------- 1 file changed, 29 insertions(+), 25 deletions(-) diff --git a/guix/scripts/pull.scm b/guix/scripts/pull.scm index 02cec999a3..a1deec8040 100644 --- a/guix/scripts/pull.scm +++ b/guix/scripts/pull.scm @@ -27,6 +27,7 @@ #:use-module (guix derivations) #:use-module (guix download) #:use-module (guix gexp) + #:use-module (guix grafts) #:use-module (guix monads) #:use-module (guix scripts build) #:use-module ((guix build utils) @@ -256,33 +257,36 @@ certificates~%")) (unless (assoc-ref opts 'dry-run?) ;XXX: not very useful (with-store store - (set-build-options-from-command-line store opts) + (parameterize ((%graft? (assoc-ref opts 'graft?))) + (set-build-options-from-command-line store opts) - ;; For reproducibility, always refer to the LE certificates when we - ;; know we're talking to Savannah. - (when (use-le-certs? url) - (honor-lets-encrypt-certificates! store)) - - (format (current-error-port) - (G_ "Updating from Git repository at '~a'...~%") - url) - - (let-values (((checkout commit) - (latest-repository-commit store url - #:ref ref - #:cache-directory cache))) + ;; For reproducibility, always refer to the LE certificates when we + ;; know we're talking to Savannah. + (when (use-le-certs? url) + (honor-lets-encrypt-certificates! store)) (format (current-error-port) - (G_ "Building from Git commit ~a...~%") - commit) - (parameterize ((%guile-for-build - (package-derivation store - (if (assoc-ref opts 'bootstrap?) - %bootstrap-guile - (canonical-package guile-2.0))))) - (run-with-store store - (build-and-install checkout (config-directory) - #:commit commit - #:verbose? (assoc-ref opts 'verbose?))))))))))) + (G_ "Updating from Git repository at '~a'...~%") + url) + + (let-values (((checkout commit) + (latest-repository-commit store url + #:ref ref + #:cache-directory cache))) + + (format (current-error-port) + (G_ "Building from Git commit ~a...~%") + commit) + (parameterize ((%guile-for-build + (package-derivation + store + (if (assoc-ref opts 'bootstrap?) + %bootstrap-guile + (canonical-package guile-2.0))))) + (run-with-store store + (build-and-install checkout (config-directory) + #:commit commit + #:verbose? + (assoc-ref opts 'verbose?)))))))))))) ;;; pull.scm ends here From aa184803f8b4cdfcd174f2999c8529b59743f652 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:21:40 +0200 Subject: [PATCH 005/162] gnu: Add r-pkgconfig. * gnu/packages/statistics.scm (r-pkgconfig): New variable. --- gnu/packages/statistics.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 99fd2e8d12..9d17df52c8 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2587,6 +2587,24 @@ the plog header-only C++ logging library, and a method to log to R's standard error stream.") (license license:expat))) +(define-public r-pkgconfig + (package + (name "r-pkgconfig") + (version "2.0.1") + (source (origin + (method url-fetch) + (uri (cran-uri "pkgconfig" version)) + (sha256 + (base32 + "0h2sp93fqqjbfqgq82a3i94ybnndx6ghaal8pbf99firnsjb40mb")))) + (build-system r-build-system) + (home-page "https://github.com/gaborcsardi/pkgconfig") + (synopsis "Private configuration for R packages") + (description "This package provides the functionality to set configuration +options on a per-package basis. Options set by a given package only apply to +that package, other packages are unaffected.") + (license license:expat))) + (define-public r-rsqlite (package (name "r-rsqlite") From 796237a9a4f30b1106e7c6c7a505fbc61e59b163 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:22:33 +0200 Subject: [PATCH 006/162] gnu: Add r-blob. * gnu/packages/statistics.scm (r-blob): New variable. --- gnu/packages/statistics.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 9d17df52c8..47a04ce328 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2605,6 +2605,27 @@ options on a per-package basis. Options set by a given package only apply to that package, other packages are unaffected.") (license license:expat))) +(define-public r-blob + (package + (name "r-blob") + (version "1.1.0") + (source (origin + (method url-fetch) + (uri (cran-uri "blob" version)) + (sha256 + (base32 + "05pazzcyz3c3vd2l70zq9cf172cgjff4dnf419zigfnxycyn1mhn")))) + (build-system r-build-system) + (propagated-inputs + `(("r-tibble" ,r-tibble))) + (home-page "https://github.com/hadley/blob") + (synopsis "Simple S3 Class for representing vectors of binary data") + (description "Raw vectors in R are useful for storing a single binary +object. What if you want to put a vector of them in a data frame? The blob +package provides the blob object, a list of raw vectors, suitable for use as +a column in data frame.") + (license license:gpl3+))) + (define-public r-rsqlite (package (name "r-rsqlite") From 8060a617989d72e829551aee18b250bacd5262c6 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:23:16 +0200 Subject: [PATCH 007/162] gnu: r-rsqlite: Update to 2.0. * gnu/packages/statistics.scm (r-rsqlite): Update to 2.0. --- gnu/packages/statistics.scm | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 47a04ce328..d13a8e8650 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2629,13 +2629,13 @@ a column in data frame.") (define-public r-rsqlite (package (name "r-rsqlite") - (version "1.1-2") + (version "2.0") (source (origin (method url-fetch) (uri (cran-uri "RSQLite" version)) (sha256 (base32 - "0mg9yhdvny3vjn72agai5ghqxd3vk8cd4x1lsc0gzc2b2dm2w0p4")))) + "1xpg1i1jkzkzv44k512k90c2vvl960pl2d4a3spwcha6yclyc3vz")))) (properties `((upstream-name . "RSQLite"))) (build-system r-build-system) (propagated-inputs @@ -2643,13 +2643,16 @@ a column in data frame.") ("r-bh" ,r-bh) ("r-memoise" ,r-memoise) ("r-plogr" ,r-plogr) - ("r-rcpp" ,r-rcpp))) + ("r-rcpp" ,r-rcpp) + ("r-bit64" ,r-bit64) + ("r-blob" ,r-blob) + ("r-pkgconfig" ,r-pkgconfig))) (home-page "https://github.com/rstats-db/RSQLite") (synopsis "SQLite interface for R") (description "This package embeds the SQLite database engine in R and provides an interface compliant with the DBI package. The source for the SQLite -engine (version 3.8.6) is included.") +engine (version 3.8.8.2) is included.") (license license:lgpl2.0+))) (define-public r-rcurl From bfa0d1e77351ee0be85c06595e6eb398731adde2 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:24:27 +0200 Subject: [PATCH 008/162] gnu: r-sva: Update to 3.24.4. * gnu/packages/bioinformatics.scm (r-sva): Update to 3.24.4. --- gnu/packages/bioinformatics.scm | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 909044f2fd..c4414ba8b5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8619,18 +8619,21 @@ number detection tools.") (define-public r-sva (package (name "r-sva") - (version "3.24.0") + (version "3.24.4") (source (origin (method url-fetch) (uri (bioconductor-uri "sva" version)) (sha256 (base32 - "04pxl61iyc845wmqca1qv8kbb8zcp0qp72zgvgki3zzmrph9a362")))) + "0wcway4ai9im81xnrzb1vij2iidq5pw24qhjfgacmhxvx3dzhbsc")))) (build-system r-build-system) (propagated-inputs `(("r-genefilter" ,r-genefilter) - ("r-mgcv" ,r-mgcv))) + ("r-mgcv" ,r-mgcv) + ("r-biocparallel" ,r-biocparallel) + ("r-matrixstats" ,r-matrixstats) + ("r-limma" ,r-limma))) (home-page "http://bioconductor.org/packages/sva") (synopsis "Surrogate variable analysis") (description From 9eb2714625a68d5108e8371c8fef23c5694b631e Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:25:00 +0200 Subject: [PATCH 009/162] gnu: r-copywriter: Update to 2.8.1. * gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.8.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c4414ba8b5..678ce454b4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8579,14 +8579,14 @@ GenomicRanges Bioconductor package.") (define-public r-copywriter (package (name "r-copywriter") - (version "2.8.0") + (version "2.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "CopywriteR" version)) (sha256 (base32 - "183nmrqmdf9syqljslvwv7mhs9ar5xizzq98imgsc80q0m25ncjf")))) + "0xgqnq5v5213b3nzvlmjysjb7w1bc0iblqpmzbjqn7n0ib0qyhbm")))) (properties `((upstream-name . "CopywriteR"))) (build-system r-build-system) (propagated-inputs From 8cfaa9ab4e7b87dffc29e6f34e3ca81a48ff92f4 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:25:26 +0200 Subject: [PATCH 010/162] gnu: r-genomicfeatures: Update to 1.28.4. * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.28.4. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 678ce454b4..c68f0c4014 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7133,13 +7133,13 @@ as well as query and modify the browser state, such as the current viewport.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.28.0") + (version "1.28.4") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "1pjxlr34ygv8pvfwpyq268wpgqzphiwpij85fyhjqdwdp0a253ik")))) + "01ylvg275iy0cvsbxkbfxcf9pi9al597v5wnlqi2xdpmrcxyc3q0")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) From 15afa9bf8f8e4a76ad03bb61e9c9e4e66d36bb5d Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:26:00 +0200 Subject: [PATCH 011/162] gnu: r-rtracklayer: Update to 1.36.4. * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.36.4. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c68f0c4014..5723947ab2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7088,13 +7088,13 @@ alignments.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.36.0") + (version "1.36.4") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "0dv7p3wzmx57inznf6fb06417zcm48g7fpazyahxny7bqgzwq0ig")))) + "050q1rv04w31168ljr975vxva31n9lqdx84rnmsk6zcr6p640ffp")))) (build-system r-build-system) (arguments `(#:phases From 26760c80cd453d56fcd78dfeddb80b105a68792b Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:26:33 +0200 Subject: [PATCH 012/162] gnu: r-genomicalignments: Update to 1.12.1. * gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.12.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5723947ab2..993cb1c371 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7055,13 +7055,13 @@ samples.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.12.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "1aagyrdk5309a7awg42lg0bpirp91i6i2ddvpmrs38pzriwahnjy")))) + "127690sys4i5q3l4vxnjg4xg8q19qlw2258vgs5d1156w9ypp04h")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) From f41150f13d1dc956c78792aa69c0d7eaad14de19 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:26:55 +0200 Subject: [PATCH 013/162] gnu: r-summarizedexperiment: Update to 1.6.3. * gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.6.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 993cb1c371..c660898e5d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7024,13 +7024,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.6.0") + (version "1.6.3") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "1szjbzzz4pyip891nji71caalxh0rhqiv7rpv6q54swlrqpfkqkw")))) + "0j7xn7pk52d383fb1wplcggacl2586c4zi0alkgfc3wz7qq9w13s")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) From adf5d0a0bc5d675a9ffff857f7121d6c49d26d75 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:27:16 +0200 Subject: [PATCH 014/162] gnu: r-delayedarray: Update to 0.2.7. * gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.2.7. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c660898e5d..a8b2f3c705 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6994,13 +6994,13 @@ files.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.2.0") + (version "0.2.7") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "0pcsk0f2dg2ldzprs1cccqrk53jrysmm6ccgjj5wh6z3x17g7g2r")))) + "02dfqp4md9xaqjj712ijc3jswghmipr5hwkd5hr0x1xi6l2fb69g")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) From 5077bc3e2e08135048b806a239b07f19b8398161 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:27:35 +0200 Subject: [PATCH 015/162] gnu: r-biostrings: Update to 2.44.2. * gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.44.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a8b2f3c705..60597cd9c8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6924,13 +6924,13 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.44.0") + (version "2.44.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "0ixgx12cx2z4n2khxq83crz9gc21qckj2v78y2p31567kfsw7clg")))) + "12c5abgshwq86357jr0r9039y6vl4d6ngysy89rsnr23ldnsirjp")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) From 1ff74d074ee06c1858daa7455a2103e542f14364 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:27:57 +0200 Subject: [PATCH 016/162] gnu: r-biocparallel: Update to 1.10.1. * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.10.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 60597cd9c8..3c9a42d8fe 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6900,13 +6900,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "01ph0kq70b5gkd7n6a4myjlvwzgc0hi4xfwz8h17h06n9p5sdwa9")))) + "08mdfxyk9nwz77v0xhlvs19p2wj0phgm5c5b25vm0xh3749njsp0")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) From 0c6494a1db94b4d0816e4b1f705b11fbba77f197 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:28:16 +0200 Subject: [PATCH 017/162] gnu: r-biomart: Update to 2.32.1. * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.32.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3c9a42d8fe..15c40c9415 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6870,13 +6870,13 @@ annotation data packages using SQLite data storage.") (define-public r-biomart (package (name "r-biomart") - (version "2.32.0") + (version "2.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "0knkxh23vl9pa0by03xr6dy9aiah714cmf54jl828k51l9wv5l2j")))) + "0fhpbjlsgbqxrpj6nzhhk9q3ph81n5x4p7mmd097xjjn6b05w1d8")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) From 62eb93a7d07d7a744260476cc5060dd338d772ff Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:28:32 +0200 Subject: [PATCH 018/162] gnu: r-annotationdbi: Update to 1.38.2. * gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.38.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 15c40c9415..6ea12caa1b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6843,13 +6843,13 @@ on Bioconductor or which replace R functions.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.38.0") + (version "1.38.2") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "1xffm98s817mfc827cnr0by6167nlrl1glxzjawzz0rkghs41g27")))) + "1lsamnbf07zzsy5asy5hn97n2a4layv58w2bzd90ikcdx0gmzarj")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) From 1898a7832fbd6d103b5e2fba07f502588b7fe0c8 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:30:27 +0200 Subject: [PATCH 019/162] gnu: r-biobase: Update to 2.36.2. * gnu/packages/bioinformatics.scm (r-biobase): Update to 2.36.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6ea12caa1b..f09399e571 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6821,13 +6821,13 @@ manipulating genomic intervals and variables defined along a genome.") (define-public r-biobase (package (name "r-biobase") - (version "2.36.0") + (version "2.36.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 - "0x7pf5xsdcj12dbf5qqki2c6bd5madqg2fbiq5xgisarpc9v6c1m")))) + "0sr48nqx5bqid4g6lr9zr9286xh842w717yvmssvddb5xxynib6f")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) From 1b4738e23c88acdb89875c9247101e00514445e0 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:30:49 +0200 Subject: [PATCH 020/162] gnu: r-limma: Update to 3.32.5. * gnu/packages/bioinformatics.scm (r-limma): Update to 3.32.5. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f09399e571..947e8000e3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6737,13 +6737,13 @@ coding changes and predict coding outcomes.") (define-public r-limma (package (name "r-limma") - (version "3.32.0") + (version "3.32.5") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "0q7rqm86nwq0rg4fjggfr7xqybjrxj425vni3cva70b4c8d1h425")))) + "0p2ayha9g9w5r8s7pgdf16mkmdbqwh6f35jh07g3b8gyra48gwiw")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") From 48f5d283b2c38e8ea3958fc141df5a630e2f267c Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:31:08 +0200 Subject: [PATCH 021/162] gnu: r-variantannotation: Update to 1.22.3. * gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.22.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 947e8000e3..bace3de0e5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6699,13 +6699,13 @@ CAGE.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.22.0") + (version "1.22.3") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "05hpm4as36kvpiqhgnkfjwfx0a05p304c21ggba29iac4nanm8b3")))) + "0sr3vdn85x5zdxh80cfwlpfdpi2hmjy3fwi00ac3jya4v145vawr")))) (properties `((upstream-name . "VariantAnnotation"))) (inputs From 6252dd0f15925969d317fcf7b26940e7ec350bd8 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:31:28 +0200 Subject: [PATCH 022/162] gnu: r-genomeinfodb: Update to 1.12.2. * gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.12.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bace3de0e5..d866510960 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6644,13 +6644,13 @@ ID and species. It is used by functions in the GenomeInfoDb package.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.12.0") + (version "1.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "1bwwhscjl376a5p43mx8ijrqajxmgypbqhv049pgagl22hkkf0y3")))) + "1hjxgmcnrngp1307ipqaq9hgxz4j0ldn7d46knhzs30k2r4qnrfp")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) From 3ec25eb2a8d10bab2e5a7c2efdaea49d435b0840 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:31:46 +0200 Subject: [PATCH 023/162] gnu: r-iranges: Update to 2.10.2. * gnu/packages/bioinformatics.scm (r-iranges): Update to 2.10.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d866510960..6e323d3890 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6592,13 +6592,13 @@ utilities for sequence data management under the ACNUC system.") (define-public r-iranges (package (name "r-iranges") - (version "2.10.0") + (version "2.10.2") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "0zp4mxm9h1p4krj7m7cinkvwa2ibqkq59jwpan97yvhb4z8q0d6n")))) + "1brmzs3rsf97gymridrh9c9r3vws8b3rpghaanxnniw36lmcajfy")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) From 9c4348d8c4532c63879ac3ea076ac255124328fb Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:32:11 +0200 Subject: [PATCH 024/162] gnu: r-dnacopy: Update to 1.50.1. * gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.50.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6e323d3890..4c21a21383 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6518,13 +6518,13 @@ that accept short and long options.") (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.50.0") + (version "1.50.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "0112ry62z18m7rdyrn3gvbxq2f6m44cawhcfb1f02z9xzlsj0k28")))) + "0f0x83db7rm5xf9fg5pjhvs4i165qqaf01lbwb8kj13fsqpwx15p")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) From 0ff478344bcbc81993395c3cb2dc81771753a1ed Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:32:31 +0200 Subject: [PATCH 025/162] gnu: r-biocstyle: Update to 2.4.1. * gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.4.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4c21a21383..8a9bd9c660 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6401,13 +6401,13 @@ authoring books and technical documents with R Markdown.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.4.0") + (version "2.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "1n2c8rj920wmk3q2khmjfnhn5i4b3lmhx1whnghk0zk3jf88hvbi")))) + "0bmgmsfll923v573g0kyzlmjd7gly5jwgd8vkrcwvbam1gz75f2c")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) From bd4a0bab5f8eb89e39884f890ea8462366b5b93a Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:32:46 +0200 Subject: [PATCH 026/162] gnu: r-category: Update to 2.42.1. * gnu/packages/bioinformatics.scm (r-category): Update to 2.42.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8a9bd9c660..c856c5065d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5867,14 +5867,14 @@ Enrichment Analysis} (GSEA).") (define-public r-category (package (name "r-category") - (version "2.42.0") + (version "2.42.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Category" version)) (sha256 (base32 - "0swcmihyjg0fhaaydl9hm24aj9zffw3bibza9y6sqs6jaqd97f09")))) + "1w186nhc85bglcgmbcrsdbb8l6rph21pl5kdwjqwkp0jnr9z0ifn")))) (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs From fd215c2978cc0abe5aca85b647446c2e8a947284 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:33:07 +0200 Subject: [PATCH 027/162] gnu: r-annotationforge: Update to 1.18.1. * gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.18.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c856c5065d..4a8edad777 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5789,14 +5789,14 @@ distribution.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "01kd86vvgpa4a5zivcy4g6z8rhcykasdskrz8yqsqz211sd1xsr3")))) + "1366qvykd9cpcvwgc5g9mm9adw9rxw6p4814dd6l5fyb0pwpmysx")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) From f1915a5dd09bb18d06b57b118efd8a537e9754ce Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:33:23 +0200 Subject: [PATCH 028/162] gnu: r-deseq2: Update to 1.16.1. * gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.16.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4a8edad777..b47d13ea55 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5752,14 +5752,14 @@ high-throughput sequencing experiments.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.16.0") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "0m0apn3xi4kdkinsj4xkw5cwysicyjr6xxlxhpa4scyv589am1s5")))) + "01pvyljxkwazxl510v7h0971nx65iqd2bdkbdhw3xzind0n9pdvq")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs From 2f06dc04356f8e6f8d210f7bbcc73a75666bc3a8 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:57:39 +0200 Subject: [PATCH 029/162] gnu: Add r-rlang. * gnu/packages/statistics.scm (r-rlang): New variable. --- gnu/packages/statistics.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index d13a8e8650..fb7431c811 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1504,6 +1504,24 @@ private members, and they support inheritance, even when the classes are defined in different packages.") (license license:expat))) +(define-public r-rlang + (package + (name "r-rlang") + (version "0.1.1") + (source (origin + (method url-fetch) + (uri (cran-uri "rlang" version)) + (sha256 + (base32 + "0grwqy3zkvz96mvpwfbfyqid4jkfrqh3ldy2n6dpv2kjd1fzj0ar")))) + (build-system r-build-system) + (home-page "http://rlang.tidyverse.org") + (synopsis "Functions for base types, core R and Tidyverse features") + (description "This package provides a toolbox for working with base types, +core R features like the condition system, and core @code{Tidyverse} features +like tidy evaluation.") + (license license:gpl3))) + (define-public r-tibble (package (name "r-tibble") From 2e508b6dc0b1e8eb40f84b077875d01ea4fd920a Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 2 Aug 2017 07:10:19 +0200 Subject: [PATCH 030/162] gnu: libvirt: Use HTTPS. * gnu/packages/virtualization.scm (libvirt)[source, home-page]: Use HTTPS. --- gnu/packages/virtualization.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index 0ac76a72d9..4aa90010ea 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -320,7 +320,7 @@ manage system or application containers.") (version "3.5.0") (source (origin (method url-fetch) - (uri (string-append "http://libvirt.org/sources/libvirt-" + (uri (string-append "https://libvirt.org/sources/libvirt-" version ".tar.xz")) (sha256 (base32 @@ -381,7 +381,7 @@ manage system or application containers.") ("iptables" ,iptables))) (native-inputs `(("pkg-config" ,pkg-config))) - (home-page "http://libvirt.org") + (home-page "https://libvirt.org") (synopsis "Simple API for virtualization") (description "Libvirt is a C toolkit to interact with the virtualization capabilities of recent versions of Linux. The library aims at providing long From ced2d2b7ca547bdc0192445dd29ea1b356b752af Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 2 Aug 2017 07:09:53 +0200 Subject: [PATCH 031/162] gnu: libvirt: Update to 3.6.0. * gnu/packages/virtualization.scm (libvirt): Update to 3.6.0. --- gnu/packages/virtualization.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index 4aa90010ea..628396e52c 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -317,14 +317,14 @@ manage system or application containers.") (define-public libvirt (package (name "libvirt") - (version "3.5.0") + (version "3.6.0") (source (origin (method url-fetch) (uri (string-append "https://libvirt.org/sources/libvirt-" version ".tar.xz")) (sha256 (base32 - "05mm4xdw6g960rwvc9189nhxpm1vrilnmpl4h4m1lha11pivlqr9")))) + "0gcyql5dp6j370kvik9hjhxirrg89m7l1q52yq0g75h7jpv9fb1s")))) (build-system gnu-build-system) (arguments `(;; FAIL: virshtest @@ -334,7 +334,7 @@ manage system or application containers.") ;; FAIL: networkxml2firewalltest ;; FAIL: nwfilterebiptablestest ;; FAIL: nwfilterxml2firewalltest - ;; Times out after PASS: virsh-vcpupin + ;; Times while running commandest. #:tests? #f #:configure-flags (list "--with-polkit" From 0abf52642043f5ed4b1a9ce51026f7e9bad2f428 Mon Sep 17 00:00:00 2001 From: Thomas Danckaert Date: Tue, 1 Aug 2017 10:26:39 +0200 Subject: [PATCH 032/162] gnu: hdf4: Update to 4.12.13. * gnu/packages/maths.scm (hdf4): Update to 4.12.13. --- gnu/packages/maths.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 6566d750b2..1761f0222d 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -561,18 +561,17 @@ computations.") (define-public hdf4 (package (name "hdf4") - (version "4.2.12") + (version "4.2.13") (source (origin (method url-fetch) (uri (string-append "https://support.hdfgroup.org/ftp/HDF/releases/HDF" version "/src/hdf-" version ".tar.bz2")) (sha256 - (base32 "020jh563sjyxsgml8l809d2i1d4ms9shivwj3gbm7n0ilxbll8id")) + (base32 "1wz0586zh91pqb95wvr0pbh71a8rz358fdj6n2ksp85x2cis9lsm")) (patches (search-patches "hdf4-architectures.patch" "hdf4-reproducibility.patch" "hdf4-shared-fortran.patch")))) - (build-system gnu-build-system) (native-inputs `(("gfortran" ,gfortran) From a70b03d413b196dbce4747f9f039ebf28d1c568a Mon Sep 17 00:00:00 2001 From: Thomas Danckaert Date: Thu, 27 Jul 2017 16:45:19 +0200 Subject: [PATCH 033/162] gnu: Add python-grako * gnu/packages/python.scm (python-grako): New variable. --- gnu/packages/python.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index 21e32c343d..cf77abdba5 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -5168,6 +5168,34 @@ Python language binding specification.") (define-public python2-drmaa (package-with-python2 python-drmaa)) +(define-public python-grako + (package + (name "python-grako") + (version "3.99.9") + (source + (origin + (method url-fetch) + (uri + (pypi-uri "grako" version ".zip")) + (sha256 + (base32 + "0r63i68wcnv63rfjkasq1ah81frz61a6mzbcnaxhrkdpx84p7hzw")))) + (build-system python-build-system) + (arguments '(#:tests? #f)) ; Test file 'grako.ebnf' is missing from archive. + (native-inputs + `(("unzip" ,unzip) + ("python-pytest" ,python-pytest-3.0) + ("python-pytest-runner" ,python-pytest-runner))) + (home-page "https://bitbucket.org/neogeny/grako") + (synopsis "EBNF parser generator") + (description + "Grako takes a grammar in a variation of EBNF as input, and outputs a +memoizing PEG/Packrat parser in Python.") + (license license:bsd-3))) + +(define-public python2-grako + (package-with-python2 python-grako)) + (define-public python-gridmap (package (name "python-gridmap") From 33485fa91316556ccc91314fab0477d3337c9d07 Mon Sep 17 00:00:00 2001 From: Thomas Danckaert Date: Thu, 27 Jul 2017 16:47:53 +0200 Subject: [PATCH 034/162] gnu: eyed3: Update to 0.8, build with python3. * gnu/packages/mp3.scm (eyed3): [source] Update to 0.8. [arguments]: Disable tests; don't use python-2. [propagated-inputs]: Add python-six and python-grako. [native-inputs]: Remove. --- gnu/packages/mp3.scm | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/gnu/packages/mp3.scm b/gnu/packages/mp3.scm index 789e596f84..37885c9e34 100644 --- a/gnu/packages/mp3.scm +++ b/gnu/packages/mp3.scm @@ -462,7 +462,7 @@ compression format (.mpc files).") (define-public eyed3 (package (name "eyed3") - (version "0.7.10") + (version "0.8") (source (origin (method url-fetch) (uri (string-append @@ -470,14 +470,13 @@ compression format (.mpc files).") version ".tar.gz")) (sha256 (base32 - "0wjicszs64ksj2y5jbk09yjd08znc1qnarlq8ssmx13f2d4x59wq")))) + "1dcswb0f6w3b05s1v43pq8fmavkd5g88ysndn9160wlaa1v9n40h")))) (build-system python-build-system) (arguments - `(#:python ,python-2)) - (native-inputs - `(("python2-nose" ,python2-nose) - ("python2-sphinx" ,python2-sphinx) - ("python2-coverage" ,python2-coverage))) + `(#:tests? #f)) ; the required test data contains copyrighted material. + (propagated-inputs + `(("python-six" ,python-six) + ("python-grako" ,python-grako))) (synopsis "MP3 tag ID3 metadata editor") (description "eyeD3 is a Python tool for working with audio files, specifically mp3 files containing ID3 metadata (i.e. song info). It provides a From e0958c2df833a5eb3b6ecfb66f8d971cd44dd49b Mon Sep 17 00:00:00 2001 From: ng0 Date: Tue, 1 Aug 2017 15:37:28 +0000 Subject: [PATCH 035/162] gnu: libpng-apng: Update to 1.6.28. Fixes . * gnu/packages/image.scm (libpng-apng): Update to 1.6.28. Remove inherit of 'libpng'. [version]: Use own version, remove 'package-version libpng'. [source]: Don't inherit the source of libpng. [arguments]: Update hash of libpng-apng source. Signed-off-by: Leo Famulari --- gnu/packages/image.scm | 32 ++++++++++++++++++++++++++------ 1 file changed, 26 insertions(+), 6 deletions(-) diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index 139be62819..ab560d2acb 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -14,7 +14,7 @@ ;;; Copyright © 2016 Eric Bavier ;;; Copyright © 2016 Arun Isaac ;;; Copyright © 2016, 2017 Kei Kebreau -;;; Copyright © 2017 ng0 +;;; Copyright © 2017 ng0 ;;; Copyright © 2017 Hartmut Goebel ;;; ;;; This file is part of GNU Guix. @@ -91,11 +91,27 @@ library. It supports almost all PNG features and is extensible.") (license license:zlib) (home-page "http://www.libpng.org/pub/png/libpng.html"))) +;; libpng-apng should be updated when the APNG patch is released: +;; (define-public libpng-apng (package - (inherit libpng) (name "libpng-apng") - (version (package-version libpng)) + (version "1.6.28") + (source + (origin + (method url-fetch) + (uri (list (string-append "mirror://sourceforge/libpng/libpng16/" + version "/libpng-" version ".tar.xz") + (string-append + "ftp://ftp.simplesystems.org/pub/libpng/png/src" + "/libpng16/libpng-" version ".tar.xz") + (string-append + "ftp://ftp.simplesystems.org/pub/libpng/png/src/history" + "/libpng16/libpng-" version ".tar.xz"))) + (sha256 + (base32 + "0ylgyx93hnk38haqrh8prd3ax5ngzwvjqw5cxw7p9nxmwsfyrlyq")))) + (build-system gnu-build-system) (arguments `(#:phases (modify-phases %standard-phases @@ -111,7 +127,7 @@ library. It supports almost all PNG features and is extensible.") (and (apply-patch "the-patch") (for-each apply-patch (find-files "\\.patch")))) - #t)) + #t)) (add-before 'configure 'no-checks (lambda _ (substitute* "Makefile.in" @@ -126,15 +142,19 @@ library. It supports almost all PNG features and is extensible.") version "/libpng-" version "-apng.patch.gz")) (sha256 (base32 - "026r0gbkf6d6v54wca02cdxln8sj4m2c1yk62sj2aasv2ki2ffh5")))))) + "0m5nv70n9903x3xzxw9qqc6sgf2rp106ha0x6gix0xf8wcrljaab")))))) (native-inputs `(("libtool" ,libtool))) + ;; libpng.la says "-lz", so propagate it. + (propagated-inputs + `(("zlib" ,zlib))) (synopsis "APNG patch for libpng") (description "APNG (Animated Portable Network Graphics) is an unofficial extension of the APNG (Portable Network Graphics) format. APNG patch provides APNG support to libpng.") - (home-page "https://sourceforge.net/projects/libpng-apng/"))) + (home-page "https://sourceforge.net/projects/libpng-apng/") + (license license:zlib))) (define-public libpng-1.2 (package From 696f1d0fb1d3f5211d9b38d0f70a5f5c9055a641 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 2 Aug 2017 11:16:30 -0400 Subject: [PATCH 036/162] gnu: libpng-apng: Be sure to apply the APNG patch. * gnu/packages/image.scm (libpng-apng)[arguments]: Check the return status of the patching procedures. --- gnu/packages/image.scm | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/gnu/packages/image.scm b/gnu/packages/image.scm index ab560d2acb..63e3fa5049 100644 --- a/gnu/packages/image.scm +++ b/gnu/packages/image.scm @@ -113,7 +113,10 @@ library. It supports almost all PNG features and is extensible.") "0ylgyx93hnk38haqrh8prd3ax5ngzwvjqw5cxw7p9nxmwsfyrlyq")))) (build-system gnu-build-system) (arguments - `(#:phases + `(#:modules ((guix build gnu-build-system) + (guix build utils) + (srfi srfi-1)) + #:phases (modify-phases %standard-phases (add-after 'unpack 'patch-apng (lambda* (#:key inputs #:allow-other-keys) @@ -123,11 +126,10 @@ library. It supports almost all PNG features and is extensible.") (let ((apng.gz (assoc-ref inputs "apng"))) (format #t "Applying APNG patch '~a'...~%" apng.gz) - (system (string-append "gunzip < " apng.gz " > the-patch")) - (and (apply-patch "the-patch") - (for-each apply-patch - (find-files "\\.patch")))) - #t)) + (and + (zero? + (system (string-append "gunzip < " apng.gz " > the-patch"))) + (apply-patch "the-patch"))))) (add-before 'configure 'no-checks (lambda _ (substitute* "Makefile.in" From 721d7a69126113c4dd068a7c86f339cf5e96b69d Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 2 Aug 2017 19:14:06 +0300 Subject: [PATCH 037/162] gnu: gcc@4.7: Don't built on aarch64. * gnu/packages/gcc.scm (gcc@4.7, gcc@4.8, gcc@4.9)[supported-systems]: New field. --- gnu/packages/gcc.scm | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gcc.scm b/gnu/packages/gcc.scm index f0e8dae3e8..bb8570bec5 100644 --- a/gnu/packages/gcc.scm +++ b/gnu/packages/gcc.scm @@ -340,6 +340,7 @@ where the OS part is overloaded to denote a specific ABI---into GCC for several languages, including C, C++, Objective-C, Fortran, Java, Ada, and Go. It also includes runtime support libraries for these languages.") (license gpl3+) + (supported-systems (delete "aarch64-linux" %supported-systems)) (home-page "https://gcc.gnu.org/")))) (define-public gcc-4.8 @@ -352,7 +353,8 @@ Go. It also includes runtime support libraries for these languages.") (sha256 (base32 "08yggr18v373a1ihj0rg2vd6psnic42b518xcgp3r9k81xz1xyr2")) - (patches (search-patches "gcc-arm-link-spec-fix.patch")))))) + (patches (search-patches "gcc-arm-link-spec-fix.patch")))) + (supported-systems %supported-systems))) (define-public gcc-4.9 (package (inherit gcc-4.7) @@ -366,7 +368,8 @@ Go. It also includes runtime support libraries for these languages.") "14l06m7nvcvb0igkbip58x59w3nq6315k6jcz3wr9ch1rn9d44bc")) (patches (search-patches "gcc-arm-bug-71399.patch" "gcc-libvtv-runpath.patch")))) - (native-inputs `(("texinfo" ,texinfo))))) + (native-inputs `(("texinfo" ,texinfo))) + (supported-systems %supported-systems))) (define-public gcc-5 ;; Note: GCC >= 5 ships with .info files but 'make install' fails to install From 9ef5940ce4b0548e7831436a8f34967e21f8d69e Mon Sep 17 00:00:00 2001 From: Manolis Ragkousis Date: Tue, 1 Aug 2017 17:56:26 +0300 Subject: [PATCH 038/162] gnu: calibre: Add python2-msgpack as an input. * gnu/packages/ebook.scm (calibre)[inputs]: Add python2-msgpack. --- gnu/packages/ebook.scm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gnu/packages/ebook.scm b/gnu/packages/ebook.scm index bbb127a7d9..32f4f3b2d1 100644 --- a/gnu/packages/ebook.scm +++ b/gnu/packages/ebook.scm @@ -41,6 +41,7 @@ #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) #:use-module (gnu packages qt) + #:use-module (gnu packages serialization) #:use-module (gnu packages tls) #:use-module (gnu packages web) #:use-module (gnu packages xorg)) @@ -126,6 +127,8 @@ ("python2-lxml" ,python2-lxml) ("python2-markdown" ,python2-markdown) ("python2-mechanize" ,python2-mechanize) + ;; python2-msgpack is needed for the network content server to work. + ("python2-msgpack" ,python2-msgpack) ("python2-netifaces" ,python2-netifaces) ("python2-pillow" ,python2-pillow) ("python2-pygments" ,python2-pygments) From 2c5cf844302e06086647a137f01a35f777ae25d7 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Wed, 2 Aug 2017 14:36:05 -0400 Subject: [PATCH 039/162] gnu: python2-conda: Fix build by building with enum34. * gnu/packages/package-management.scm (python2-conda): Use 'python2-variant'. [native-inputs]: Add python2-enum34. --- gnu/packages/package-management.scm | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index 5c0e5a9c7d..d9ba5f6ce1 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -661,7 +661,12 @@ This package provides Conda as a library.") (license bsd-3))) (define-public python2-conda - (package-with-python2 python-conda)) + (let ((base (package-with-python2 + (strip-python2-variant python-conda)))) + (package (inherit base) + (native-inputs + `(("python2-enum34" ,python2-enum34) + ,@(package-native-inputs base)))))) (define-public conda (package (inherit python-conda) From 575e5e4e51e01aed1044cd8ba9e00a9631eba794 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 2 Aug 2017 20:48:12 +0300 Subject: [PATCH 040/162] gnu: glibc@2.24: Fix CVE-2015-5180. * gnu/packages/base.scm (glibc@2.24)[source]: Add patch. * gnu/packages/patches/glibc-CVE-2015-5180.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. --- gnu/local.mk | 1 + gnu/packages/base.scm | 1 + .../patches/glibc-CVE-2015-5180.patch | 311 ++++++++++++++++++ 3 files changed, 313 insertions(+) create mode 100644 gnu/packages/patches/glibc-CVE-2015-5180.patch diff --git a/gnu/local.mk b/gnu/local.mk index db8be36fb4..5cc8b64aa0 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -644,6 +644,7 @@ dist_patch_DATA = \ %D%/packages/patches/ghostscript-runpath.patch \ %D%/packages/patches/glib-networking-ssl-cert-file.patch \ %D%/packages/patches/glib-tests-timer.patch \ + %D%/packages/patches/glibc-CVE-2015-5180.patch \ %D%/packages/patches/glibc-CVE-2017-1000366-pt1.patch \ %D%/packages/patches/glibc-CVE-2017-1000366-pt2.patch \ %D%/packages/patches/glibc-CVE-2017-1000366-pt3.patch \ diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm index 2040f84bf1..f23db9a778 100644 --- a/gnu/packages/base.scm +++ b/gnu/packages/base.scm @@ -933,6 +933,7 @@ GLIBC/HURD for a Hurd host" "glibc-versioned-locpath.patch" "glibc-o-largefile.patch" "glibc-vectorized-strcspn-guards.patch" + "glibc-CVE-2015-5180.patch" "glibc-CVE-2017-1000366-pt1.patch" "glibc-CVE-2017-1000366-pt2.patch" "glibc-CVE-2017-1000366-pt3.patch")))))) diff --git a/gnu/packages/patches/glibc-CVE-2015-5180.patch b/gnu/packages/patches/glibc-CVE-2015-5180.patch new file mode 100644 index 0000000000..92e3740fc1 --- /dev/null +++ b/gnu/packages/patches/glibc-CVE-2015-5180.patch @@ -0,0 +1,311 @@ +From b3b37f1a5559a7620e31c8053ed1b44f798f2b6d Mon Sep 17 00:00:00 2001 +From: Florian Weimer +Date: Sat, 31 Dec 2016 20:22:09 +0100 +Subject: [PATCH] CVE-2015-5180: resolv: Fix crash with internal QTYPE [BZ + #18784] + +Also rename T_UNSPEC because an upcoming public header file +update will use that name. + +(cherry picked from commit fc82b0a2dfe7dbd35671c10510a8da1043d746a5) +--- + ChangeLog | 14 ++++ + NEWS | 6 ++ + include/arpa/nameser_compat.h | 6 +- + resolv/Makefile | 5 ++ + resolv/nss_dns/dns-host.c | 2 +- + resolv/res_mkquery.c | 4 + + resolv/res_query.c | 6 +- + resolv/tst-resolv-qtypes.c | 185 ++++++++++++++++++++++++++++++++++++++++++ + 8 files changed, 221 insertions(+), 7 deletions(-) + create mode 100644 resolv/tst-resolv-qtypes.c + +diff --git a/include/arpa/nameser_compat.h b/include/arpa/nameser_compat.h +index 2e735ed..7c0deed 100644 +--- a/include/arpa/nameser_compat.h ++++ b/include/arpa/nameser_compat.h +@@ -1,8 +1,8 @@ + #ifndef _ARPA_NAMESER_COMPAT_ + #include + +-/* Picksome unused number to represent lookups of IPv4 and IPv6 (i.e., +- T_A and T_AAAA). */ +-#define T_UNSPEC 62321 ++/* The number is outside the 16-bit RR type range and is used ++ internally by the implementation. */ ++#define T_QUERY_A_AND_AAAA 439963904 + + #endif +diff --git a/resolv/Makefile b/resolv/Makefile +index 8be41d3..a4c86b9 100644 +--- a/resolv/Makefile ++++ b/resolv/Makefile +@@ -40,6 +40,9 @@ ifeq ($(have-thread-library),yes) + extra-libs += libanl + routines += gai_sigqueue + tests += tst-res_hconf_reorder ++ ++# This test sends millions of packets and is rather slow. ++xtests += tst-resolv-qtypes + endif + extra-libs-others = $(extra-libs) + libresolv-routines := gethnamaddr res_comp res_debug \ +@@ -117,3 +120,5 @@ tst-leaks2-ENV = MALLOC_TRACE=$(objpfx)tst-leaks2.mtrace + $(objpfx)mtrace-tst-leaks2.out: $(objpfx)tst-leaks2.out + $(common-objpfx)malloc/mtrace $(objpfx)tst-leaks2.mtrace > $@; \ + $(evaluate-test) ++ ++$(objpfx)tst-resolv-qtypes: $(objpfx)libresolv.so $(shared-thread-library) +diff --git a/resolv/nss_dns/dns-host.c b/resolv/nss_dns/dns-host.c +index 5f9e357..d16fa4b 100644 +--- a/resolv/nss_dns/dns-host.c ++++ b/resolv/nss_dns/dns-host.c +@@ -323,7 +323,7 @@ _nss_dns_gethostbyname4_r (const char *name, struct gaih_addrtuple **pat, + + int olderr = errno; + enum nss_status status; +- int n = __libc_res_nsearch (&_res, name, C_IN, T_UNSPEC, ++ int n = __libc_res_nsearch (&_res, name, C_IN, T_QUERY_A_AND_AAAA, + host_buffer.buf->buf, 2048, &host_buffer.ptr, + &ans2p, &nans2p, &resplen2, &ans2p_malloced); + if (n >= 0) +diff --git a/resolv/res_mkquery.c b/resolv/res_mkquery.c +index 12f9730..d80b531 100644 +--- a/resolv/res_mkquery.c ++++ b/resolv/res_mkquery.c +@@ -103,6 +103,10 @@ res_nmkquery(res_state statp, + int n; + u_char *dnptrs[20], **dpp, **lastdnptr; + ++ if (class < 0 || class > 65535 ++ || type < 0 || type > 65535) ++ return -1; ++ + #ifdef DEBUG + if (statp->options & RES_DEBUG) + printf(";; res_nmkquery(%s, %s, %s, %s)\n", +diff --git a/resolv/res_query.c b/resolv/res_query.c +index 944d1a9..07dc6f6 100644 +--- a/resolv/res_query.c ++++ b/resolv/res_query.c +@@ -122,7 +122,7 @@ __libc_res_nquery(res_state statp, + int n, use_malloc = 0; + u_int oflags = statp->_flags; + +- size_t bufsize = (type == T_UNSPEC ? 2 : 1) * QUERYSIZE; ++ size_t bufsize = (type == T_QUERY_A_AND_AAAA ? 2 : 1) * QUERYSIZE; + u_char *buf = alloca (bufsize); + u_char *query1 = buf; + int nquery1 = -1; +@@ -137,7 +137,7 @@ __libc_res_nquery(res_state statp, + printf(";; res_query(%s, %d, %d)\n", name, class, type); + #endif + +- if (type == T_UNSPEC) ++ if (type == T_QUERY_A_AND_AAAA) + { + n = res_nmkquery(statp, QUERY, name, class, T_A, NULL, 0, NULL, + query1, bufsize); +@@ -190,7 +190,7 @@ __libc_res_nquery(res_state statp, + if (__builtin_expect (n <= 0, 0) && !use_malloc) { + /* Retry just in case res_nmkquery failed because of too + short buffer. Shouldn't happen. */ +- bufsize = (type == T_UNSPEC ? 2 : 1) * MAXPACKET; ++ bufsize = (type == T_QUERY_A_AND_AAAA ? 2 : 1) * MAXPACKET; + buf = malloc (bufsize); + if (buf != NULL) { + query1 = buf; +diff --git a/resolv/tst-resolv-qtypes.c b/resolv/tst-resolv-qtypes.c +new file mode 100644 +index 0000000..b3e60c6 +--- /dev/null ++++ b/resolv/tst-resolv-qtypes.c +@@ -0,0 +1,185 @@ ++/* Exercise low-level query functions with different QTYPEs. ++ Copyright (C) 2016 Free Software Foundation, Inc. ++ This file is part of the GNU C Library. ++ ++ The GNU C Library is free software; you can redistribute it and/or ++ modify it under the terms of the GNU Lesser General Public ++ License as published by the Free Software Foundation; either ++ version 2.1 of the License, or (at your option) any later version. ++ ++ The GNU C Library is distributed in the hope that it will be useful, ++ but WITHOUT ANY WARRANTY; without even the implied warranty of ++ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU ++ Lesser General Public License for more details. ++ ++ You should have received a copy of the GNU Lesser General Public ++ License along with the GNU C Library; if not, see ++ . */ ++ ++#include ++#include ++#include ++#include ++#include ++#include ++#include ++#include ++ ++/* If ture, the response function will send the actual response packet ++ over TCP instead of UDP. */ ++static volatile bool force_tcp; ++ ++/* Send back a fake resource record matching the QTYPE. */ ++static void ++response (const struct resolv_response_context *ctx, ++ struct resolv_response_builder *b, ++ const char *qname, uint16_t qclass, uint16_t qtype) ++{ ++ if (force_tcp && ctx->tcp) ++ { ++ resolv_response_init (b, (struct resolv_response_flags) { .tc = 1 }); ++ resolv_response_add_question (b, qname, qclass, qtype); ++ return; ++ } ++ ++ resolv_response_init (b, (struct resolv_response_flags) { }); ++ resolv_response_add_question (b, qname, qclass, qtype); ++ resolv_response_section (b, ns_s_an); ++ resolv_response_open_record (b, qname, qclass, qtype, 0); ++ resolv_response_add_data (b, &qtype, sizeof (qtype)); ++ resolv_response_close_record (b); ++} ++ ++static const const char *domain = "www.example.com"; ++ ++static int ++wrap_res_query (int type, unsigned char *answer, int answer_length) ++{ ++ return res_query (domain, C_IN, type, answer, answer_length); ++} ++ ++static int ++wrap_res_search (int type, unsigned char *answer, int answer_length) ++{ ++ return res_query (domain, C_IN, type, answer, answer_length); ++} ++ ++static int ++wrap_res_querydomain (int type, unsigned char *answer, int answer_length) ++{ ++ return res_querydomain ("www", "example.com", C_IN, type, ++ answer, answer_length); ++} ++ ++static int ++wrap_res_send (int type, unsigned char *answer, int answer_length) ++{ ++ unsigned char buf[512]; ++ int ret = res_mkquery (QUERY, domain, C_IN, type, ++ (const unsigned char *) "", 0, NULL, ++ buf, sizeof (buf)); ++ if (type < 0 || type >= 65536) ++ { ++ /* res_mkquery fails for out-of-range record types. */ ++ TEST_VERIFY_EXIT (ret == -1); ++ return -1; ++ } ++ TEST_VERIFY_EXIT (ret > 12); /* DNS header length. */ ++ return res_send (buf, ret, answer, answer_length); ++} ++ ++static int ++wrap_res_nquery (int type, unsigned char *answer, int answer_length) ++{ ++ return res_nquery (&_res, domain, C_IN, type, answer, answer_length); ++} ++ ++static int ++wrap_res_nsearch (int type, unsigned char *answer, int answer_length) ++{ ++ return res_nquery (&_res, domain, C_IN, type, answer, answer_length); ++} ++ ++static int ++wrap_res_nquerydomain (int type, unsigned char *answer, int answer_length) ++{ ++ return res_nquerydomain (&_res, "www", "example.com", C_IN, type, ++ answer, answer_length); ++} ++ ++static int ++wrap_res_nsend (int type, unsigned char *answer, int answer_length) ++{ ++ unsigned char buf[512]; ++ int ret = res_nmkquery (&_res, QUERY, domain, C_IN, type, ++ (const unsigned char *) "", 0, NULL, ++ buf, sizeof (buf)); ++ if (type < 0 || type >= 65536) ++ { ++ /* res_mkquery fails for out-of-range record types. */ ++ TEST_VERIFY_EXIT (ret == -1); ++ return -1; ++ } ++ TEST_VERIFY_EXIT (ret > 12); /* DNS header length. */ ++ return res_nsend (&_res, buf, ret, answer, answer_length); ++} ++ ++static void ++test_function (const char *fname, ++ int (*func) (int type, ++ unsigned char *answer, int answer_length)) ++{ ++ unsigned char buf[512]; ++ for (int tcp = 0; tcp < 2; ++tcp) ++ { ++ force_tcp = tcp; ++ for (unsigned int type = 1; type <= 65535; ++type) ++ { ++ if (test_verbose) ++ printf ("info: sending QTYPE %d with %s (tcp=%d)\n", ++ type, fname, tcp); ++ int ret = func (type, buf, sizeof (buf)); ++ if (ret != 47) ++ FAIL_EXIT1 ("%s tcp=%d qtype=%d return value %d", ++ fname,tcp, type, ret); ++ /* One question, one answer record. */ ++ TEST_VERIFY (memcmp (buf + 4, "\0\1\0\1\0\0\0\0", 8) == 0); ++ /* Question section. */ ++ static const char qname[] = "\3www\7example\3com"; ++ size_t qname_length = sizeof (qname); ++ TEST_VERIFY (memcmp (buf + 12, qname, qname_length) == 0); ++ /* RDATA part of answer. */ ++ uint16_t type16 = type; ++ TEST_VERIFY (memcmp (buf + ret - 2, &type16, sizeof (type16)) == 0); ++ } ++ } ++ ++ TEST_VERIFY (func (-1, buf, sizeof (buf) == -1)); ++ TEST_VERIFY (func (65536, buf, sizeof (buf) == -1)); ++} ++ ++static int ++do_test (void) ++{ ++ struct resolv_redirect_config config = ++ { ++ .response_callback = response, ++ }; ++ struct resolv_test *obj = resolv_test_start (config); ++ ++ test_function ("res_query", &wrap_res_query); ++ test_function ("res_search", &wrap_res_search); ++ test_function ("res_querydomain", &wrap_res_querydomain); ++ test_function ("res_send", &wrap_res_send); ++ ++ test_function ("res_nquery", &wrap_res_nquery); ++ test_function ("res_nsearch", &wrap_res_nsearch); ++ test_function ("res_nquerydomain", &wrap_res_nquerydomain); ++ test_function ("res_nsend", &wrap_res_nsend); ++ ++ resolv_test_end (obj); ++ return 0; ++} ++ ++#define TIMEOUT 300 ++#include +-- +2.9.3 + From a0ae64a334ce4dda269828bbb3c9182842e5cd50 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 2 Aug 2017 21:11:57 +0300 Subject: [PATCH 041/162] gnu: glibc@2.23: Fix CVE-2015-5180, CVE-2016-{3075,3706,4429}. * gnu/packages/base.scm (glibc@2.23)[source]: Add patches. * gnu/packages/patches/glibc-CVE-2016-3075.patch, gnu/packages/patches/glibc-CVE-2016-3706.patch, gnu/packages/patches/glibc-CVE-2016-4429.patch: New files. * gnu/local.mk (dist_patch_DATA): Register them. --- gnu/local.mk | 3 + gnu/packages/base.scm | 4 + .../patches/glibc-CVE-2016-3075.patch | 43 ++++ .../patches/glibc-CVE-2016-3706.patch | 188 ++++++++++++++++++ .../patches/glibc-CVE-2016-4429.patch | 58 ++++++ 5 files changed, 296 insertions(+) create mode 100644 gnu/packages/patches/glibc-CVE-2016-3075.patch create mode 100644 gnu/packages/patches/glibc-CVE-2016-3706.patch create mode 100644 gnu/packages/patches/glibc-CVE-2016-4429.patch diff --git a/gnu/local.mk b/gnu/local.mk index 5cc8b64aa0..67150aed67 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -645,6 +645,9 @@ dist_patch_DATA = \ %D%/packages/patches/glib-networking-ssl-cert-file.patch \ %D%/packages/patches/glib-tests-timer.patch \ %D%/packages/patches/glibc-CVE-2015-5180.patch \ + %D%/packages/patches/glibc-CVE-2016-3075.patch \ + %D%/packages/patches/glibc-CVE-2016-3706.patch \ + %D%/packages/patches/glibc-CVE-2016-4429.patch \ %D%/packages/patches/glibc-CVE-2017-1000366-pt1.patch \ %D%/packages/patches/glibc-CVE-2017-1000366-pt2.patch \ %D%/packages/patches/glibc-CVE-2017-1000366-pt3.patch \ diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm index f23db9a778..37e09eb8ce 100644 --- a/gnu/packages/base.scm +++ b/gnu/packages/base.scm @@ -953,6 +953,10 @@ GLIBC/HURD for a Hurd host" "glibc-versioned-locpath.patch" "glibc-o-largefile.patch" "glibc-vectorized-strcspn-guards.patch" + "glibc-CVE-2015-5180.patch" + "glibc-CVE-2016-3075.patch" + "glibc-CVE-2016-3706.patch" + "glibc-CVE-2016-4429.patch" "glibc-CVE-2017-1000366-pt1.patch" "glibc-CVE-2017-1000366-pt2.patch" "glibc-CVE-2017-1000366-pt3.patch")))))) diff --git a/gnu/packages/patches/glibc-CVE-2016-3075.patch b/gnu/packages/patches/glibc-CVE-2016-3075.patch new file mode 100644 index 0000000000..d16722806e --- /dev/null +++ b/gnu/packages/patches/glibc-CVE-2016-3075.patch @@ -0,0 +1,43 @@ +From 146b58d11fddbef15b888906e3be4f33900c416f Mon Sep 17 00:00:00 2001 +From: Florian Weimer +Date: Tue, 29 Mar 2016 12:57:56 +0200 +Subject: [PATCH] CVE-2016-3075: Stack overflow in _nss_dns_getnetbyname_r [BZ + #19879] + +The defensive copy is not needed because the name may not alias the +output buffer. + +(cherry picked from commit 317b199b4aff8cfa27f2302ab404d2bb5032b9a4) +(cherry picked from commit 883dceebc8f11921a9890211a4e202e5be17562f) +--- + ChangeLog | 7 +++++++ + NEWS | 10 ++++++++-- + resolv/nss_dns/dns-network.c | 5 +---- + 3 files changed, 16 insertions(+), 6 deletions(-) + +diff --git a/resolv/nss_dns/dns-network.c b/resolv/nss_dns/dns-network.c +index 2eb2f67..8f301a7 100644 +--- a/resolv/nss_dns/dns-network.c ++++ b/resolv/nss_dns/dns-network.c +@@ -118,17 +118,14 @@ _nss_dns_getnetbyname_r (const char *name, struct netent *result, + } net_buffer; + querybuf *orig_net_buffer; + int anslen; +- char *qbuf; + enum nss_status status; + + if (__res_maybe_init (&_res, 0) == -1) + return NSS_STATUS_UNAVAIL; + +- qbuf = strdupa (name); +- + net_buffer.buf = orig_net_buffer = (querybuf *) alloca (1024); + +- anslen = __libc_res_nsearch (&_res, qbuf, C_IN, T_PTR, net_buffer.buf->buf, ++ anslen = __libc_res_nsearch (&_res, name, C_IN, T_PTR, net_buffer.buf->buf, + 1024, &net_buffer.ptr, NULL, NULL, NULL, NULL); + if (anslen < 0) + { +-- +2.9.3 + diff --git a/gnu/packages/patches/glibc-CVE-2016-3706.patch b/gnu/packages/patches/glibc-CVE-2016-3706.patch new file mode 100644 index 0000000000..617242df24 --- /dev/null +++ b/gnu/packages/patches/glibc-CVE-2016-3706.patch @@ -0,0 +1,188 @@ +From 1a8a7c12950a0026a3c406a7cb1608f96aa1460e Mon Sep 17 00:00:00 2001 +From: Florian Weimer +Date: Fri, 29 Apr 2016 10:35:34 +0200 +Subject: [PATCH] CVE-2016-3706: getaddrinfo: stack overflow in hostent + conversion [BZ #20010] + +When converting a struct hostent response to struct gaih_addrtuple, the +gethosts macro (which is called from gaih_inet) used alloca, without +malloc fallback for large responses. This commit changes this code to +use calloc unconditionally. + +This commit also consolidated a second hostent-to-gaih_addrtuple +conversion loop (in gaih_inet) to use the new conversion function. + +(cherry picked from commit 4ab2ab03d4351914ee53248dc5aef4a8c88ff8b9) +--- + ChangeLog | 10 ++++ + sysdeps/posix/getaddrinfo.c | 130 +++++++++++++++++++++++--------------------- + 2 files changed, 79 insertions(+), 61 deletions(-) + +diff --git a/sysdeps/posix/getaddrinfo.c b/sysdeps/posix/getaddrinfo.c +index 1ef3f20..fed2d3b 100644 +--- a/sysdeps/posix/getaddrinfo.c ++++ b/sysdeps/posix/getaddrinfo.c +@@ -168,9 +168,58 @@ gaih_inet_serv (const char *servicename, const struct gaih_typeproto *tp, + return 0; + } + ++/* Convert struct hostent to a list of struct gaih_addrtuple objects. ++ h_name is not copied, and the struct hostent object must not be ++ deallocated prematurely. *RESULT must be NULL or a pointer to an ++ object allocated using malloc, which is freed. */ ++static bool ++convert_hostent_to_gaih_addrtuple (const struct addrinfo *req, ++ int family, ++ struct hostent *h, ++ struct gaih_addrtuple **result) ++{ ++ free (*result); ++ *result = NULL; ++ ++ /* Count the number of addresses in h->h_addr_list. */ ++ size_t count = 0; ++ for (char **p = h->h_addr_list; *p != NULL; ++p) ++ ++count; ++ ++ /* Report no data if no addresses are available, or if the incoming ++ address size is larger than what we can store. */ ++ if (count == 0 || h->h_length > sizeof (((struct gaih_addrtuple) {}).addr)) ++ return true; ++ ++ struct gaih_addrtuple *array = calloc (count, sizeof (*array)); ++ if (array == NULL) ++ return false; ++ ++ for (size_t i = 0; i < count; ++i) ++ { ++ if (family == AF_INET && req->ai_family == AF_INET6) ++ { ++ /* Perform address mapping. */ ++ array[i].family = AF_INET6; ++ memcpy(array[i].addr + 3, h->h_addr_list[i], sizeof (uint32_t)); ++ array[i].addr[2] = htonl (0xffff); ++ } ++ else ++ { ++ array[i].family = family; ++ memcpy (array[i].addr, h->h_addr_list[i], h->h_length); ++ } ++ array[i].next = array + i + 1; ++ } ++ array[0].name = h->h_name; ++ array[count - 1].next = NULL; ++ ++ *result = array; ++ return true; ++} ++ + #define gethosts(_family, _type) \ + { \ +- int i; \ + int herrno; \ + struct hostent th; \ + struct hostent *h; \ +@@ -219,36 +268,23 @@ gaih_inet_serv (const char *servicename, const struct gaih_typeproto *tp, + } \ + else if (h != NULL) \ + { \ +- for (i = 0; h->h_addr_list[i]; i++) \ ++ /* Make sure that addrmem can be freed. */ \ ++ if (!malloc_addrmem) \ ++ addrmem = NULL; \ ++ if (!convert_hostent_to_gaih_addrtuple (req, _family,h, &addrmem)) \ + { \ +- if (*pat == NULL) \ +- { \ +- *pat = __alloca (sizeof (struct gaih_addrtuple)); \ +- (*pat)->scopeid = 0; \ +- } \ +- uint32_t *addr = (*pat)->addr; \ +- (*pat)->next = NULL; \ +- (*pat)->name = i == 0 ? strdupa (h->h_name) : NULL; \ +- if (_family == AF_INET && req->ai_family == AF_INET6) \ +- { \ +- (*pat)->family = AF_INET6; \ +- addr[3] = *(uint32_t *) h->h_addr_list[i]; \ +- addr[2] = htonl (0xffff); \ +- addr[1] = 0; \ +- addr[0] = 0; \ +- } \ +- else \ +- { \ +- (*pat)->family = _family; \ +- memcpy (addr, h->h_addr_list[i], sizeof(_type)); \ +- } \ +- pat = &((*pat)->next); \ ++ _res.options |= old_res_options & RES_USE_INET6; \ ++ result = -EAI_SYSTEM; \ ++ goto free_and_return; \ + } \ ++ *pat = addrmem; \ ++ /* The conversion uses malloc unconditionally. */ \ ++ malloc_addrmem = true; \ + \ + if (localcanon != NULL && canon == NULL) \ + canon = strdupa (localcanon); \ + \ +- if (_family == AF_INET6 && i > 0) \ ++ if (_family == AF_INET6 && *pat != NULL) \ + got_ipv6 = true; \ + } \ + } +@@ -612,44 +648,16 @@ gaih_inet (const char *name, const struct gaih_service *service, + { + if (h != NULL) + { +- int i; +- /* We found data, count the number of addresses. */ +- for (i = 0; h->h_addr_list[i]; ++i) +- ; +- if (i > 0 && *pat != NULL) +- --i; +- +- if (__libc_use_alloca (alloca_used +- + i * sizeof (struct gaih_addrtuple))) +- addrmem = alloca_account (i * sizeof (struct gaih_addrtuple), +- alloca_used); +- else +- { +- addrmem = malloc (i +- * sizeof (struct gaih_addrtuple)); +- if (addrmem == NULL) +- { +- result = -EAI_MEMORY; +- goto free_and_return; +- } +- malloc_addrmem = true; +- } +- +- /* Now convert it into the list. */ +- struct gaih_addrtuple *addrfree = addrmem; +- for (i = 0; h->h_addr_list[i]; ++i) ++ /* We found data, convert it. */ ++ if (!convert_hostent_to_gaih_addrtuple ++ (req, AF_INET, h, &addrmem)) + { +- if (*pat == NULL) +- { +- *pat = addrfree++; +- (*pat)->scopeid = 0; +- } +- (*pat)->next = NULL; +- (*pat)->family = AF_INET; +- memcpy ((*pat)->addr, h->h_addr_list[i], +- h->h_length); +- pat = &((*pat)->next); ++ result = -EAI_MEMORY; ++ goto free_and_return; + } ++ *pat = addrmem; ++ /* The conversion uses malloc unconditionally. */ ++ malloc_addrmem = true; + } + } + else +-- +2.9.3 + diff --git a/gnu/packages/patches/glibc-CVE-2016-4429.patch b/gnu/packages/patches/glibc-CVE-2016-4429.patch new file mode 100644 index 0000000000..5eebd10543 --- /dev/null +++ b/gnu/packages/patches/glibc-CVE-2016-4429.patch @@ -0,0 +1,58 @@ +From bdce95930e1d9a7d013d1ba78740243491262879 Mon Sep 17 00:00:00 2001 +From: Florian Weimer +Date: Mon, 23 May 2016 20:18:34 +0200 +Subject: [PATCH] CVE-2016-4429: sunrpc: Do not use alloca in clntudp_call [BZ + #20112] + +The call is technically in a loop, and under certain circumstances +(which are quite difficult to reproduce in a test case), alloca +can be invoked repeatedly during a single call to clntudp_call. +As a result, the available stack space can be exhausted (even +though individual alloca sizes are bounded implicitly by what +can fit into a UDP packet, as a side effect of the earlier +successful send operation). + +(cherry picked from commit bc779a1a5b3035133024b21e2f339fe4219fb11c) +--- + ChangeLog | 7 +++++++ + NEWS | 4 ++++ + sunrpc/clnt_udp.c | 10 +++++++++- + 3 files changed, 20 insertions(+), 1 deletion(-) + +diff --git a/sunrpc/clnt_udp.c b/sunrpc/clnt_udp.c +index a6cf5f1..4d9acb1 100644 +--- a/sunrpc/clnt_udp.c ++++ b/sunrpc/clnt_udp.c +@@ -388,9 +388,15 @@ send_again: + struct sock_extended_err *e; + struct sockaddr_in err_addr; + struct iovec iov; +- char *cbuf = (char *) alloca (outlen + 256); ++ char *cbuf = malloc (outlen + 256); + int ret; + ++ if (cbuf == NULL) ++ { ++ cu->cu_error.re_errno = errno; ++ return (cu->cu_error.re_status = RPC_CANTRECV); ++ } ++ + iov.iov_base = cbuf + 256; + iov.iov_len = outlen; + msg.msg_name = (void *) &err_addr; +@@ -415,10 +421,12 @@ send_again: + cmsg = CMSG_NXTHDR (&msg, cmsg)) + if (cmsg->cmsg_level == SOL_IP && cmsg->cmsg_type == IP_RECVERR) + { ++ free (cbuf); + e = (struct sock_extended_err *) CMSG_DATA(cmsg); + cu->cu_error.re_errno = e->ee_errno; + return (cu->cu_error.re_status = RPC_CANTRECV); + } ++ free (cbuf); + } + #endif + do +-- +2.9.3 + From edd08fb7ac86afe1886f348001bbf088e48a8741 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 2 Aug 2017 21:45:37 +0300 Subject: [PATCH 042/162] gnu: glibc@2.22: Fix security issues. Fixes CVE-2015-{5180,7547}, CVE-2016-{3075,3706,4429}. * gnu/packages/base.scm (glibc@2.22)[source]: Add patches. * gnu/packages/patches/glibc-CVE-2015-7547.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it. --- gnu/local.mk | 1 + gnu/packages/base.scm | 5 + .../patches/glibc-CVE-2015-7547.patch | 590 ++++++++++++++++++ 3 files changed, 596 insertions(+) create mode 100644 gnu/packages/patches/glibc-CVE-2015-7547.patch diff --git a/gnu/local.mk b/gnu/local.mk index 67150aed67..f4fef78f31 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -645,6 +645,7 @@ dist_patch_DATA = \ %D%/packages/patches/glib-networking-ssl-cert-file.patch \ %D%/packages/patches/glib-tests-timer.patch \ %D%/packages/patches/glibc-CVE-2015-5180.patch \ + %D%/packages/patches/glibc-CVE-2015-7547.patch \ %D%/packages/patches/glibc-CVE-2016-3075.patch \ %D%/packages/patches/glibc-CVE-2016-3706.patch \ %D%/packages/patches/glibc-CVE-2016-4429.patch \ diff --git a/gnu/packages/base.scm b/gnu/packages/base.scm index 37e09eb8ce..da2c6dead6 100644 --- a/gnu/packages/base.scm +++ b/gnu/packages/base.scm @@ -974,6 +974,11 @@ GLIBC/HURD for a Hurd host" "0j49682pm2nh4qbdw35bas82p1pgfnz4d2l7iwfyzvrvj0318wzb")) (patches (search-patches "glibc-ldd-x86_64.patch" "glibc-vectorized-strcspn-guards.patch" + "glibc-CVE-2015-5180.patch" + "glibc-CVE-2015-7547.patch" + "glibc-CVE-2016-3075.patch" + "glibc-CVE-2016-3706.patch" + "glibc-CVE-2016-4429.patch" "glibc-CVE-2017-1000366-pt1.patch" "glibc-CVE-2017-1000366-pt2.patch" "glibc-CVE-2017-1000366-pt3.patch")))) diff --git a/gnu/packages/patches/glibc-CVE-2015-7547.patch b/gnu/packages/patches/glibc-CVE-2015-7547.patch new file mode 100644 index 0000000000..12abeb76d4 --- /dev/null +++ b/gnu/packages/patches/glibc-CVE-2015-7547.patch @@ -0,0 +1,590 @@ +From b995d95a5943785be3ab862b2d3276f3b4a22481 Mon Sep 17 00:00:00 2001 +From: Carlos O'Donell +Date: Tue, 16 Feb 2016 21:26:37 -0500 +Subject: [PATCH] CVE-2015-7547: getaddrinfo() stack-based buffer overflow (Bug + 18665). + +* A stack-based buffer overflow was found in libresolv when invoked from + libnss_dns, allowing specially crafted DNS responses to seize control + of execution flow in the DNS client. The buffer overflow occurs in + the functions send_dg (send datagram) and send_vc (send TCP) for the + NSS module libnss_dns.so.2 when calling getaddrinfo with AF_UNSPEC + family. The use of AF_UNSPEC triggers the low-level resolver code to + send out two parallel queries for A and AAAA. A mismanagement of the + buffers used for those queries could result in the response of a query + writing beyond the alloca allocated buffer created by + _nss_dns_gethostbyname4_r. Buffer management is simplified to remove + the overflow. Thanks to the Google Security Team and Red Hat for + reporting the security impact of this issue, and Robert Holiday of + Ciena for reporting the related bug 18665. (CVE-2015-7547) + +See also: +https://sourceware.org/ml/libc-alpha/2016-02/msg00416.html +https://sourceware.org/ml/libc-alpha/2016-02/msg00418.html + +(cherry picked from commit e9db92d3acfe1822d56d11abcea5bfc4c41cf6ca) +--- + ChangeLog | 15 +++ + NEWS | 14 +++ + resolv/nss_dns/dns-host.c | 111 ++++++++++++++++++- + resolv/res_query.c | 3 + + resolv/res_send.c | 264 ++++++++++++++++++++++++++++++++++------------ + 5 files changed, 338 insertions(+), 69 deletions(-) + +diff --git a/resolv/nss_dns/dns-host.c b/resolv/nss_dns/dns-host.c +index 357ac04..a0fe9a8 100644 +--- a/resolv/nss_dns/dns-host.c ++++ b/resolv/nss_dns/dns-host.c +@@ -1031,7 +1031,10 @@ gaih_getanswer_slice (const querybuf *answer, int anslen, const char *qname, + int h_namelen = 0; + + if (ancount == 0) +- return NSS_STATUS_NOTFOUND; ++ { ++ *h_errnop = HOST_NOT_FOUND; ++ return NSS_STATUS_NOTFOUND; ++ } + + while (ancount-- > 0 && cp < end_of_message && had_error == 0) + { +@@ -1208,7 +1211,14 @@ gaih_getanswer_slice (const querybuf *answer, int anslen, const char *qname, + /* Special case here: if the resolver sent a result but it only + contains a CNAME while we are looking for a T_A or T_AAAA record, + we fail with NOTFOUND instead of TRYAGAIN. */ +- return canon == NULL ? NSS_STATUS_TRYAGAIN : NSS_STATUS_NOTFOUND; ++ if (canon != NULL) ++ { ++ *h_errnop = HOST_NOT_FOUND; ++ return NSS_STATUS_NOTFOUND; ++ } ++ ++ *h_errnop = NETDB_INTERNAL; ++ return NSS_STATUS_TRYAGAIN; + } + + +@@ -1222,11 +1232,101 @@ gaih_getanswer (const querybuf *answer1, int anslen1, const querybuf *answer2, + + enum nss_status status = NSS_STATUS_NOTFOUND; + ++ /* Combining the NSS status of two distinct queries requires some ++ compromise and attention to symmetry (A or AAAA queries can be ++ returned in any order). What follows is a breakdown of how this ++ code is expected to work and why. We discuss only SUCCESS, ++ TRYAGAIN, NOTFOUND and UNAVAIL, since they are the only returns ++ that apply (though RETURN and MERGE exist). We make a distinction ++ between TRYAGAIN (recoverable) and TRYAGAIN' (not-recoverable). ++ A recoverable TRYAGAIN is almost always due to buffer size issues ++ and returns ERANGE in errno and the caller is expected to retry ++ with a larger buffer. ++ ++ Lastly, you may be tempted to make significant changes to the ++ conditions in this code to bring about symmetry between responses. ++ Please don't change anything without due consideration for ++ expected application behaviour. Some of the synthesized responses ++ aren't very well thought out and sometimes appear to imply that ++ IPv4 responses are always answer 1, and IPv6 responses are always ++ answer 2, but that's not true (see the implementation of send_dg ++ and send_vc to see response can arrive in any order, particularly ++ for UDP). However, we expect it holds roughly enough of the time ++ that this code works, but certainly needs to be fixed to make this ++ a more robust implementation. ++ ++ ---------------------------------------------- ++ | Answer 1 Status / | Synthesized | Reason | ++ | Answer 2 Status | Status | | ++ |--------------------------------------------| ++ | SUCCESS/SUCCESS | SUCCESS | [1] | ++ | SUCCESS/TRYAGAIN | TRYAGAIN | [5] | ++ | SUCCESS/TRYAGAIN' | SUCCESS | [1] | ++ | SUCCESS/NOTFOUND | SUCCESS | [1] | ++ | SUCCESS/UNAVAIL | SUCCESS | [1] | ++ | TRYAGAIN/SUCCESS | TRYAGAIN | [2] | ++ | TRYAGAIN/TRYAGAIN | TRYAGAIN | [2] | ++ | TRYAGAIN/TRYAGAIN' | TRYAGAIN | [2] | ++ | TRYAGAIN/NOTFOUND | TRYAGAIN | [2] | ++ | TRYAGAIN/UNAVAIL | TRYAGAIN | [2] | ++ | TRYAGAIN'/SUCCESS | SUCCESS | [3] | ++ | TRYAGAIN'/TRYAGAIN | TRYAGAIN | [3] | ++ | TRYAGAIN'/TRYAGAIN' | TRYAGAIN' | [3] | ++ | TRYAGAIN'/NOTFOUND | TRYAGAIN' | [3] | ++ | TRYAGAIN'/UNAVAIL | UNAVAIL | [3] | ++ | NOTFOUND/SUCCESS | SUCCESS | [3] | ++ | NOTFOUND/TRYAGAIN | TRYAGAIN | [3] | ++ | NOTFOUND/TRYAGAIN' | TRYAGAIN' | [3] | ++ | NOTFOUND/NOTFOUND | NOTFOUND | [3] | ++ | NOTFOUND/UNAVAIL | UNAVAIL | [3] | ++ | UNAVAIL/SUCCESS | UNAVAIL | [4] | ++ | UNAVAIL/TRYAGAIN | UNAVAIL | [4] | ++ | UNAVAIL/TRYAGAIN' | UNAVAIL | [4] | ++ | UNAVAIL/NOTFOUND | UNAVAIL | [4] | ++ | UNAVAIL/UNAVAIL | UNAVAIL | [4] | ++ ---------------------------------------------- ++ ++ [1] If the first response is a success we return success. ++ This ignores the state of the second answer and in fact ++ incorrectly sets errno and h_errno to that of the second ++ answer. However because the response is a success we ignore ++ *errnop and *h_errnop (though that means you touched errno on ++ success). We are being conservative here and returning the ++ likely IPv4 response in the first answer as a success. ++ ++ [2] If the first response is a recoverable TRYAGAIN we return ++ that instead of looking at the second response. The ++ expectation here is that we have failed to get an IPv4 response ++ and should retry both queries. ++ ++ [3] If the first response was not a SUCCESS and the second ++ response is not NOTFOUND (had a SUCCESS, need to TRYAGAIN, ++ or failed entirely e.g. TRYAGAIN' and UNAVAIL) then use the ++ result from the second response, otherwise the first responses ++ status is used. Again we have some odd side-effects when the ++ second response is NOTFOUND because we overwrite *errnop and ++ *h_errnop that means that a first answer of NOTFOUND might see ++ its *errnop and *h_errnop values altered. Whether it matters ++ in practice that a first response NOTFOUND has the wrong ++ *errnop and *h_errnop is undecided. ++ ++ [4] If the first response is UNAVAIL we return that instead of ++ looking at the second response. The expectation here is that ++ it will have failed similarly e.g. configuration failure. ++ ++ [5] Testing this code is complicated by the fact that truncated ++ second response buffers might be returned as SUCCESS if the ++ first answer is a SUCCESS. To fix this we add symmetry to ++ TRYAGAIN with the second response. If the second response ++ is a recoverable error we now return TRYAGIN even if the first ++ response was SUCCESS. */ ++ + if (anslen1 > 0) + status = gaih_getanswer_slice(answer1, anslen1, qname, + &pat, &buffer, &buflen, + errnop, h_errnop, ttlp, + &first); ++ + if ((status == NSS_STATUS_SUCCESS || status == NSS_STATUS_NOTFOUND + || (status == NSS_STATUS_TRYAGAIN + /* We want to look at the second answer in case of an +@@ -1242,8 +1342,15 @@ gaih_getanswer (const querybuf *answer1, int anslen1, const querybuf *answer2, + &pat, &buffer, &buflen, + errnop, h_errnop, ttlp, + &first); ++ /* Use the second response status in some cases. */ + if (status != NSS_STATUS_SUCCESS && status2 != NSS_STATUS_NOTFOUND) + status = status2; ++ /* Do not return a truncated second response (unless it was ++ unavoidable e.g. unrecoverable TRYAGAIN). */ ++ if (status == NSS_STATUS_SUCCESS ++ && (status2 == NSS_STATUS_TRYAGAIN ++ && *errnop == ERANGE && *h_errnop != NO_RECOVERY)) ++ status = NSS_STATUS_TRYAGAIN; + } + + return status; +diff --git a/resolv/res_query.c b/resolv/res_query.c +index 4a9b3b3..95470a9 100644 +--- a/resolv/res_query.c ++++ b/resolv/res_query.c +@@ -396,6 +396,7 @@ __libc_res_nsearch(res_state statp, + { + free (*answerp2); + *answerp2 = NULL; ++ *nanswerp2 = 0; + *answerp2_malloced = 0; + } + } +@@ -447,6 +448,7 @@ __libc_res_nsearch(res_state statp, + { + free (*answerp2); + *answerp2 = NULL; ++ *nanswerp2 = 0; + *answerp2_malloced = 0; + } + +@@ -521,6 +523,7 @@ __libc_res_nsearch(res_state statp, + { + free (*answerp2); + *answerp2 = NULL; ++ *nanswerp2 = 0; + *answerp2_malloced = 0; + } + if (saved_herrno != -1) +diff --git a/resolv/res_send.c b/resolv/res_send.c +index 5e53cc2..6511bb1 100644 +--- a/resolv/res_send.c ++++ b/resolv/res_send.c +@@ -1,3 +1,20 @@ ++/* Copyright (C) 2016 Free Software Foundation, Inc. ++ This file is part of the GNU C Library. ++ ++ The GNU C Library is free software; you can redistribute it and/or ++ modify it under the terms of the GNU Lesser General Public ++ License as published by the Free Software Foundation; either ++ version 2.1 of the License, or (at your option) any later version. ++ ++ The GNU C Library is distributed in the hope that it will be useful, ++ but WITHOUT ANY WARRANTY; without even the implied warranty of ++ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU ++ Lesser General Public License for more details. ++ ++ You should have received a copy of the GNU Lesser General Public ++ License along with the GNU C Library; if not, see ++ . */ ++ + /* + * Copyright (c) 1985, 1989, 1993 + * The Regents of the University of California. All rights reserved. +@@ -363,6 +380,8 @@ __libc_res_nsend(res_state statp, const u_char *buf, int buflen, + #ifdef USE_HOOKS + if (__glibc_unlikely (statp->qhook || statp->rhook)) { + if (anssiz < MAXPACKET && ansp) { ++ /* Always allocate MAXPACKET, callers expect ++ this specific size. */ + u_char *buf = malloc (MAXPACKET); + if (buf == NULL) + return (-1); +@@ -638,6 +657,77 @@ get_nsaddr (res_state statp, int n) + return (struct sockaddr *) (void *) &statp->nsaddr_list[n]; + } + ++/* The send_vc function is responsible for sending a DNS query over TCP ++ to the nameserver numbered NS from the res_state STATP i.e. ++ EXT(statp).nssocks[ns]. The function supports sending both IPv4 and ++ IPv6 queries at the same serially on the same socket. ++ ++ Please note that for TCP there is no way to disable sending both ++ queries, unlike UDP, which honours RES_SNGLKUP and RES_SNGLKUPREOP ++ and sends the queries serially and waits for the result after each ++ sent query. This implemetnation should be corrected to honour these ++ options. ++ ++ Please also note that for TCP we send both queries over the same ++ socket one after another. This technically violates best practice ++ since the server is allowed to read the first query, respond, and ++ then close the socket (to service another client). If the server ++ does this, then the remaining second query in the socket data buffer ++ will cause the server to send the client an RST which will arrive ++ asynchronously and the client's OS will likely tear down the socket ++ receive buffer resulting in a potentially short read and lost ++ response data. This will force the client to retry the query again, ++ and this process may repeat until all servers and connection resets ++ are exhausted and then the query will fail. It's not known if this ++ happens with any frequency in real DNS server implementations. This ++ implementation should be corrected to use two sockets by default for ++ parallel queries. ++ ++ The query stored in BUF of BUFLEN length is sent first followed by ++ the query stored in BUF2 of BUFLEN2 length. Queries are sent ++ serially on the same socket. ++ ++ Answers to the query are stored firstly in *ANSP up to a max of ++ *ANSSIZP bytes. If more than *ANSSIZP bytes are needed and ANSCP ++ is non-NULL (to indicate that modifying the answer buffer is allowed) ++ then malloc is used to allocate a new response buffer and ANSCP and ++ ANSP will both point to the new buffer. If more than *ANSSIZP bytes ++ are needed but ANSCP is NULL, then as much of the response as ++ possible is read into the buffer, but the results will be truncated. ++ When truncation happens because of a small answer buffer the DNS ++ packets header field TC will bet set to 1, indicating a truncated ++ message and the rest of the socket data will be read and discarded. ++ ++ Answers to the query are stored secondly in *ANSP2 up to a max of ++ *ANSSIZP2 bytes, with the actual response length stored in ++ *RESPLEN2. If more than *ANSSIZP bytes are needed and ANSP2 ++ is non-NULL (required for a second query) then malloc is used to ++ allocate a new response buffer, *ANSSIZP2 is set to the new buffer ++ size and *ANSP2_MALLOCED is set to 1. ++ ++ The ANSP2_MALLOCED argument will eventually be removed as the ++ change in buffer pointer can be used to detect the buffer has ++ changed and that the caller should use free on the new buffer. ++ ++ Note that the answers may arrive in any order from the server and ++ therefore the first and second answer buffers may not correspond to ++ the first and second queries. ++ ++ It is not supported to call this function with a non-NULL ANSP2 ++ but a NULL ANSCP. Put another way, you can call send_vc with a ++ single unmodifiable buffer or two modifiable buffers, but no other ++ combination is supported. ++ ++ It is the caller's responsibility to free the malloc allocated ++ buffers by detecting that the pointers have changed from their ++ original values i.e. *ANSCP or *ANSP2 has changed. ++ ++ If errors are encountered then *TERRNO is set to an appropriate ++ errno value and a zero result is returned for a recoverable error, ++ and a less-than zero result is returned for a non-recoverable error. ++ ++ If no errors are encountered then *TERRNO is left unmodified and ++ a the length of the first response in bytes is returned. */ + static int + send_vc(res_state statp, + const u_char *buf, int buflen, const u_char *buf2, int buflen2, +@@ -647,11 +737,7 @@ send_vc(res_state statp, + { + const HEADER *hp = (HEADER *) buf; + const HEADER *hp2 = (HEADER *) buf2; +- u_char *ans = *ansp; +- int orig_anssizp = *anssizp; +- // XXX REMOVE +- // int anssiz = *anssizp; +- HEADER *anhp = (HEADER *) ans; ++ HEADER *anhp = (HEADER *) *ansp; + struct sockaddr *nsap = get_nsaddr (statp, ns); + int truncating, connreset, n; + /* On some architectures compiler might emit a warning indicating +@@ -743,6 +829,8 @@ send_vc(res_state statp, + * Receive length & response + */ + int recvresp1 = 0; ++ /* Skip the second response if there is no second query. ++ To do that we mark the second response as received. */ + int recvresp2 = buf2 == NULL; + uint16_t rlen16; + read_len: +@@ -779,40 +867,14 @@ send_vc(res_state statp, + u_char **thisansp; + int *thisresplenp; + if ((recvresp1 | recvresp2) == 0 || buf2 == NULL) { ++ /* We have not received any responses ++ yet or we only have one response to ++ receive. */ + thisanssizp = anssizp; + thisansp = anscp ?: ansp; + assert (anscp != NULL || ansp2 == NULL); + thisresplenp = &resplen; + } else { +- if (*anssizp != MAXPACKET) { +- /* No buffer allocated for the first +- reply. We can try to use the rest +- of the user-provided buffer. */ +-#if __GNUC_PREREQ (4, 7) +- DIAG_PUSH_NEEDS_COMMENT; +- DIAG_IGNORE_NEEDS_COMMENT (5, "-Wmaybe-uninitialized"); +-#endif +-#if _STRING_ARCH_unaligned +- *anssizp2 = orig_anssizp - resplen; +- *ansp2 = *ansp + resplen; +-#else +- int aligned_resplen +- = ((resplen + __alignof__ (HEADER) - 1) +- & ~(__alignof__ (HEADER) - 1)); +- *anssizp2 = orig_anssizp - aligned_resplen; +- *ansp2 = *ansp + aligned_resplen; +-#endif +-#if __GNUC_PREREQ (4, 7) +- DIAG_POP_NEEDS_COMMENT; +-#endif +- } else { +- /* The first reply did not fit into the +- user-provided buffer. Maybe the second +- answer will. */ +- *anssizp2 = orig_anssizp; +- *ansp2 = *ansp; +- } +- + thisanssizp = anssizp2; + thisansp = ansp2; + thisresplenp = resplen2; +@@ -820,10 +882,14 @@ send_vc(res_state statp, + anhp = (HEADER *) *thisansp; + + *thisresplenp = rlen; +- if (rlen > *thisanssizp) { +- /* Yes, we test ANSCP here. If we have two buffers +- both will be allocatable. */ +- if (__glibc_likely (anscp != NULL)) { ++ /* Is the answer buffer too small? */ ++ if (*thisanssizp < rlen) { ++ /* If the current buffer is not the the static ++ user-supplied buffer then we can reallocate ++ it. */ ++ if (thisansp != NULL && thisansp != ansp) { ++ /* Always allocate MAXPACKET, callers expect ++ this specific size. */ + u_char *newp = malloc (MAXPACKET); + if (newp == NULL) { + *terrno = ENOMEM; +@@ -835,6 +901,9 @@ send_vc(res_state statp, + if (thisansp == ansp2) + *ansp2_malloced = 1; + anhp = (HEADER *) newp; ++ /* A uint16_t can't be larger than MAXPACKET ++ thus it's safe to allocate MAXPACKET but ++ read RLEN bytes instead. */ + len = rlen; + } else { + Dprint(statp->options & RES_DEBUG, +@@ -997,6 +1066,66 @@ reopen (res_state statp, int *terrno, int ns) + return 1; + } + ++/* The send_dg function is responsible for sending a DNS query over UDP ++ to the nameserver numbered NS from the res_state STATP i.e. ++ EXT(statp).nssocks[ns]. The function supports IPv4 and IPv6 queries ++ along with the ability to send the query in parallel for both stacks ++ (default) or serially (RES_SINGLKUP). It also supports serial lookup ++ with a close and reopen of the socket used to talk to the server ++ (RES_SNGLKUPREOP) to work around broken name servers. ++ ++ The query stored in BUF of BUFLEN length is sent first followed by ++ the query stored in BUF2 of BUFLEN2 length. Queries are sent ++ in parallel (default) or serially (RES_SINGLKUP or RES_SNGLKUPREOP). ++ ++ Answers to the query are stored firstly in *ANSP up to a max of ++ *ANSSIZP bytes. If more than *ANSSIZP bytes are needed and ANSCP ++ is non-NULL (to indicate that modifying the answer buffer is allowed) ++ then malloc is used to allocate a new response buffer and ANSCP and ++ ANSP will both point to the new buffer. If more than *ANSSIZP bytes ++ are needed but ANSCP is NULL, then as much of the response as ++ possible is read into the buffer, but the results will be truncated. ++ When truncation happens because of a small answer buffer the DNS ++ packets header field TC will bet set to 1, indicating a truncated ++ message, while the rest of the UDP packet is discarded. ++ ++ Answers to the query are stored secondly in *ANSP2 up to a max of ++ *ANSSIZP2 bytes, with the actual response length stored in ++ *RESPLEN2. If more than *ANSSIZP bytes are needed and ANSP2 ++ is non-NULL (required for a second query) then malloc is used to ++ allocate a new response buffer, *ANSSIZP2 is set to the new buffer ++ size and *ANSP2_MALLOCED is set to 1. ++ ++ The ANSP2_MALLOCED argument will eventually be removed as the ++ change in buffer pointer can be used to detect the buffer has ++ changed and that the caller should use free on the new buffer. ++ ++ Note that the answers may arrive in any order from the server and ++ therefore the first and second answer buffers may not correspond to ++ the first and second queries. ++ ++ It is not supported to call this function with a non-NULL ANSP2 ++ but a NULL ANSCP. Put another way, you can call send_vc with a ++ single unmodifiable buffer or two modifiable buffers, but no other ++ combination is supported. ++ ++ It is the caller's responsibility to free the malloc allocated ++ buffers by detecting that the pointers have changed from their ++ original values i.e. *ANSCP or *ANSP2 has changed. ++ ++ If an answer is truncated because of UDP datagram DNS limits then ++ *V_CIRCUIT is set to 1 and the return value non-zero to indicate to ++ the caller to retry with TCP. The value *GOTSOMEWHERE is set to 1 ++ if any progress was made reading a response from the nameserver and ++ is used by the caller to distinguish between ECONNREFUSED and ++ ETIMEDOUT (the latter if *GOTSOMEWHERE is 1). ++ ++ If errors are encountered then *TERRNO is set to an appropriate ++ errno value and a zero result is returned for a recoverable error, ++ and a less-than zero result is returned for a non-recoverable error. ++ ++ If no errors are encountered then *TERRNO is left unmodified and ++ a the length of the first response in bytes is returned. */ + static int + send_dg(res_state statp, + const u_char *buf, int buflen, const u_char *buf2, int buflen2, +@@ -1006,8 +1135,6 @@ send_dg(res_state statp, + { + const HEADER *hp = (HEADER *) buf; + const HEADER *hp2 = (HEADER *) buf2; +- u_char *ans = *ansp; +- int orig_anssizp = *anssizp; + struct timespec now, timeout, finish; + struct pollfd pfd[1]; + int ptimeout; +@@ -1040,6 +1167,8 @@ send_dg(res_state statp, + int need_recompute = 0; + int nwritten = 0; + int recvresp1 = 0; ++ /* Skip the second response if there is no second query. ++ To do that we mark the second response as received. */ + int recvresp2 = buf2 == NULL; + pfd[0].fd = EXT(statp).nssocks[ns]; + pfd[0].events = POLLOUT; +@@ -1203,55 +1332,56 @@ send_dg(res_state statp, + int *thisresplenp; + + if ((recvresp1 | recvresp2) == 0 || buf2 == NULL) { ++ /* We have not received any responses ++ yet or we only have one response to ++ receive. */ + thisanssizp = anssizp; + thisansp = anscp ?: ansp; + assert (anscp != NULL || ansp2 == NULL); + thisresplenp = &resplen; + } else { +- if (*anssizp != MAXPACKET) { +- /* No buffer allocated for the first +- reply. We can try to use the rest +- of the user-provided buffer. */ +-#if _STRING_ARCH_unaligned +- *anssizp2 = orig_anssizp - resplen; +- *ansp2 = *ansp + resplen; +-#else +- int aligned_resplen +- = ((resplen + __alignof__ (HEADER) - 1) +- & ~(__alignof__ (HEADER) - 1)); +- *anssizp2 = orig_anssizp - aligned_resplen; +- *ansp2 = *ansp + aligned_resplen; +-#endif +- } else { +- /* The first reply did not fit into the +- user-provided buffer. Maybe the second +- answer will. */ +- *anssizp2 = orig_anssizp; +- *ansp2 = *ansp; +- } +- + thisanssizp = anssizp2; + thisansp = ansp2; + thisresplenp = resplen2; + } + + if (*thisanssizp < MAXPACKET +- /* Yes, we test ANSCP here. If we have two buffers +- both will be allocatable. */ +- && anscp ++ /* If the current buffer is not the the static ++ user-supplied buffer then we can reallocate ++ it. */ ++ && (thisansp != NULL && thisansp != ansp) + #ifdef FIONREAD ++ /* Is the size too small? */ + && (ioctl (pfd[0].fd, FIONREAD, thisresplenp) < 0 + || *thisanssizp < *thisresplenp) + #endif + ) { ++ /* Always allocate MAXPACKET, callers expect ++ this specific size. */ + u_char *newp = malloc (MAXPACKET); + if (newp != NULL) { +- *anssizp = MAXPACKET; +- *thisansp = ans = newp; ++ *thisanssizp = MAXPACKET; ++ *thisansp = newp; + if (thisansp == ansp2) + *ansp2_malloced = 1; + } + } ++ /* We could end up with truncation if anscp was NULL ++ (not allowed to change caller's buffer) and the ++ response buffer size is too small. This isn't a ++ reliable way to detect truncation because the ioctl ++ may be an inaccurate report of the UDP message size. ++ Therefore we use this only to issue debug output. ++ To do truncation accurately with UDP we need ++ MSG_TRUNC which is only available on Linux. We ++ can abstract out the Linux-specific feature in the ++ future to detect truncation. */ ++ if (__glibc_unlikely (*thisanssizp < *thisresplenp)) { ++ Dprint(statp->options & RES_DEBUG, ++ (stdout, ";; response may be truncated (UDP)\n") ++ ); ++ } ++ + HEADER *anhp = (HEADER *) *thisansp; + socklen_t fromlen = sizeof(struct sockaddr_in6); + assert (sizeof(from) <= fromlen); +-- +2.9.3 + From ec5495ba3f06655252959aebe9d9d273387c6125 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 3 Aug 2017 00:14:53 +0200 Subject: [PATCH 043/162] doc: 'patches' field of can list file-like objects. Fixes . Reported by sirgazil . * doc/guix.texi (origin Reference): 'patches' can contain file-like objects. --- doc/guix.texi | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/doc/guix.texi b/doc/guix.texi index 0ea677387b..2bb820b46c 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -3290,7 +3290,8 @@ used. For version control checkouts, it is recommended to provide the file name explicitly because the default is not very descriptive. @item @code{patches} (default: @code{'()}) -A list of file names containing patches to be applied to the source. +A list of file names, origins, or file-like objects (@pxref{G-Expressions, +file-like objects}) pointing to patches to be applied to the source. This list of patches must be unconditional. In particular, it cannot depend on the value of @code{%current-system} or From 49962b15a1c4e72a55b6cf273806d203906de2ed Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Thu, 3 Aug 2017 00:20:05 +0200 Subject: [PATCH 044/162] activation: Make sure /etc exists. Fixes . Reported by ng0 . * gnu/build/activation.scm (activate-etc): Add call to 'mkdir-p'. --- gnu/build/activation.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/build/activation.scm b/gnu/build/activation.scm index 299c0728cb..9c58370ec3 100644 --- a/gnu/build/activation.scm +++ b/gnu/build/activation.scm @@ -313,6 +313,7 @@ they already exist." (false-if-exception (delete-file file))) (format #t "populating /etc from ~a...~%" etc) + (mkdir-p "/etc") ;; Create the /etc/ssl -> /run/current-system/profile/etc/ssl symlink. This ;; symlink, to a target outside of the store, probably doesn't belong in the From 6862c723738a846adeed34adbdb4b554f5fa04f3 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 3 Aug 2017 01:56:22 +0200 Subject: [PATCH 045/162] gnu: tor: Update to 0.3.0.10. * gnu/packages/tor.scm (tor): Update to 0.3.0.10. --- gnu/packages/tor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/tor.scm b/gnu/packages/tor.scm index 1d5a1f1612..64acb44490 100644 --- a/gnu/packages/tor.scm +++ b/gnu/packages/tor.scm @@ -44,14 +44,14 @@ (define-public tor (package (name "tor") - (version "0.3.0.9") + (version "0.3.0.10") (source (origin (method url-fetch) (uri (string-append "https://dist.torproject.org/tor-" version ".tar.gz")) (sha256 (base32 - "0hhyb1wil8japynqnm07r1f67w3wdnafdg9amzlrrcfcyq5qim28")))) + "1cas30wk4bhcivi6l9dj7wwlz6pc2jj883x1vijax3b8l54nx3ls")))) (build-system gnu-build-system) (arguments `(#:configure-flags (list "--enable-gcc-hardening" From 5d8312f1c649afbf727eaa17ce1879989908508b Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 3 Aug 2017 05:31:24 +0200 Subject: [PATCH 046/162] gnu: youtube-dl: Update to 2017.07.30.1. * gnu/packages/video.scm (youtube-dl): Update to 2017.07.30.1. --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 0a551c74f4..1152cdf0a0 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -1121,7 +1121,7 @@ access to mpv's powerful playback capabilities.") (define-public youtube-dl (package (name "youtube-dl") - (version "2017.07.23") + (version "2017.07.30.1") (source (origin (method url-fetch) (uri (string-append "https://yt-dl.org/downloads/" @@ -1129,7 +1129,7 @@ access to mpv's powerful playback capabilities.") version ".tar.gz")) (sha256 (base32 - "0h8jim7qx7b97wg7s8izz3and1xp70b9clqwpxl33xls9linh04m")))) + "1m1n5d06xh8hnild6kssiv9yaq2sm7vy0c8h506v3nff7i9wf0a7")))) (build-system python-build-system) (arguments ;; The problem here is that the directory for the man page and completion From 68a29ab8d00be37f5e084d16a8971d7cf5fb2714 Mon Sep 17 00:00:00 2001 From: Eric Bavier Date: Thu, 3 Aug 2017 00:32:30 -0500 Subject: [PATCH 047/162] gnu: Add LeoCAD. * gnu/packages/lego.scm (leocad): New variable. --- gnu/packages/lego.scm | 61 +++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 59 insertions(+), 2 deletions(-) diff --git a/gnu/packages/lego.scm b/gnu/packages/lego.scm index d47be5dfb4..d5e5de1c1f 100644 --- a/gnu/packages/lego.scm +++ b/gnu/packages/lego.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2016 Eric Bavier +;;; Copyright © 2016, 2017 Eric Bavier ;;; ;;; This file is part of GNU Guix. ;;; @@ -23,7 +23,10 @@ #:use-module (guix build-system gnu) #:use-module (gnu packages) #:use-module (gnu packages bison) - #:use-module (gnu packages flex)) + #:use-module (gnu packages compression) + #:use-module (gnu packages flex) + #:use-module (gnu packages gl) + #:use-module (gnu packages qt)) (define-public nqc (package @@ -65,3 +68,57 @@ MINDSTORMS products. The preprocessor and control structures of NQC are very similar to C. NQC is not a general purpose language -- there are many restrictions that stem from limitations of the standard RCX firmware.") (license license:mpl1.0))) + +(define-public leocad + (package + (name "leocad") + (version "17.07") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/leozide/leocad/" + "archive/v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "02gm4950zlmsw4sxmdwypgkybn51b02qnmmk6rzjdr8si4k6gikq")))) + (build-system gnu-build-system) + (native-inputs + `(("qttools" ,qttools))) ;for lrelease + (inputs + `(("mesa" ,mesa) + ("qtbase" ,qtbase) + ("zlib" ,zlib))) + (arguments + '(#:tests? #f + #:phases + (modify-phases %standard-phases + (replace 'configure + (lambda* (#:key outputs inputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (zero? (system* "qmake" + (string-append "INSTALL_PREFIX=" out) + ;; Otherwise looks for lrelease-qt4 + "QMAKE_LRELEASE=lrelease" + ;; Don't pester users about updates + "DISABLE_UPDATE_CHECK=1"))))) + (add-after 'configure 'reset-resource-timestamps + (lambda _ + ;; The contents of build/release/.qrc/qrc_leocad.cpp generated by + ;; qt's rcc tool depends on the timestamps in resources/*, in + ;; particular the leocad_*.qm files that are created by qmake + ;; above. So reset those timestamps for a reproducible build. + (with-directory-excursion "resources" + (for-each (lambda (file) + (let* ((base (basename file ".qm")) + (src (string-append base ".ts")) + (st (stat src))) + (set-file-time file st))) + (find-files "." "leocad_.*\\.qm")))))))) + (home-page "http://www.leocad.org") + (synopsis "Create virtual Lego models") + (description + "LeoCAD is a program for creating virtual LEGO models. It has an +intuitive interface, designed to allow new users to start creating new models +without having to spend too much time learning the application. LeoCAD is +fully compatible with the LDraw Standard and related tools.") + (license license:gpl2+))) From 5638d7150229bcc63bf26e484f81ff310dafd263 Mon Sep 17 00:00:00 2001 From: Manolis Ragkousis Date: Wed, 2 Aug 2017 20:32:22 +0300 Subject: [PATCH 048/162] gnu: openscenegraph: Add 'Release' configure flag. * gnu/packages/graphics.scm (openscenegraph)[arguments]: Add "-DCMAKE_BUILD_TYPE=Release". --- gnu/packages/graphics.scm | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/gnu/packages/graphics.scm b/gnu/packages/graphics.scm index 6c813e8a37..d0e50106fa 100644 --- a/gnu/packages/graphics.scm +++ b/gnu/packages/graphics.scm @@ -339,7 +339,11 @@ visual effects work for film.") #:configure-flags (list (string-append "-DCMAKE_INSTALL_RPATH=" (assoc-ref %outputs "out") "/lib:" - (assoc-ref %outputs "out") "/lib64")))) + (assoc-ref %outputs "out") "/lib64") + ;; We need to set this flag or otherwise 'rd' will be added + ;; to the name of the library binaries and break linking + ;; with other programs. + "-DCMAKE_BUILD_TYPE=Release"))) (native-inputs `(("unzip" ,unzip))) (inputs From a8ead6f91b74dbc5c776a5029a62e15bd84d7b0e Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 3 Aug 2017 13:34:18 +0300 Subject: [PATCH 049/162] gnu: vc: Limit to x86_64 and i686. * gnu/packages/maths.scm (vc)[supported-systems]: New field. --- gnu/packages/maths.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 1761f0222d..6ed51b027e 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -3067,6 +3067,8 @@ instruction sets. Thus, an application written with Vc can be compiled for: @item NVIDIA GPUs / CUDA (in development) @end enumerate\n") (home-page "https://github.com/VcDevel/Vc") + ;; "No support_???.cpp file exists for this architecture." + (supported-systems '("x86_64-linux" "i686-linux")) (license license:bsd-3))) (define-public reducelcs From 92971d68ac942cd4a38092b4ccb20a8192a56aaf Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Thu, 3 Aug 2017 20:37:25 +1000 Subject: [PATCH 050/162] gnu: htseq: Update to 0.9.1. * gnu/packages/bioinformatics.scm (htseq): Update to 0.9.1. [arguments]: Use python-3 by removing field. [native-inputs]: Add 'python-cython'. [propagated-inputs]: Use python3 numpy package. [inputs]: Use python3 pysam package. Add 'python-matplotlib'. (python2-htseq): New variable. (clipper)[inputs]: Use it. --- gnu/packages/bioinformatics.scm | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b47d13ea55..4de245abe6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1636,7 +1636,7 @@ databases.") (build-system python-build-system) (arguments `(#:python ,python-2)) ; only Python 2 is supported (inputs - `(("htseq" ,htseq) + `(("htseq" ,python2-htseq) ("python-pybedtools" ,python2-pybedtools) ("python-cython" ,python2-cython) ("python-scikit-learn" ,python2-scikit-learn) @@ -2981,7 +2981,7 @@ HMMs).") (define-public htseq (package (name "htseq") - (version "0.6.1") + (version "0.9.1") (source (origin (method url-fetch) (uri (string-append @@ -2989,14 +2989,16 @@ HMMs).") version ".tar.gz")) (sha256 (base32 - "1i85ppf2j2lj12m0x690qq5nn17xxk23pbbx2c83r8ayb5wngzwv")))) + "11flgb1381xdhk43bzbfm3vhnszkpqg6jk76rpa5xd1zbrvvlnxg")))) (build-system python-build-system) - (arguments `(#:python ,python-2)) ; only Python 2 is supported + (native-inputs + `(("python-cython" ,python-cython))) ;; Numpy needs to be propagated when htseq is used as a Python library. (propagated-inputs - `(("python-numpy" ,python2-numpy))) + `(("python-numpy" ,python-numpy))) (inputs - `(("python-pysam" ,python2-pysam))) + `(("python-pysam" ,python-pysam) + ("python-matplotlib" ,python-matplotlib))) (home-page "http://www-huber.embl.de/users/anders/HTSeq/") (synopsis "Analysing high-throughput sequencing data with Python") (description @@ -3004,6 +3006,9 @@ HMMs).") from high-throughput sequencing assays.") (license license:gpl3+))) +(define-public python2-htseq + (package-with-python2 htseq)) + (define-public java-htsjdk (package (name "java-htsjdk") From 75e6639f364d77378edbc10022bca09040336a56 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Thu, 3 Aug 2017 21:08:13 +1000 Subject: [PATCH 051/162] gnu: htseq: Use PyPI URI. This is a follow-up to 92971d68ac942cd4a38092b4ccb20a8192a56aaf. * gnu/packages/bioinformatics.scm (htseq)[source]: Use 'pypi-uri'. --- gnu/packages/bioinformatics.scm | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4de245abe6..e3c3bbc52f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2984,9 +2984,7 @@ HMMs).") (version "0.9.1") (source (origin (method url-fetch) - (uri (string-append - "https://pypi.python.org/packages/source/H/HTSeq/HTSeq-" - version ".tar.gz")) + (uri (pypi-uri "HTSeq" version)) (sha256 (base32 "11flgb1381xdhk43bzbfm3vhnszkpqg6jk76rpa5xd1zbrvvlnxg")))) From dd4b7476ec2c8c1d790f1366173a15bd6042eeee Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Fri, 21 Jul 2017 01:06:47 +0200 Subject: [PATCH 052/162] gnu: Add grub-hybrid. * gnu/packages/bootloaders.scm (grub-hybrid): New variable. --- gnu/packages/bootloaders.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/bootloaders.scm b/gnu/packages/bootloaders.scm index 34b8953aa7..c0d16b6c88 100644 --- a/gnu/packages/bootloaders.scm +++ b/gnu/packages/bootloaders.scm @@ -183,6 +183,39 @@ menu to select one of the installed operating systems.") "/bin/mcopy\""))) #t)))))))))) +;; Because grub searches hardcoded paths it's easiest to just build grub +;; again to make it find both grub-pc and grub-efi. There is a command +;; line argument which allows you to specify ONE platform - but +;; grub-mkrescue will use multiple platforms if they are available +;; in the installation directory (without command line argument). +(define-public grub-hybrid + (package + (inherit grub-efi) + (name "grub-hybrid") + (synopsis "GRand Unified Boot loader (hybrid version)") + (inputs + `(("grub" ,grub) + ,@(package-inputs grub-efi))) + (arguments + (substitute-keyword-arguments (package-arguments grub-efi) + ((#:modules modules `((guix build utils) (guix build gnu-build-system))) + `((ice-9 ftw) ,@modules)) + ((#:phases phases) + `(modify-phases ,phases + (add-after 'install 'install-non-efi + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((input-dir (string-append (assoc-ref inputs "grub") + "/lib/grub")) + (output-dir (string-append (assoc-ref outputs "out") + "/lib/grub"))) + (for-each + (lambda (basename) + (if (not (string-prefix? "." basename)) + (symlink (string-append input-dir "/" basename) + (string-append output-dir "/" basename)))) + (scandir input-dir)) + #t))))))))) + (define-public syslinux (let ((commit "bb41e935cc83c6242de24d2271e067d76af3585c")) (package From 5bee6bf409dd36b0671ff59bac09d7ad4aa9e09e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Aug 2017 15:47:56 +0200 Subject: [PATCH 053/162] gnu: Add r-glue. * gnu/packages/cran.scm (r-glue): New variable. --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 9ebfbbed2d..61c6496022 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -42,3 +42,23 @@ including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided.") (license license:bsd-3))) + +(define-public r-glue + (package + (name "r-glue") + (version "1.1.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "glue" version)) + (sha256 + (base32 + "01awmqby7rwzhzr51m7d87wqibx7ggl6xair8fi3z3q1hkyyv7ih")))) + (build-system r-build-system) + (home-page "https://github.com/tidyverse/glue") + (synopsis "Interpreted string literals") + (description + "This package provides an implementation of interpreted string literals, +inspired by Python's Literal String Interpolation (PEP-0498) and +Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.") + (license license:expat))) From 847b4572535819379a92dcc45d123936ba0729ab Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Aug 2017 15:49:42 +0200 Subject: [PATCH 054/162] gnu: r-plogr: Move to (gnu packages cran). * gnu/packages/statistics.scm (r-plogr): Move from here... * gnu/packages/cran.scm (r-plogr): ...to here. --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ gnu/packages/statistics.scm | 20 -------------------- 2 files changed, 20 insertions(+), 20 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 61c6496022..083eed1dbf 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -62,3 +62,23 @@ colors are provided.") inspired by Python's Literal String Interpolation (PEP-0498) and Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.") (license license:expat))) + +(define-public r-plogr + (package + (name "r-plogr") + (version "0.1-1") + (source + (origin + (method url-fetch) + (uri (cran-uri "plogr" version)) + (sha256 + (base32 + "13zliqlbkl8b04k9ga0sx5jsh7k867gracgl84l2a9kcqy9mqx92")))) + (build-system r-build-system) + (home-page "https://github.com/krlmlr/plogr") + (synopsis "R bindings for the plog C++ logging library") + (description + "This package provides the header files for a stripped-down version of +the plog header-only C++ logging library, and a method to log to R's standard +error stream.") + (license license:expat))) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index fb7431c811..02811f3fdc 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2585,26 +2585,6 @@ variety of formats.") and draw tables.") (license license:gpl2+))) -(define-public r-plogr - (package - (name "r-plogr") - (version "0.1-1") - (source - (origin - (method url-fetch) - (uri (cran-uri "plogr" version)) - (sha256 - (base32 - "13zliqlbkl8b04k9ga0sx5jsh7k867gracgl84l2a9kcqy9mqx92")))) - (build-system r-build-system) - (home-page "https://github.com/krlmlr/plogr") - (synopsis "R bindings for the plog C++ logging library") - (description - "This package provides the header files for a stripped-down version of -the plog header-only C++ logging library, and a method to log to R's standard -error stream.") - (license license:expat))) - (define-public r-pkgconfig (package (name "r-pkgconfig") From 736332c79c17fa76282ae8468927eea0ccc90541 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Aug 2017 15:51:44 +0200 Subject: [PATCH 055/162] gnu: r-rcpp: Update to 0.12.12. * gnu/packages/statistics.scm (r-rcpp): Update to 0.12.12. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 02811f3fdc..428e2a073f 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -796,13 +796,13 @@ Munsell colour system.") (define-public r-rcpp (package (name "r-rcpp") - (version "0.12.10") + (version "0.12.12") (source (origin (method url-fetch) (uri (cran-uri "Rcpp" version)) (sha256 - (base32 "108p485agxwgmnl9p54vsyy94w96lcimlk08v71ddm77gfl13y2f")))) + (base32 "1byyqvlgb2p46p1gv243k73rk69fa8pa4l5m5asmckag2pkb2glz")))) (build-system r-build-system) (home-page "http://www.rcpp.org") (synopsis "Seamless R and C++ Integration") From a8cba9dd112528d67a946eee057c838221eb5249 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Aug 2017 15:52:39 +0200 Subject: [PATCH 056/162] gnu: r-rcpp: Move to (gnu packages cran). * gnu/packages/statistics.scm (r-rcpp): Move from here... * gnu/packages/cran.scm (r-rcpp): ...to here. --- gnu/packages/cran.scm | 24 ++++++++++++++++++++++++ gnu/packages/statistics.scm | 24 ------------------------ gnu/packages/web.scm | 1 + 3 files changed, 25 insertions(+), 24 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 083eed1dbf..863c872d14 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -82,3 +82,27 @@ Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.") the plog header-only C++ logging library, and a method to log to R's standard error stream.") (license license:expat))) + +(define-public r-rcpp + (package + (name "r-rcpp") + (version "0.12.12") + (source + (origin + (method url-fetch) + (uri (cran-uri "Rcpp" version)) + (sha256 + (base32 "1byyqvlgb2p46p1gv243k73rk69fa8pa4l5m5asmckag2pkb2glz")))) + (build-system r-build-system) + (home-page "http://www.rcpp.org") + (synopsis "Seamless R and C++ integration") + (description + "The Rcpp package provides R functions as well as C++ classes which offer +a seamless integration of R and C++. Many R data types and objects can be +mapped back and forth to C++ equivalents which facilitates both writing of new +code as well as easier integration of third-party libraries. Documentation +about Rcpp is provided by several vignettes included in this package, via the +'Rcpp Gallery' site at , the paper by Eddelbuettel +and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see +'citation(\"Rcpp\")' for details on these last two.") + (license license:gpl2+))) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 428e2a073f..1b7c4d3b60 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -793,30 +793,6 @@ see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"") Munsell colour system.") (license license:expat))) -(define-public r-rcpp - (package - (name "r-rcpp") - (version "0.12.12") - (source - (origin - (method url-fetch) - (uri (cran-uri "Rcpp" version)) - (sha256 - (base32 "1byyqvlgb2p46p1gv243k73rk69fa8pa4l5m5asmckag2pkb2glz")))) - (build-system r-build-system) - (home-page "http://www.rcpp.org") - (synopsis "Seamless R and C++ Integration") - (description - "The Rcpp package provides R functions as well as C++ classes which offer -a seamless integration of R and C++. Many R data types and objects can be -mapped back and forth to C++ equivalents which facilitates both writing of new -code as well as easier integration of third-party libraries. Documentation -about Rcpp is provided by several vignettes included in this package, via the -'Rcpp Gallery' site at , the paper by Eddelbuettel -and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see -'citation(\"Rcpp\")' for details on these last two.") - (license license:gpl2+))) - (define-public r-permute (package (name "r-permute") diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index f03f67bf8c..1550454241 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -54,6 +54,7 @@ #:use-module (gnu packages) #:use-module (gnu packages apr) #:use-module (gnu packages check) + #:use-module (gnu packages cran) #:use-module (gnu packages documentation) #:use-module (gnu packages docbook) #:use-module (gnu packages autotools) From eed58a0886433195fd610fc2b7d19c11c11c4ca1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Aug 2017 15:53:33 +0200 Subject: [PATCH 057/162] gnu: Add r-bindr. * gnu/packages/cran.scm (r-bindr): New variable. --- gnu/packages/cran.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 863c872d14..c0f34f1375 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -106,3 +106,22 @@ about Rcpp is provided by several vignettes included in this package, via the and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see 'citation(\"Rcpp\")' for details on these last two.") (license license:gpl2+))) + +(define-public r-bindr + (package + (name "r-bindr") + (version "0.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "bindr" version)) + (sha256 + (base32 + "0d95ifm0x4mrfzi20xf39f5pzd7rfzqsld0vjqf6xzga5rhnd8fc")))) + (build-system r-build-system) + (home-page "https://github.com/krlmlr/bindr") + (synopsis "Parametrized active bindings") + (description + "This package provides a simple interface for creating active bindings +where the bound function accepts additional arguments.") + (license license:expat))) From 4bb0b4cc0aeffcc97d67c257e0c839aedb87f680 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Aug 2017 15:53:49 +0200 Subject: [PATCH 058/162] gnu: Add r-bindrcpp. * gnu/packages/cran.scm (r-bindrcpp): New variable. --- gnu/packages/cran.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index c0f34f1375..feae801116 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -125,3 +125,26 @@ and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see "This package provides a simple interface for creating active bindings where the bound function accepts additional arguments.") (license license:expat))) + +(define-public r-bindrcpp + (package + (name "r-bindrcpp") + (version "0.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "bindrcpp" version)) + (sha256 + (base32 + "0l1l22zl87wiyl79m3gj2vlxmkhxvrkl4alhyy08h55q7hqs3vyh")))) + (build-system r-build-system) + (propagated-inputs + `(("r-bindr" ,r-bindr) + ("r-plogr" ,r-plogr) + ("r-rcpp" ,r-rcpp))) + (home-page "https://github.com/krlmlr/bindrcpp") + (synopsis "Rcpp interface to active bindings") + (description + "This package provides an easy way to fill an environment with active +bindings that call a C++ function.") + (license license:expat))) From a40b2c212944bfffd4d29869589bb64ca9d0fa0c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Aug 2017 16:15:13 +0200 Subject: [PATCH 059/162] gnu: r-dplyr: Update to 0.7.2. * gnu/packages/statistics.scm (r-dplyr): Update to 0.7.2. [propagated-inputs]: Remove r-lazyeval, r-dbi; add r-rlang, r-plogr, r-glue, r-pkgconfig, r-bindrcpp. --- gnu/packages/statistics.scm | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 1b7c4d3b60..e78e0802c7 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1523,20 +1523,23 @@ and printing capabilities than traditional data frames.") (define-public r-dplyr (package (name "r-dplyr") - (version "0.5.0") + (version "0.7.2") (source (origin (method url-fetch) (uri (cran-uri "dplyr" version)) (sha256 (base32 - "0ks5cklb03laqf5ygcw986g1lv7wk1ipvypjlha8xly2y4lvilwk")))) + "0jpb32ca1c0mr660igna4yw4fmzydzfhxshd0g8wgmggkynx2qi2")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) ("r-r6" ,r-r6) ("r-magrittr" ,r-magrittr) - ("r-lazyeval" ,r-lazyeval) - ("r-dbi" ,r-dbi) + ("r-rlang" ,r-rlang) + ("r-plogr" ,r-plogr) + ("r-glue" ,r-glue) + ("r-pkgconfig" ,r-pkgconfig) + ("r-bindrcpp" ,r-bindrcpp) ("r-tibble" ,r-tibble))) (native-inputs `(("r-rcpp" ,r-rcpp) From aad948a0eaea550cbc8e524717a6e74b68bb35b0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Aug 2017 16:16:09 +0200 Subject: [PATCH 060/162] gnu: r-tibble: Update to 1.3.3. * gnu/packages/statistics.scm (r-tibble): Update to 1.3.3. [propagated-inputs]: Remove r-lazyeval, add r-rlang. --- gnu/packages/statistics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index e78e0802c7..1159f2c42e 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1501,17 +1501,17 @@ like tidy evaluation.") (define-public r-tibble (package (name "r-tibble") - (version "1.3.0") + (version "1.3.3") (source (origin (method url-fetch) (uri (cran-uri "tibble" version)) (sha256 (base32 - "1q25i1cv3qms6d3lw7jd3z142w188znkcbyam460gn9si8l8g2bk")))) + "1bhq4pm56l7l6s1k44ajrcr7hz56h37m9ck4zji9f8xfdqschbl0")))) (build-system r-build-system) (propagated-inputs - `(("r-lazyeval" ,r-lazyeval) + `(("r-rlang" ,r-rlang) ("r-rcpp" ,r-rcpp))) (home-page "https://github.com/hadley/tibble") (synopsis "Simple data frames") From 5fc74f24bf96970d783147f60b2b36a87c089ea0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Aug 2017 16:17:04 +0200 Subject: [PATCH 061/162] gnu: r-devtools: Update to 1.13.3. * gnu/packages/statistics.scm (r-devtools): Update to 1.13.3. [propagated-inputs]: Remove r-curl, r-digest, r-evaluate, r-roxygen2, and r-rversions. --- gnu/packages/statistics.scm | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 1159f2c42e..012df8343d 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2251,25 +2251,21 @@ informative error messages when it's not available.") (define-public r-devtools (package (name "r-devtools") - (version "1.13.2") + (version "1.13.3") (source (origin (method url-fetch) (uri (cran-uri "devtools" version)) (sha256 (base32 - "08ajsr12wd31lsx3jv5l9mq4063dc5fpr9lcnzra6kl59vi5pa7v")))) + "146wb09cmfh10vhn1ps2nmzx104zldb3nj9qv2ic0gbcikbbryp6")))) (build-system r-build-system) (propagated-inputs - `(("r-curl" ,r-curl) - ("r-digest" ,r-digest) - ("r-evaluate" ,r-evaluate) + `(("r-digest" ,r-digest) ("r-git2r" ,r-git2r) ("r-httr" ,r-httr) ("r-jsonlite" ,r-jsonlite) ("r-memoise" ,r-memoise) - ("r-roxygen2" ,r-roxygen2) ("r-rstudioapi" ,r-rstudioapi) - ("r-rversions" ,r-rversions) ("r-whisker" ,r-whisker) ("r-withr" ,r-withr))) (home-page "https://github.com/hadley/devtools") From 7b3688150be542f1f3bc27cf350552c0de7026a9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 16:16:38 +0200 Subject: [PATCH 062/162] gnu: r-purrr: Update to 0.2.2.2. * gnu/packages/statistics.scm (r-purrr): Update to 0.2.2.2. [propagated-inputs]: Remove r-bh and r-dplyr; add r-tibble. --- gnu/packages/statistics.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 012df8343d..5002e09d22 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3590,18 +3590,17 @@ It uses and relies on grid graphics and formal (S4) classes and methods.") (define-public r-purrr (package (name "r-purrr") - (version "0.2.2") + (version "0.2.2.2") (source (origin (method url-fetch) (uri (cran-uri "purrr" version)) (sha256 (base32 - "0lss8q733nv7s154wargm6vnxq55qygnxakib8xdj4jv0y86sxc3")))) + "1i1n651xf15489pd6xjdvyp8wyayn8p33d27br39mddn1xdjrpc1")))) (build-system r-build-system) (propagated-inputs - `(("r-bh" ,r-bh) - ("r-dplyr" ,r-dplyr) + `(("r-tibble" ,r-tibble) ("r-lazyeval" ,r-lazyeval) ("r-magrittr" ,r-magrittr) ("r-rcpp" ,r-rcpp))) From d59050823e64a3c6c352487ad1e56d9c6b04216c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 16:17:32 +0200 Subject: [PATCH 063/162] gnu: r-igraph: Update to 1.1.2. * gnu/packages/statistics.scm (r-igraph): Update to 1.1.2. [propagated-inputs]: Remove r-nmf; add r-matrix and r-pkgconfig. --- gnu/packages/statistics.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 5002e09d22..a07c07ab60 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3283,14 +3283,14 @@ performing parallel computations on multicore machines.") (define-public r-igraph (package (name "r-igraph") - (version "1.0.1") + (version "1.1.2") (source (origin (method url-fetch) (uri (cran-uri "igraph" version)) (sha256 (base32 - "00jnm8v3kvxpxav5klld2z2nnkcpj4sdwv4ksipddy5mp04ysr6w")))) + "1v26wyk52snh8z6m5p7yqwcd9dbqifhm57j112i9x53ppi0npcc9")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -3300,7 +3300,8 @@ performing parallel computations on multicore machines.") (propagated-inputs `(("r-irlba" ,r-irlba) ("r-magrittr" ,r-magrittr) - ("r-nmf" ,r-nmf))) + ("r-matrix" ,r-matrix) + ("r-pkgconfig" ,r-pkgconfig))) (home-page "http://igraph.org") (synopsis "Network analysis and visualization") (description From f9b376063643ae4b7c4403d0debad590fba5942d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 16:34:13 +0200 Subject: [PATCH 064/162] gnu: r-plotly: Update to 4.7.1. * gnu/packages/statistics.scm (r-plotly): Update to 4.7.1. [propagated-inputs]: Add r-crosstalk, r-data-table, r-htmltools, and r-rcolorbrewer. --- gnu/packages/statistics.scm | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index a07c07ab60..fd991d6434 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3615,26 +3615,30 @@ features present in other programming languages.") (define-public r-plotly (package (name "r-plotly") - (version "4.5.6") + (version "4.7.1") (source (origin (method url-fetch) (uri (cran-uri "plotly" version)) (sha256 (base32 - "09yw977yxlcxv57kni3q899zrxyxa6pznr06cylr9lqkyr7llfhx")))) + "0wj9lw7w28z8w9ip9vadv6sydjhqyg65kfiai9m3bndzz50b1m3w")))) (build-system r-build-system) (propagated-inputs `(("r-base64enc" ,r-base64enc) + ("r-crosstalk" ,r-crosstalk) ("r-digest" ,r-digest) + ("r-data-table" ,r-data-table) ("r-dplyr" ,r-dplyr) ("r-ggplot2" ,r-ggplot2) ("r-hexbin" ,r-hexbin) + ("r-htmltools" ,r-htmltools) ("r-htmlwidgets" ,r-htmlwidgets) ("r-httr" ,r-httr) ("r-jsonlite" ,r-jsonlite) ("r-lazyeval" ,r-lazyeval) ("r-magrittr" ,r-magrittr) ("r-purrr" ,r-purrr) + ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-scales" ,r-scales) ("r-tibble" ,r-tibble) ("r-tidyr" ,r-tidyr) From cc9a778ecc39371602903850ac9f2f090c2d0381 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 16:49:12 +0200 Subject: [PATCH 065/162] gnu: r-hmisc: Update to 4.0-3. * gnu/packages/statistics.scm (r-hmisc): Update to 4.0-3. [propagated-inputs]: Remove r-base64. --- gnu/packages/statistics.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index fd991d6434..22e35f8aa8 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3814,21 +3814,20 @@ package instead.") (define-public r-hmisc (package (name "r-hmisc") - (version "4.0-2") + (version "4.0-3") (source (origin (method url-fetch) (uri (cran-uri "Hmisc" version)) (sha256 (base32 - "1lg9k0kj803wsm3h0a991q9l2lrgsqryzfv2z79b88kjbfapqpqr")))) + "1a7i7azag6pldgala85d8hh7wnx1shamyiriy4jfc65nxrr2lq8w")))) (properties `((upstream-name . "Hmisc"))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (propagated-inputs `(("r-acepack" ,r-acepack) - ("r-base64" ,r-base64) ("r-base64enc" ,r-base64enc) ("r-cluster" ,r-cluster) ("r-data-table" ,r-data-table) From c628b8418a0e16ebab6af739732bacb9163f3246 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 16:51:23 +0200 Subject: [PATCH 066/162] gnu: r-ranger: Update to 0.8.0. * gnu/packages/statistics.scm (r-ranger): Update to 0.8.0. [propagated-inputs]: Add r-matrix and r-rcppeigen. --- gnu/packages/statistics.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 22e35f8aa8..2ee9879b42 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -5126,17 +5126,19 @@ diagnostic tools (@code{ctlcurves} and @code{DiscrFact}).") (define-public r-ranger (package (name "r-ranger") - (version "0.7.0") + (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "ranger" version)) (sha256 (base32 - "0g1rnpk4c06lmy0r5n0j7i2xna190kqalmxp42d9gnk3drnb1x43")))) + "1fdbm879wx3hlng8s4c4f8f2x5yxz57llakcqnpa0lymybidw3vz")))) (build-system r-build-system) (propagated-inputs - `(("r-rcpp" ,r-rcpp))) + `(("r-rcpp" ,r-rcpp) + ("r-matrix" ,r-matrix) + ("r-rcppeigen" ,r-rcppeigen))) (home-page "https://github.com/imbs-hl/ranger") (synopsis "Fast implementation of random forests") (description From 64c6712d03254ff40fe05f3eaccd2258d2eb8d78 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:06:40 +0200 Subject: [PATCH 067/162] gnu: r-knitrbootstrap: Update to 1.0.1. * gnu/packages/statistics.scm (r-knitrbootstrap): Update to 1.0.1. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 2ee9879b42..f189fd001f 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1309,14 +1309,14 @@ generation in R using Literate Programming techniques.") (define-public r-knitrbootstrap (package (name "r-knitrbootstrap") - (version "1.0.0") + (version "1.0.1") (source (origin (method url-fetch) (uri (cran-uri "knitrBootstrap" version)) (sha256 (base32 - "0pshn2slzqwpryklslsxwh1dmqcnwv6bwi7yfm6m342wjybpk0wl")))) + "089147g7nqp99rwdxxsfmklsrwc8aia09sr8ndmrc335r33v6r6p")))) (properties `((upstream-name . "knitrBootstrap"))) (build-system r-build-system) (propagated-inputs From 0f2eee0d969b27d12a4e5789ff1f27af0e87959d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:07:37 +0200 Subject: [PATCH 068/162] gnu: r-pracma: Update to 2.0.7. * gnu/packages/maths.scm (r-pracma): Update to 2.0.7. --- gnu/packages/maths.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 6ed51b027e..00732a5756 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1626,12 +1626,12 @@ programming problems.") (define-public r-pracma (package (name "r-pracma") - (version "2.0.4") + (version "2.0.7") (source (origin (method url-fetch) (uri (cran-uri "pracma" version)) (sha256 - (base32 "1z3i90mkzwvp9di17caf4934z2xlb2imm3hwxllcrbwvmnmhrwyc")))) + (base32 "0hxa0rbbp54j0c05qj7vfwhqfdmiz5ax8vhqxd09g33x7c0hqbc5")))) (build-system r-build-system) (propagated-inputs `(("r-quadprog" ,r-quadprog))) From 2d81bc16a90944d6e7225ab562c3de117411f1cf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:08:24 +0200 Subject: [PATCH 069/162] gnu: r-httpuv: Update to 1.3.5. * gnu/packages/web.scm (r-httpuv): Update to 1.3.5. --- gnu/packages/web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 1550454241..51533ee0a3 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -3347,13 +3347,13 @@ CDF, Atom 0.3, and Atom 1.0 feeds.") (define-public r-httpuv (package (name "r-httpuv") - (version "1.3.3") + (version "1.3.5") (source (origin (method url-fetch) (uri (cran-uri "httpuv" version)) (sha256 (base32 - "0aibs0hf38n8f6xxx4g2i2lzd6l5h92m5pscx2z834sdvhnladxv")))) + "1sg4f223zfyd265b28rlhsn3b6mqflcpnmya98cjmjncmy9vjdj3")))) (build-system r-build-system) (native-inputs `(("r-rcpp" ,r-rcpp))) (home-page "https://github.com/rstudio/httpuv") From 9fe794f0f73eca2563c122d6d5ea25cad6eb4682 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:09:11 +0200 Subject: [PATCH 070/162] gnu: r-jsonlite: Update to 1.5. * gnu/packages/web.scm (r-jsonlite): Update to 1.5. --- gnu/packages/web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 51533ee0a3..9a923a7f88 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -3371,13 +3371,13 @@ particularly easy to create complete web applications using httpuv alone.") (define-public r-jsonlite (package (name "r-jsonlite") - (version "1.4") + (version "1.5") (source (origin (method url-fetch) (uri (cran-uri "jsonlite" version)) (sha256 (base32 - "11rgkjp5qir79niad0aizjxvjzyvkl6l9nsrv3ikv446vllmrasn")))) + "00lfg464jhf7k01bal9pcjvbdf5cxk6xi2h46hccp1x3h883g434")))) (build-system r-build-system) (home-page "http://arxiv.org/abs/1403.2805") (synopsis "Robust, high performance JSON parser and generator for R") From a1e54db2ace516db7d7f52672f10cafa0ed3131c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:10:05 +0200 Subject: [PATCH 071/162] gnu: r-servr: Update to 0.6. * gnu/packages/web.scm (r-servr): Update to 0.6. --- gnu/packages/web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 9a923a7f88..4e096f19d3 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -3395,13 +3395,13 @@ in systems and applications.") (define-public r-servr (package (name "r-servr") - (version "0.5") + (version "0.6") (source (origin (method url-fetch) (uri (cran-uri "servr" version)) (sha256 (base32 - "1ixcl9xjc1k9zvl6v6bsw4kpramr1h53b4s46qg8kahkqy6kqd8a")))) + "0sqz3wssxa19g9mpmf9s4gx2a5rvzl8nrd11qkgpz5v3iqsc6ysr")))) (build-system r-build-system) (propagated-inputs `(("r-httpuv" ,r-httpuv) From 850151058dcb99dedced7ceb00d1203e649f9898 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:10:46 +0200 Subject: [PATCH 072/162] gnu: r-htmltools: Update to 0.3.6. * gnu/packages/web.scm (r-htmltools): Update to 0.3.6. --- gnu/packages/web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 4e096f19d3..e6dc13500a 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -3420,13 +3420,13 @@ directory.") (define-public r-htmltools (package (name "r-htmltools") - (version "0.3.5") + (version "0.3.6") (source (origin (method url-fetch) (uri (cran-uri "htmltools" version)) (sha256 (base32 - "0j9bf80grd6gwh7116m575pycv87c0wcwkxsz3gzzfs4aw3pxyr9")))) + "18k8r1s8sz1jy7dkz35n69wj20xhmllr53xmwb4pdzf2z61gpbs4")))) (build-system r-build-system) (arguments `(#:phases From 53deffe5e9e4fd24d57c0f34059f6be04a7d8cf9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:11:14 +0200 Subject: [PATCH 073/162] gnu: r-htmlwidgets: Update to 0.9. * gnu/packages/web.scm (r-htmlwidgets): Update to 0.9. --- gnu/packages/web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index e6dc13500a..45526f2cc0 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -3454,13 +3454,13 @@ directory.") (define-public r-htmlwidgets (package (name "r-htmlwidgets") - (version "0.8") + (version "0.9") (source (origin (method url-fetch) (uri (cran-uri "htmlwidgets" version)) (sha256 (base32 - "1df3pwl34rvdbr9sgr5h27q9bmqpckvpwq4frl3d1v614y3vfclj")))) + "0plqkfqys1ca3ki7sb7yc6gwjpi7yy4g3mzh7hfy8s6qri0vam0i")))) (build-system r-build-system) (propagated-inputs `(("r-htmltools" ,r-htmltools) From e584b9fc1b201a79212910251cf2fbae0f9e1526 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:11:59 +0200 Subject: [PATCH 074/162] gnu: r-curl: Update to 2.8.1. * gnu/packages/web.scm (r-curl): Update to 2.8.1. --- gnu/packages/web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 45526f2cc0..972f1bdbce 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -3508,13 +3508,13 @@ LaTeX.") (define-public r-curl (package (name "r-curl") - (version "2.5") + (version "2.8.1") (source (origin (method url-fetch) (uri (cran-uri "curl" version)) (sha256 (base32 - "09p86i5f88gx1i7cidm1ka56g0jjkghqfam96p1jhwlh2fv6nrks")))) + "0dgfl7wn4r8inv55xnk4ybf1y2x4qmi4cbr6phr3lfi1dnjm4hsm")))) (build-system r-build-system) (arguments `(#:phases From af1eeabe899342d19ebaabbc6e34733758b8c350 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:12:26 +0200 Subject: [PATCH 075/162] gnu: r-boot: Update to 1.3-20. * gnu/packages/statistics.scm (r-boot): Update to 1.3-20. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index f189fd001f..810a2ad688 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -264,14 +264,14 @@ available, greatly increasing its breadth and scope.") (define-public r-boot (package (name "r-boot") - (version "1.3-19") + (version "1.3-20") (source (origin (method url-fetch) (uri (cran-uri "boot" version)) (sha256 (base32 - "16hsw4bw9pkfc2lqxfwycm1sbvbrm4linvm0ci71n8sxc7srvkis")))) + "0ai1qpm0p4z07xr0dvag8sdn9jrxcwanrsk9khzmww094jvr1jxd")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/boot") (synopsis "Bootstrap functions for R") From 74b037df64914254f5539ccaca697310459b6b79 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:12:51 +0200 Subject: [PATCH 076/162] gnu: r-foreign: Update to 0.8-69. * gnu/packages/statistics.scm (r-foreign): Update to 0.8-69. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 810a2ad688..ae03f9ca8d 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -366,14 +366,14 @@ Hubert, based on Kaufman and Rousseeuw (1990) \"Finding Groups in Data\".") (define-public r-foreign (package (name "r-foreign") - (version "0.8-67") + (version "0.8-69") (source (origin (method url-fetch) (uri (cran-uri "foreign" version)) (sha256 (base32 - "0j0z815zyp8n97rk6hlk68d1r8b26vls39s03viq0pnx3cbpwyga")))) + "0s1lxmd85dd0kxx8hwk02w9l7pmpk4bpy7787fbyh2dbq5g9ys0k")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/foreign") (synopsis "Read data stored by other statistics software") From dbeda1b4a0fd1d6b59ba95ef036441c83f50642e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:13:15 +0200 Subject: [PATCH 077/162] gnu: r-matrix: Update to 1.2-10. * gnu/packages/statistics.scm (r-matrix): Update to 1.2-10. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index ae03f9ca8d..63166bea32 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -428,14 +428,14 @@ also flexible enough to handle most nonstandard requirements.") (define-public r-matrix (package (name "r-matrix") - (version "1.2-8") + (version "1.2-10") (source (origin (method url-fetch) (uri (cran-uri "Matrix" version)) (sha256 (base32 - "1dyv42d7ranb85y8hvi57hbg5xnvhdzqn56wcq3qmhazqj3s3liw")))) + "0r3qjcz92xwgdzrfz444mqzwnja5sv9abaf252fh6k48qbyahahh")))) (properties `((upstream-name . "Matrix"))) (build-system r-build-system) (propagated-inputs From 6fb21ed2a346e426571c088098b642fd20fe0aa7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:13:46 +0200 Subject: [PATCH 078/162] gnu: r-mgcv: Update to 1.8-18. * gnu/packages/statistics.scm (r-mgcv): Update to 1.8-18. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 63166bea32..95d106035e 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -473,14 +473,14 @@ nonlinear mixed-effects models.") (define-public r-mgcv (package (name "r-mgcv") - (version "1.8-17") + (version "1.8-18") (source (origin (method url-fetch) (uri (cran-uri "mgcv" version)) (sha256 (base32 - "1zj223l4a3j15d3c01wv7dkzn9w6084gxrq5600ck9rvr0lfpwwg")))) + "011mgcypr56xvm9nizsfsb2285kzql93x0d3lzg849g39vbpp4s2")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix) From 831858a7d3215f4b17700260845675deeb9f6d75 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:14:14 +0200 Subject: [PATCH 079/162] gnu: r-bit64: Update to 0.9-7. * gnu/packages/statistics.scm (r-bit64): Update to 0.9-7. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 95d106035e..30f83d098c 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -622,14 +622,14 @@ binary booleans, @code{TRUE} and @code{FALSE} can be stored with 1 bit only.") (define-public r-bit64 (package (name "r-bit64") - (version "0.9-5") + (version "0.9-7") (source (origin (method url-fetch) (uri (cran-uri "bit64" version)) (sha256 (base32 - "0fz5m3fhvxgwjl76maag7yn0zdw24rx34gy6v77378fajag9yllg")))) + "07znvz9vp1nz1y5ljng4qyskvm943cdbmy996s67560ijxzsm6kv")))) (build-system r-build-system) (propagated-inputs `(("r-bit" ,r-bit))) From d5ce3807114123abd8d3e84f054edd6f26f45309 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:14:42 +0200 Subject: [PATCH 080/162] gnu: r-dbi: Update to 0.7. * gnu/packages/statistics.scm (r-dbi): Update to 0.7. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 30f83d098c..5d0f675a71 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1120,13 +1120,13 @@ evaluation (NSE) in R.") (define-public r-dbi (package (name "r-dbi") - (version "0.6-1") + (version "0.7") (source (origin (method url-fetch) (uri (cran-uri "DBI" version)) (sha256 (base32 - "1fg158k4n6l3rzx9nrwhp4nwkwpbmv1q7z2xz5rw138zws68fkgr")))) + "04fyrxdpqcygg5wviy637y6lgk64xqjjq31lvv4hwqj5kbaxamr5")))) (build-system r-build-system) (home-page "https://github.com/rstats-db/DBI") (synopsis "R database interface") From 12cd7975410669c687c9285bcc97d1e720129aad Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:15:09 +0200 Subject: [PATCH 081/162] gnu: r-evaluate: Update to 0.10.1. * gnu/packages/statistics.scm (r-evaluate): Update to 0.10.1. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 5d0f675a71..3e1b64cf9e 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1158,13 +1158,13 @@ for template use among CRAN packages.") (define-public r-evaluate (package (name "r-evaluate") - (version "0.10") + (version "0.10.1") (source (origin (method url-fetch) (uri (cran-uri "evaluate" version)) (sha256 (base32 - "0mwna7rjyrmc76651a1fm7c76ippdsc2wsp3sj3iwb1c73mvlqv1")))) + "070vvmnbdlp7sz2zhza7fhd2a6mlwiln8fn4hyzhsiizbn4n79y9")))) (build-system r-build-system) (propagated-inputs `(("r-stringr" ,r-stringr))) From 6dc86e8dfc4fa22b1a320283c8bb2188efd8e39a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:15:34 +0200 Subject: [PATCH 082/162] gnu: r-formatr: Update to 1.5. * gnu/packages/statistics.scm (r-formatr): Update to 1.5. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 3e1b64cf9e..cd01c733ec 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1180,13 +1180,13 @@ adapted for other output formats, such as HTML or LaTeX.") (define-public r-formatr (package (name "r-formatr") - (version "1.4") + (version "1.5") (source (origin (method url-fetch) (uri (cran-uri "formatR" version)) (sha256 (base32 - "1fvynq0fj1r9grg9vvfdh5fl2riv6qki9f2rfpyvbvqq3xxpmi3f")))) + "19sd23vgs4ac0fwlw40j3676k6mramb0ajlq8hdw23kjwdx1jk47")))) (build-system r-build-system) (home-page "http://yihui.name/formatR") (synopsis "Format R code automatically") From b07c8c01565b23cc4c5ae5313c8302e0227fa6db Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:15:57 +0200 Subject: [PATCH 083/162] gnu: r-knitr: Update to 1.16. * gnu/packages/statistics.scm (r-knitr): Update to 1.16. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index cd01c733ec..9ef4d166ce 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1281,13 +1281,13 @@ emitter (http://pyyaml.org/wiki/LibYAML) for R.") (define-public r-knitr (package (name "r-knitr") - (version "1.15.1") + (version "1.16") (source (origin (method url-fetch) (uri (cran-uri "knitr" version)) (sha256 (base32 - "1pbxd3k7kv5sa1a5gxm0zc2bhjxdgx2nfch9xap5k85djmgsfqc1")))) + "02balmhvc955rkqv4v0wkxbw4vjphydajgcpy4ml0s3b4sziyj0h")))) (build-system r-build-system) (propagated-inputs `(("r-evaluate" ,r-evaluate) From f05c6275b762b7d2abf0280330d8018065d6da8c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:16:17 +0200 Subject: [PATCH 084/162] gnu: r-r6: Update to 2.2.2. * gnu/packages/statistics.scm (r-r6): Update to 2.2.2. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 9ef4d166ce..d1f8f08c44 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1461,13 +1461,13 @@ flexible and easy to set up.") (define-public r-r6 (package (name "r-r6") - (version "2.2.0") + (version "2.2.2") (source (origin (method url-fetch) (uri (cran-uri "R6" version)) (sha256 (base32 - "1ir51pb0y6yj05qaxsflk4a6hv8n73cwlb0qajcskbrz632dsyvx")))) + "13xfdr19ca7ymisidsanm6w7hsk3qmy5l8c0mlz3nk48f7s5cxq8")))) (build-system r-build-system) (home-page "https://github.com/wch/R6/") (synopsis "Classes with reference semantics in R") From c832d326a1671d0f6741a48cea8a7bd45600d2a8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:16:39 +0200 Subject: [PATCH 085/162] gnu: r-formula: Update to 1.2-2. * gnu/packages/statistics.scm (r-formula): Update to 1.2-2. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index d1f8f08c44..1529d1135a 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1602,14 +1602,14 @@ Groups in Data\".") (define-public r-formula (package (name "r-formula") - (version "1.2-1") + (version "1.2-2") (source (origin (method url-fetch) (uri (cran-uri "Formula" version)) (sha256 (base32 - "02in5325zzrqbhlygx6s0dinj6ymw845q70y56frqacv25ayzcax")))) + "0ad49bzip1zqmpj1d8jajwl4bd81fm3k6dq8p26x6mvlzc04dvwd")))) (properties `((upstream-name . "Formula"))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/Formula") From 63f934e67243bc4cfb887655de92369cf819ab71 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:16:59 +0200 Subject: [PATCH 086/162] gnu: r-backports: Update to 1.1.0. * gnu/packages/statistics.scm (r-backports): Update to 1.1.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 1529d1135a..3489068273 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1934,14 +1934,14 @@ limited to R.") (define-public r-backports (package (name "r-backports") - (version "1.0.5") + (version "1.1.0") (source (origin (method url-fetch) (uri (cran-uri "backports" version)) (sha256 (base32 - "1pn1ii8vbkgxcqvx52kzsbwf9gkn9fp33388087zky2hmdzdirn0")))) + "1kcz6j82by28cjk5wi2j6dfqdin1kib4y7d2r4h3zabcxmk6jly5")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/backports") (synopsis "Reimplementations of functions introduced since R 3.0.0") From 58e1ce86abf2ee636b2ec5eca27738357cd8db03 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:17:49 +0200 Subject: [PATCH 087/162] gnu: r-checkmate: Update to 1.8.3. * gnu/packages/statistics.scm (r-checkmate): Update to 1.8.3. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 3489068273..d568e6e6c7 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -1957,14 +1957,14 @@ R version.") (define-public r-checkmate (package (name "r-checkmate") - (version "1.8.2") + (version "1.8.3") (source (origin (method url-fetch) (uri (cran-uri "checkmate" version)) (sha256 (base32 - "1zqcggl9m7slvc0q6zyhssdypb7jzf3l9byl5vxh1qdwjiw2y64g")))) + "04rxabzamhv6ybynx627sxk02qvq8znkv0y10vmq67xx6pxhqvla")))) (build-system r-build-system) (propagated-inputs `(("r-backports" ,r-backports))) From f212bf84abfc00cc536778a64b8400082ff78826 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:18:22 +0200 Subject: [PATCH 088/162] gnu: r-git2r: Update to 0.19.0. * gnu/packages/statistics.scm (r-git2r): Update to 0.19.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index d568e6e6c7..3c89612437 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2207,13 +2207,13 @@ functions make it easy to control additional request components.") (define-public r-git2r (package (name "r-git2r") - (version "0.18.0") + (version "0.19.0") (source (origin (method url-fetch) (uri (cran-uri "git2r" version)) (sha256 (base32 - "0bgzdsdi9n6l8pchivs6a2g4ksa56qs8hygpyv2c0ndqmx4jxcwi")))) + "0ws6fbndmaafk2am4dwnz24qizxhld0yh54hgx0z6lzv3p1j209q")))) (build-system r-build-system) ;; This R package contains modified sources of libgit2. This modified ;; version of libgit2 is built as the package is built. Hence libgit2 is From d8048a1212e880ce360aaf1b32f4bf3c84e51028 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:18:45 +0200 Subject: [PATCH 089/162] gnu: r-withr: Update to 2.0.0. * gnu/packages/statistics.scm (r-withr): Update to 2.0.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 3c89612437..f8c637f163 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2277,13 +2277,13 @@ tools to simplify the devolpment of R packages.") (define-public r-withr (package (name "r-withr") - (version "1.0.2") + (version "2.0.0") (source (origin (method url-fetch) (uri (cran-uri "withr" version)) (sha256 (base32 - "042z8nmqqilgrvhmbqrjc05qys3gzwq1rqy2wxp2bi5d41859493")))) + "0ncq9ygx33rx7aazn53p0a0vbr5xv0r6wbkzcwbhbwyd8k55bgin")))) (build-system r-build-system) (home-page "https://github.com/jimhester/withr") (synopsis "Run code with temporarily modified global state") From 76040b85613a2dd99d27c485a12e57d9cb221fb5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:19:03 +0200 Subject: [PATCH 090/162] gnu: r-readr: Update to 1.1.1. * gnu/packages/statistics.scm (r-readr): Update to 1.1.1. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index f8c637f163..d47d03126e 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2315,13 +2315,13 @@ time-of-day values, based on the @code{difftime} class.") (define-public r-readr (package (name "r-readr") - (version "1.1.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "readr" version)) (sha256 (base32 - "1g7g3gdmvq7nj8asw6fi13k38c420sy9696nqgkrhlvv5h13yqs7")))) + "1cvw5wdcqk88cp5fyv678mnmp66l3whcd2yh33p2qvx0168bja8s")))) (build-system r-build-system) (propagated-inputs `(("r-rcpp" ,r-rcpp) From 1c41d51743864245620eff0f2ba2cb1b9ad0ec44 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:19:22 +0200 Subject: [PATCH 091/162] gnu: r-plotrix: Update to 3.6-5. * gnu/packages/statistics.scm (r-plotrix): Update to 3.6-5. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index d47d03126e..a7a3ca8cab 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2339,13 +2339,13 @@ disk (or a connection).") (define-public r-plotrix (package (name "r-plotrix") - (version "3.6-4") + (version "3.6-5") (source (origin (method url-fetch) (uri (cran-uri "plotrix" version)) (sha256 (base32 - "1wxzjnzvkl3aga51ad2xhv4s7v46kvnp4z0nz4cb9cn10057sfw8")))) + "01655y3qzy0283ppc85bi0g42g20zrqzcl0qb30cl6rcbflhymlb")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/plotrix") (synopsis "Various plotting functions") From 7c172eacfa082fe1a2f8ae284fe4ef604fb0ce44 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:20:00 +0200 Subject: [PATCH 092/162] gnu: r-rcpparmadillo: Update to 0.7.900.2.0. * gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.7.900.2.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index a7a3ca8cab..10ad5fc708 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2398,13 +2398,13 @@ well as additional utilities such as panel and axis annotation functions.") (define-public r-rcpparmadillo (package (name "r-rcpparmadillo") - (version "0.7.800.2.0") + (version "0.7.900.2.0") (source (origin (method url-fetch) (uri (cran-uri "RcppArmadillo" version)) (sha256 (base32 - "025lh504nw7ir1f2xsqnvfkq9rg0rb2xzfn3a2s0b2a9snqdzzwr")))) + "01qsff2p1fp5i9lq7rsykrskgr6smz24ddspbl5ad9a8rkmczwyv")))) (properties `((upstream-name . "RcppArmadillo"))) (build-system r-build-system) (propagated-inputs From cc8ba9b69c1b546b182156f7b2b4aec5612533e8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:20:31 +0200 Subject: [PATCH 093/162] gnu: r-rmarkdown: Update to 1.6. * gnu/packages/statistics.scm (r-rmarkdown): Update to 1.6. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 10ad5fc708..db78a8bc31 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2490,14 +2490,14 @@ certain criterion, e.g., it contains a certain regular file.") (define-public r-rmarkdown (package (name "r-rmarkdown") - (version "1.4") + (version "1.6") (source (origin (method url-fetch) (uri (cran-uri "rmarkdown" version)) (sha256 (base32 - "1dvs9cq88g61wfimifagq6y98yxavxzjan39jvpdsg98mafckq9g")))) + "0p8ph5z5pifk1nxc1bppkfs1ir5gjc6ap9n64b4255m2fdaqfrc7")))) (properties `((upstream-name . "rmarkdown"))) (build-system r-build-system) (propagated-inputs From fe9917284f7df172392db16993f1eb41a44b59ac Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:20:51 +0200 Subject: [PATCH 094/162] gnu: r-xml: Update to 3.98-1.9. * gnu/packages/statistics.scm (r-xml): Update to 3.98-1.9. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index db78a8bc31..c0da1a80d8 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2662,13 +2662,13 @@ ldap, and also supports cookies, redirects, authentication, etc.") (define-public r-xml (package (name "r-xml") - (version "3.98-1.6") + (version "3.98-1.9") (source (origin (method url-fetch) (uri (cran-uri "XML" version)) (sha256 (base32 - "1amxx7fpik162nimrr7m5lvv6rhx9cwdyg44fxp1i5wm3y4skwnz")))) + "1hzkdkgs0nzmfg9wm7kyh1j9i0i2g7925whzlihqvg9grdlh3dx3")))) (properties `((upstream-name . "XML"))) (build-system r-build-system) From 127b926bc1dcf71c9bbb2dc3ccd93bfc02ea125c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:21:18 +0200 Subject: [PATCH 095/162] gnu: r-segmented: Update to 0.5-2.1. * gnu/packages/statistics.scm (r-segmented): Update to 0.5-2.1. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index c0da1a80d8..5423e132fa 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2780,14 +2780,14 @@ statements.") (define-public r-segmented (package (name "r-segmented") - (version "0.5-1.4") + (version "0.5-2.1") (source (origin (method url-fetch) (uri (cran-uri "segmented" version)) (sha256 (base32 - "1740cvx2q4v23g4q0zkvg50s5bv8jcrlzzhm7fac4xn0riwmzp5i")))) + "1i576xksc761nyv2dmq86nwbgqvp0plz6bjcn69nkdwq2wbizmw8")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/segmented") (synopsis "Regression models with breakpoints estimation") From 81c057ced9d81728e3218508ca85e9ce038404eb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:21:46 +0200 Subject: [PATCH 096/162] gnu: r-sparsem: Update to 1.77. * gnu/packages/statistics.scm (r-sparsem): Update to 1.77. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 5423e132fa..a6be7df3b5 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2821,13 +2821,13 @@ worker processes and collect and return the results on the master.") (define-public r-sparsem (package (name "r-sparsem") - (version "1.76") + (version "1.77") (source (origin (method url-fetch) (uri (cran-uri "SparseM" version)) (sha256 (base32 - "16xnl9cacim35aawq6bmd2y6rrhnh1kg6dwsy3k5yslkfr1y9j62")))) + "0p6ljma2h12cq1xmy0cxb48ih8dhxxbnwkqzvx3cckxf2kprycm9")))) (properties `((upstream-name . "SparseM"))) (inputs From 1c576cbadb88258b03d78091c1037ad906aea6bf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:22:07 +0200 Subject: [PATCH 097/162] gnu: r-irlba: Update to 2.2.1. * gnu/packages/statistics.scm (r-irlba): Update to 2.2.1. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index a6be7df3b5..fe00155675 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3008,14 +3008,14 @@ flexible than the orphaned \"base64\" package.") (define-public r-irlba (package (name "r-irlba") - (version "2.1.2") + (version "2.2.1") (source (origin (method url-fetch) (uri (cran-uri "irlba" version)) (sha256 (base32 - "1qbcn0ix85pmk296jhpi419kvh06vxm5cq24yk013ps3g7fyi0si")))) + "0zfb7x1701n6gask0f8y2yq0vmb82xkxf6limp43ivx551hx600s")))) (build-system r-build-system) (propagated-inputs `(("r-matrix" ,r-matrix))) From e1cd25bc7871d8f9d2bc81c96c1ac3b015d7b868 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:22:36 +0200 Subject: [PATCH 098/162] gnu: r-glmnet: Update to 2.0-10. * gnu/packages/statistics.scm (r-glmnet): Update to 2.0-10. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index fe00155675..7deb27e015 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3030,14 +3030,14 @@ analysis of large sparse or dense matrices.") (define-public r-glmnet (package (name "r-glmnet") - (version "2.0-5") + (version "2.0-10") (source (origin (method url-fetch) (uri (cran-uri "glmnet" version)) (sha256 (base32 - "1cbpzmbv837fvq88rgn6mgzgr9f1wqp9fg8gh2kkmngvr1957a9c")))) + "07n2hz4fvjyv0siai8z8wqwfj8d58i8n1vzf1ckdfzp4kxa3z08d")))) (build-system r-build-system) (inputs `(("gfortran" ,gfortran))) From 9b9fef0eafe4c3dc448c0d779cbbb8bbc6cb6e2d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:22:55 +0200 Subject: [PATCH 099/162] gnu: r-tidyr: Update to 0.6.3. * gnu/packages/statistics.scm (r-tidyr): Update to 0.6.3. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 7deb27e015..7ca656664b 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3535,14 +3535,14 @@ the 'lite' version of the more complete @code{viridis} package.") (define-public r-tidyr (package (name "r-tidyr") - (version "0.6.1") + (version "0.6.3") (source (origin (method url-fetch) (uri (cran-uri "tidyr" version)) (sha256 (base32 - "11hs3gqpbaw3w281as4m7j9n594ix5axfpwbyjsd0l62pwnzj217")))) + "14s57zrjm2phiy600z9ivq4az71z0ggmp6nj0js7yrybxf0dlah6")))) (build-system r-build-system) (propagated-inputs `(("r-dplyr" ,r-dplyr) From 1d256438c84862906d95e860502170c9a968aca0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:23:31 +0200 Subject: [PATCH 100/162] gnu: r-googlesheets: Update to 0.2.2. * gnu/packages/statistics.scm (r-googlesheets): Update to 0.2.2. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 7ca656664b..7f1d6593cc 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3720,14 +3720,14 @@ character vector.") (define-public r-googlesheets (package (name "r-googlesheets") - (version "0.2.1") + (version "0.2.2") (source (origin (method url-fetch) (uri (cran-uri "googlesheets" version)) (sha256 (base32 - "0ps13h1cv7fj5dh8s4nvwi64wnnyqdsadcaa4iizq1c5s615cwk3")))) + "18q0xmxn09b52rmky7gr5flp0awndcnsgb7zcvkzvkrkvmwad52b")))) (build-system r-build-system) (propagated-inputs `(("r-cellranger" ,r-cellranger) From 2c75199c56b6558a6c717febba018ddd77f850b2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:23:53 +0200 Subject: [PATCH 101/162] gnu: r-sfsmisc: Update to 1.1-1. * gnu/packages/statistics.scm (r-sfsmisc): Update to 1.1-1. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 7f1d6593cc..5d53852028 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3944,14 +3944,14 @@ existing packages provide.") (define-public r-sfsmisc (package (name "r-sfsmisc") - (version "1.1-0") + (version "1.1-1") (source (origin (method url-fetch) (uri (cran-uri "sfsmisc" version)) (sha256 (base32 - "0580piv4n1nispl3pa8nfjjfnb8iwaqky2dzdy0aqnxrxgrhqhvz")))) + "0jzmbywlyzfxs7hlmyd0iynghfc9qp5sa5lnhr73y8r360yv1ahf")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/sfsmisc") (synopsis "Utilities from \"Seminar fuer Statistik\" ETH Zurich") From 80d1185076be3366a7eb9e006f4871af85093a17 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:24:19 +0200 Subject: [PATCH 102/162] gnu: r-gdata: Update to 2.18.0. * gnu/packages/statistics.scm (r-gdata): Update to 2.18.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 5d53852028..2e42ff7af9 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3985,14 +3985,14 @@ tests for whether a value is missing, empty or contains only @code{NA} and (define-public r-gdata (package (name "r-gdata") - (version "2.17.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (cran-uri "gdata" version)) (sha256 (base32 - "0kiy3jbcszlpmarg311spdsfi5pn89wgy742dxsbzxk8907fr5w0")))) + "0zwdj7lscgxr8r62ii8hbdh4mb7sa9w4f5nv32zzrxdvymcpya2b")))) (build-system r-build-system) (inputs `(("perl" ,perl))) From a8c2706de21f2cbeb709e3e72618756d5507d595 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:24:46 +0200 Subject: [PATCH 103/162] gnu: r-statmod: Update to 1.4.30. * gnu/packages/statistics.scm (r-statmod): Update to 1.4.30. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 2e42ff7af9..6ab5379ee5 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4266,13 +4266,13 @@ Wall Street Journal, among others. This package also provides (define-public r-statmod (package (name "r-statmod") - (version "1.4.29") + (version "1.4.30") (source (origin (method url-fetch) (uri (cran-uri "statmod" version)) (sha256 (base32 - "1fgzkwriba39d7946lq892f0si2fjdy37pvxki6ix8xyj8qgnci4")))) + "07v4x8af60alcw6vbiwf5fp25bhra61kvxz9kqx64lszm0i1fb4x")))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/statmod") (native-inputs From d58faa7f447bbccc1b8714dc43a7940177ab3e62 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:25:18 +0200 Subject: [PATCH 104/162] gnu: r-rann: Update to 2.5.1. * gnu/packages/statistics.scm (r-rann): Update to 2.5.1. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 6ab5379ee5..dd47cee905 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4292,13 +4292,13 @@ dispersion modeling and Tweedie power-law families.") (define-public r-rann (package (name "r-rann") - (version "2.5") + (version "2.5.1") (source (origin (method url-fetch) (uri (cran-uri "RANN" version)) (sha256 (base32 - "007cgqg9bybg2zlljbv5m6cmlm3r6i251018rpgjcn0xnm9sjsj7")))) + "0il5i99vbcagnxvb15af5n37g04a4q1x96bz73zh3jhki9fpw9vm")))) (properties `((upstream-name . "RANN"))) (build-system r-build-system) From df03b6f90c0613472b9306679ff95a7bcc3aaa22 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:25:45 +0200 Subject: [PATCH 105/162] gnu: r-cowplot: Update to 0.8.0. * gnu/packages/statistics.scm (r-cowplot): Update to 0.8.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index dd47cee905..13f6639e40 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4361,14 +4361,14 @@ Farebrother's algorithm or Liu et al.'s algorithm.") (define-public r-cowplot (package (name "r-cowplot") - (version "0.7.0") + (version "0.8.0") (source (origin (method url-fetch) (uri (cran-uri "cowplot" version)) (sha256 (base32 - "03iimcsh1pk7iqzjdlfcj43b8khijdk4hg00j4jdllv19xsfb0hx")))) + "03bh0r6ynr95gk4lc8asfi3kpmskm59vfzwn417pdziha3igs5x6")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) From 62d3afc3d6c38b3d60fb754ff2b9916e86cc839a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:26:06 +0200 Subject: [PATCH 106/162] gnu: r-fastica: Update to 1.2-1. * gnu/packages/statistics.scm (r-fastica): Update to 1.2-1. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 13f6639e40..8fd757a003 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4434,14 +4434,14 @@ regression.") (define-public r-fastica (package (name "r-fastica") - (version "1.2-0") + (version "1.2-1") (source (origin (method url-fetch) (uri (cran-uri "fastICA" version)) (sha256 (base32 - "0ykk78fsk5da2g16i4wji85bvji7nayjvkfp07hyaxq9d15jmf0r")))) + "108z2ymby5y4h8l4l2krqwm28rya93gq09yylgilnm3afvfrfabg")))) (properties `((upstream-name . "fastICA"))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/fastICA") From 60869fb2f857de565499e859e67a226d9cc769eb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:26:37 +0200 Subject: [PATCH 107/162] gnu: r-flexmix: Update to 2.3-14. * gnu/packages/statistics.scm (r-flexmix): Update to 2.3-14. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 8fd757a003..81e92359b0 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4517,14 +4517,14 @@ to change in the future.") (define-public r-flexmix (package (name "r-flexmix") - (version "2.3-13") + (version "2.3-14") (source (origin (method url-fetch) (uri (cran-uri "flexmix" version)) (sha256 (base32 - "1i205yw3kkxs27gqcs6zx0c2mh16p332a2p06wq6fdzb20bazg3z")))) + "0sl4zxh1sb2sr5q7svjw9ihrm219jzn82yrc9d43q6r1b8bpyz43")))) (build-system r-build-system) (propagated-inputs `(("r-lattice" ,r-lattice) From 41692b29636c1e492b35fa5b02c229bb003a6438 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:27:10 +0200 Subject: [PATCH 108/162] gnu: r-mclust: Update to 5.3. * gnu/packages/statistics.scm (r-mclust): Update to 5.3. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 81e92359b0..10305d73e5 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4543,14 +4543,14 @@ models, generalized linear models and model-based clustering.") (define-public r-mclust (package (name "r-mclust") - (version "5.2.3") + (version "5.3") (source (origin (method url-fetch) (uri (cran-uri "mclust" version)) (sha256 (base32 - "0045msdw1xndfmlylbnm1ss716iiqzqwj454a97gmcq5kph86qzz")))) + "0h5syvpg3azrz5d10z2afilaa27jb4azi38idzlv05mfcs16s6rb")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) From 4431dd3a4eb9f8c9ee074e70475d5215f48e40d3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:27:40 +0200 Subject: [PATCH 109/162] gnu: r-vgam: Update to 1.0-4. * gnu/packages/statistics.scm (r-vgam): Update to 1.0-4. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 10305d73e5..82972c8646 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4690,14 +4690,14 @@ groupings.") (define-public r-vgam (package (name "r-vgam") - (version "1.0-3") + (version "1.0-4") (source (origin (method url-fetch) (uri (cran-uri "VGAM" version)) (sha256 (base32 - "0wr6szcpj8r4a1rlzgd6iym7khin69fmvxcf37iyvs8mms86dfr3")))) + "0r59hyp3afmvms890b3v2yyckf8v0qkjf2w11rnqd2zgg1gri0g5")))) (properties `((upstream-name . "VGAM"))) (build-system r-build-system) (inputs From 12c3bbb6629c3e9412929b5d5d1f6dae80eba032 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:28:01 +0200 Subject: [PATCH 110/162] gnu: r-pbapply: Update to 1.3-3. * gnu/packages/statistics.scm (r-pbapply): Update to 1.3-3. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 82972c8646..04e2a749c6 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4715,14 +4715,14 @@ VGLMs can be loosely thought of as multivariate generalised linear models.") (define-public r-pbapply (package (name "r-pbapply") - (version "1.3-2") + (version "1.3-3") (source (origin (method url-fetch) (uri (cran-uri "pbapply" version)) (sha256 (base32 - "1sdmjlnwxb99f95g5v8k8mirrkzw99yig377v0qi9lzwjgd6fqqr")))) + "0iqhymf65jffh00qf056h1p76xf92bfmij6aymlmgnvn24fv4ybk")))) (build-system r-build-system) (home-page "https://github.com/psolymos/pbapply") (synopsis "Adding progress bar to apply functions") From 0f008abe7a52691c8f9849d4db90029a77a1d10c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:28:29 +0200 Subject: [PATCH 111/162] gnu: r-rcppeigen: Update to 0.3.3.3.0. * gnu/packages/statistics.scm (r-rcppeigen): Update to 0.3.3.3.0. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 04e2a749c6..13249c70e4 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4779,14 +4779,14 @@ based on an interface to Fortran implementations by M. J. D. Powell.") (define-public r-rcppeigen (package (name "r-rcppeigen") - (version "0.3.2.9.1") + (version "0.3.3.3.0") (source (origin (method url-fetch) (uri (cran-uri "RcppEigen" version)) (sha256 (base32 - "1ih940yjbc530cmpl6kx1jic7pz2ps1w5vrvy32qizh6m5s3lk7x")))) + "0zz9v0f8nnlvhhqv91lkyfblvjnmav84l89mr6vmbqjc2hzqd3n8")))) (properties `((upstream-name . "RcppEigen"))) (build-system r-build-system) (propagated-inputs From 6bb4bfa4bc282e93de77f68bd4461e25c05b0775 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:28:49 +0200 Subject: [PATCH 112/162] gnu: r-car: Update to 2.1-5. * gnu/packages/statistics.scm (r-car): Update to 2.1-5. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 13249c70e4..6467e9e131 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -4957,14 +4957,14 @@ bootstrap test for generalized linear mixed models.") (define-public r-car (package (name "r-car") - (version "2.1-4") + (version "2.1-5") (source (origin (method url-fetch) (uri (cran-uri "car" version)) (sha256 (base32 - "0a6v7rsd1xsdyapnfqy37m7c4kx9wslkzsizc9k0lmnba0bwyfgx")))) + "1bm0ks9ga60z3izgq0d4kvirr9v4yf1820d1wznkihnbb55bc3m6")))) (build-system r-build-system) (propagated-inputs `(("r-mass" ,r-mass) From 85cd755417bc398e1de126039dc16e654f7d5716 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:29:20 +0200 Subject: [PATCH 113/162] gnu: r-tclust: Update to 1.2-7. * gnu/packages/statistics.scm (r-tclust): Update to 1.2-7. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 6467e9e131..5e14391dce 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -5101,14 +5101,14 @@ multivariate case.") (define-public r-tclust (package (name "r-tclust") - (version "1.2-3") + (version "1.2-7") (source (origin (method url-fetch) (uri (cran-uri "tclust" version)) (sha256 (base32 - "0a1b7yp4l9wf6ic5czizyl2cnxrc1virj0icr8i6m1vv23jd8jfp")))) + "1mvqr280c6kwpg98byd0r1y0qf238xn2x15y8npqch6lpcszlb3x")))) (build-system r-build-system) (propagated-inputs `(("r-cluster" ,r-cluster) From 3f6ec083ecfd698f85841d04efe5f15794b2f75e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:29:47 +0200 Subject: [PATCH 114/162] gnu: r-bookdown: Update to 0.4. * gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.4. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e3c3bbc52f..8e1da7c4a9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6382,13 +6382,13 @@ also known as views, in a controlled vocabulary.") (define-public r-bookdown (package (name "r-bookdown") - (version "0.3") + (version "0.4") (source (origin (method url-fetch) (uri (cran-uri "bookdown" version)) (sha256 (base32 - "0r9bchzg7im6psc3jphvshzbidc5bv5xaih1qg7b5518jy4iyvb9")))) + "1fp1k7hivrb7s2dwgrsqy9s7xg6pk9hczhrc149y1dwh901j6qvv")))) (build-system r-build-system) (propagated-inputs `(("r-htmltools" ,r-htmltools) From 7150f1c30c6f3da0114b56332d9860473c48760e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:30:08 +0200 Subject: [PATCH 115/162] gnu: r-optparse: Update to 1.4.4. * gnu/packages/bioinformatics.scm (r-optparse): Update to 1.4.4. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8e1da7c4a9..19826a333e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6498,14 +6498,14 @@ support for default values, positional argument support, etc.") (define-public r-optparse (package (name "r-optparse") - (version "1.3.2") + (version "1.4.4") (source (origin (method url-fetch) (uri (cran-uri "optparse" version)) (sha256 (base32 - "1g8as89r91xxi5j5azsd6vrfrhg84mnfx2683j7pacdp8s33radw")))) + "1ff4wmsszrb3spwfp7ynfs8w11qpy1sdzfxm1wk8dqqvdwris7qb")))) (build-system r-build-system) (propagated-inputs `(("r-getopt" ,r-getopt))) From 023aa8ff5839a295b4b42287ba50713775866131 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:30:31 +0200 Subject: [PATCH 116/162] gnu: r-seqinr: Update to 3.4-5. * gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.4-5. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 19826a333e..ccb31d0960 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6570,14 +6570,14 @@ S4Vectors package itself.") (define-public r-seqinr (package (name "r-seqinr") - (version "3.3-6") + (version "3.4-5") (source (origin (method url-fetch) (uri (cran-uri "seqinr" version)) (sha256 (base32 - "13d0qxm2244wgdl2dy2s8vnrnf5fx4n47if9gkb49dqx6c0sx8s2")))) + "17zv0n5cji17izwmwg0jcbxbjl3w5rls91w15svcnlpxjms38ahn")))) (build-system r-build-system) (propagated-inputs `(("r-ade4" ,r-ade4) From c8a9b2bcbff2d78609f8d34ad4d9ca41f17f4602 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:30:59 +0200 Subject: [PATCH 117/162] gnu: r-qtl: Update to 1.41-6. * gnu/packages/bioinformatics.scm (r-qtl): Update to 1.41-6. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ccb31d0960..907309d591 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7815,7 +7815,7 @@ throughput genetic sequencing data sets using regression methods.") (define-public r-qtl (package (name "r-qtl") - (version "1.40-8") + (version "1.41-6") (source (origin (method url-fetch) @@ -7823,7 +7823,7 @@ throughput genetic sequencing data sets using regression methods.") version ".tar.gz")) (sha256 (base32 - "05bj1x2ry0i7yqiydlswb3d2h4pxg70z8w1072az1mrv1m54k8sp")))) + "067az4v432zxp6lxck8d7vlh9w4r13r0mvw5zsglyaqwsh3d9sad")))) (build-system r-build-system) (home-page "http://rqtl.org/") (synopsis "R package for analyzing QTL experiments in genetics") From 4e0c847d5965d86d334d04458387cedbd5b4e9d4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:31:27 +0200 Subject: [PATCH 118/162] gnu: r-wgcna: Update to 1.60. * gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.60. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 907309d591..76dfc88cbb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8065,14 +8065,14 @@ in SNV base substitution data.") (define-public r-wgcna (package (name "r-wgcna") - (version "1.51") + (version "1.60") (source (origin (method url-fetch) (uri (cran-uri "WGCNA" version)) (sha256 (base32 - "0hzvnhw76vwg8bl8x368f0c5szpwb8323bmrb3bir93i5bmfjsxx")))) + "16mxhwzhh5q48wmz1iba2r21cp0n0v8g11am4pi52iv6g0663ixl")))) (properties `((upstream-name . "WGCNA"))) (build-system r-build-system) (propagated-inputs From 5e0de298926e3a4d6e444f91427e240cd1c3c4cc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:31:50 +0200 Subject: [PATCH 119/162] gnu: r-seqminer: Update to 6.0. * gnu/packages/bioinformatics.scm (r-seqminer): Update to 6.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 76dfc88cbb..768f0897a4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8652,14 +8652,14 @@ unmodeled, or latent sources of noise.") (define-public r-seqminer (package (name "r-seqminer") - (version "5.9") + (version "6.0") (source (origin (method url-fetch) (uri (cran-uri "seqminer" version)) (sha256 (base32 - "0sfkxrc9gy5a8fadzyzfzh7l5grasm8cj6cd2nnpv85ws6mqr6qd")))) + "057j1l6dip35l1aivilapl2zv9db677b3di2pb3sfgq2sxg0ps3l")))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) From ceb802a31cd0bf1a39282e0032689a5d9d2c8332 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:45:10 +0200 Subject: [PATCH 120/162] gnu: r-desc: Update to 1.1.1. * gnu/packages/statistics.scm (r-desc): Update to 1.1.1. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 5e14391dce..e4feed377c 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -2073,14 +2073,14 @@ module, Java Server Pages, and Python's psp module.") (define-public r-desc (package (name "r-desc") - (version "1.1.0") + (version "1.1.1") (source (origin (method url-fetch) (uri (cran-uri "desc" version)) (sha256 (base32 - "0mc1jmiwqyj7s6gzxz6fyamzjpmdn3rpfpllby2fq11ml30c6jpr")))) + "0k07qighac1xzmm8k988zi7i88a0yfvia3gk5hbz0fyvb2v9kzrj")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) From 2267e4d3f64c9224997f8d48d69c505fa91c9aa6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:45:27 +0200 Subject: [PATCH 121/162] gnu: r-purrr: Update to 0.2.3. * gnu/packages/statistics.scm (r-purrr): Update to 0.2.3. [propagated-inputs]: Remove r-rcpp and r-lazyeval; add r-rlang. --- gnu/packages/statistics.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index e4feed377c..55a8a2a483 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3591,20 +3591,19 @@ It uses and relies on grid graphics and formal (S4) classes and methods.") (define-public r-purrr (package (name "r-purrr") - (version "0.2.2.2") + (version "0.2.3") (source (origin (method url-fetch) (uri (cran-uri "purrr" version)) (sha256 (base32 - "1i1n651xf15489pd6xjdvyp8wyayn8p33d27br39mddn1xdjrpc1")))) + "0j1y0nbvljcis9hgic4wbbzslcsidhpw0wzs7d2hx7a2ygi6mkma")))) (build-system r-build-system) (propagated-inputs `(("r-tibble" ,r-tibble) - ("r-lazyeval" ,r-lazyeval) ("r-magrittr" ,r-magrittr) - ("r-rcpp" ,r-rcpp))) + ("r-rlang" ,r-rlang))) (home-page "https://github.com/hadley/purrr") (synopsis "Functional programming tools") (description From cf189709bcbc96e0e24c132f2a55a5347531ab44 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Fri, 21 Jul 2017 01:06:48 +0200 Subject: [PATCH 122/162] vm: Use grub-hybrid's grub-mkrescue. * gnu/system/vm.scm (system-disk-image): Use grub-hybrid's grub-mkrescue. * gnu/bootlader/grub.scm (grub-mkrescue-bootloader): New variable. --- gnu/bootloader/grub.scm | 6 ++++++ gnu/system/vm.scm | 7 +++++++ 2 files changed, 13 insertions(+) diff --git a/gnu/bootloader/grub.scm b/gnu/bootloader/grub.scm index 3a3456ca46..ef62fe059b 100644 --- a/gnu/bootloader/grub.scm +++ b/gnu/bootloader/grub.scm @@ -55,6 +55,7 @@ grub-bootloader grub-efi-bootloader + grub-mkrescue-bootloader grub-configuration)) @@ -410,6 +411,11 @@ submenu \"GNU system, old configurations...\" {~%") (name 'grub-efi) (package grub-efi))) +(define* grub-mkrescue-bootloader + (bootloader + (inherit grub-efi-bootloader) + (package grub-hybrid))) + ;;; ;;; Compatibility macros. diff --git a/gnu/system/vm.scm b/gnu/system/vm.scm index 90d29b0783..4494af0031 100644 --- a/gnu/system/vm.scm +++ b/gnu/system/vm.scm @@ -49,6 +49,7 @@ #:use-module (gnu packages admin) #:use-module (gnu bootloader) + #:use-module ((gnu bootloader grub) #:select (grub-mkrescue-bootloader)) #:use-module (gnu system shadow) #:use-module (gnu system pam) #:use-module (gnu system linux-initrd) @@ -369,6 +370,12 @@ to USB sticks meant to be read-only." #:volatile-root? #t rest))) + (bootloader (if (string=? "iso9660" file-system-type) + (bootloader-configuration + (inherit (operating-system-bootloader os)) + (bootloader grub-mkrescue-bootloader)) + (operating-system-bootloader os))) + ;; Force our own root file system. (file-systems (cons (file-system (mount-point "/") From 7cb6155088ee10300d0247077b3bf48089912e86 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 3 Aug 2017 21:39:12 +0300 Subject: [PATCH 123/162] gnu: bioinformatics.scm: Use (gnu packages cran) module. This is a follow up to a8cba9dd112528d67a946eee057c838221eb5249. * gnu/packages/bioinformatics.scm: Add (gnu packages cran) to #:use-modules. --- gnu/packages/bioinformatics.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 768f0897a4..3ec8b5ec71 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -48,6 +48,7 @@ #:use-module (gnu packages boost) #:use-module (gnu packages compression) #:use-module (gnu packages cpio) + #:use-module (gnu packages cran) #:use-module (gnu packages curl) #:use-module (gnu packages documentation) #:use-module (gnu packages databases) From 9e37e537a2d76d6f28a1790cae2e14b8ba1a55e3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 22:14:48 +0200 Subject: [PATCH 124/162] gnu: Add missing references to (gnu packages cran). This is a follow-up to commit a8cba9dd112528d67a946eee057c838221eb5249. Reported-by: Efraim Flashner --- gnu/packages/machine-learning.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm index d39e77d978..c5132faf58 100644 --- a/gnu/packages/machine-learning.scm +++ b/gnu/packages/machine-learning.scm @@ -32,6 +32,7 @@ #:use-module (gnu packages autotools) #:use-module (gnu packages boost) #:use-module (gnu packages compression) + #:use-module (gnu packages cran) #:use-module (gnu packages dejagnu) #:use-module (gnu packages gcc) #:use-module (gnu packages image) From 81ca29a6d6ac3be4f35f0e1148eec9e8bb39bbb9 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 3 Aug 2017 18:00:45 -0400 Subject: [PATCH 125/162] gnu: gnupg@1.4: Update to 1.4.22 [fixes CVE-2017-7526]. * gnu/packages/gnupg.scm (gnupg-1): Update to 1.4.22. --- gnu/packages/gnupg.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/gnupg.scm b/gnu/packages/gnupg.scm index 5b46257948..a9d8679a29 100644 --- a/gnu/packages/gnupg.scm +++ b/gnu/packages/gnupg.scm @@ -355,14 +355,14 @@ libskba (working with X.509 certificates and CMS data).") (define-public gnupg-1 (package (inherit gnupg) - (version "1.4.21") + (version "1.4.22") (source (origin (method url-fetch) (uri (string-append "mirror://gnupg/gnupg/gnupg-" version ".tar.bz2")) (sha256 (base32 - "0xi2mshq8f6zbarb5f61c9w2qzwrdbjm4q8fqsrwlzc51h8a6ivb")))) + "1d1hz4szh1kvwhsw7w2zxa6q5ndrk3qy6hj289l1b8k3xi5s554m")))) (native-inputs '()) (inputs `(("zlib" ,zlib) From c9f4f56b24801718d89c2520bec08867516e1371 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Thu, 3 Aug 2017 23:02:02 +0200 Subject: [PATCH 126/162] gnu: git: Enable tests. * gnu/packages/version-control.scm (git)[arguments]: Remove #:tests?. Add 'patch-tests' phase. --- gnu/packages/version-control.scm | 33 +++++++++++++++++++++++++++++++- 1 file changed, 32 insertions(+), 1 deletion(-) diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index 9274a93f6a..08a6f3aae8 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -15,6 +15,7 @@ ;;; Copyright © 2017 Vasile Dumitrascu ;;; Copyright © 2017 Clément Lassieur ;;; Copyright © 2017 André +;;; Copyright © 2017 Marius Bakke ;;; ;;; This file is part of GNU Guix. ;;; @@ -176,7 +177,6 @@ as well as the classic centralized workflow.") ;; nars; see . "NO_INSTALL_HARDLINKS=indeed") #:test-target "test" - #:tests? #f ; FIXME: Many tests are failing ;; The explicit --with-tcltk forces the build system to hardcode the ;; absolute file name to 'wish'. @@ -203,6 +203,37 @@ as well as the classic centralized workflow.") ;; Add the "PM.stamp" to avoid "no rule to make target". (call-with-output-file "perl/PM.stamp" (const #t)) #t)) + (add-before 'check 'patch-tests + (lambda _ + ;; These files contain some funny bytes that Guile is unable + ;; to decode for shebang patching. Just delete them. + (for-each delete-file '("t/t4201-shortlog.sh" + "t/t7813-grep-icase-iso.sh")) + ;; Many tests contain inline shell scripts (hooks etc). + (substitute* (find-files "t" "\\.sh$") + (("#!/bin/sh") (string-append "#!" (which "sh")))) + ;; Un-do shebang patching here to prevent checksum mismatch. + (substitute* '("t/t4034/perl/pre" "t/t4034/perl/post") + (("^#!.*/bin/perl") "#!/usr/bin/perl")) + (substitute* "t/t5003-archive-zip.sh" + (("cp /bin/sh") (string-append "cp " (which "sh")))) + (substitute* "t/t6030-bisect-porcelain.sh" + (("\"/bin/sh\"") (string-append "\"" (which "sh") "\""))) + ;; FIXME: This test runs `git commit` with a bogus EDITOR + ;; and empty commit message, but does not fail the way it's + ;; expected to. The test passes when invoked interactively. + (substitute* "t/t7508-status.sh" + (("\tcommit_template_commented") "\ttrue")) + ;; More checksum mismatches due to odd shebangs. + (substitute* "t/t9100-git-svn-basic.sh" + (("\"#!/gnu.*/bin/sh") "\"#!/bin/sh")) + (substitute* "t/t9300-fast-import.sh" + (("\t#!/gnu.*/bin/sh") "\t#!/bin/sh") + (("'#!/gnu.*/bin/sh") "'#!/bin/sh")) + ;; FIXME: Some hooks fail with "basename: command not found". + ;; See 't/trash directory.t9164.../svn-hook.log'. + (delete-file "t/t9164-git-svn-dcommit-concurrent.sh") + #t)) (add-after 'install 'install-shell-completion (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) From c89091459f24dee4ba4959d65e38589efc1d8d9e Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Fri, 4 Aug 2017 00:47:07 +0200 Subject: [PATCH 127/162] gnu: freerdp: Update to 2.0.0-rc0 [security fixes]. Fixes CVE-2017-{2834,2835,2836,2837,2838,2839}. Reported by Leo Famulari in . * gnu/packages/rdesktop.scm (freerdp): Update to 2.0.0-rc0. [source]: Use tarball release. Adjust file-name. [arguments]: Remove #:phases. --- gnu/packages/rdesktop.scm | 22 ++++++---------------- 1 file changed, 6 insertions(+), 16 deletions(-) diff --git a/gnu/packages/rdesktop.scm b/gnu/packages/rdesktop.scm index 3eb82f22f3..7946cde790 100644 --- a/gnu/packages/rdesktop.scm +++ b/gnu/packages/rdesktop.scm @@ -72,15 +72,14 @@ to remotely control a user's Windows desktop.") (define-public freerdp (package (name "freerdp") - (version "1.2.0-beta1+android9") + (version "2.0.0-rc0") (source (origin - (method git-fetch) - (uri (git-reference - (url "git://github.com/FreeRDP/FreeRDP.git") - (commit version))) - (file-name (git-file-name name version)) + (method url-fetch) + (uri (string-append "https://github.com/FreeRDP/FreeRDP/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "1m0lzrr7hkxfvc5f9p8snimv0rmin2463zhg25mv36wig8g5k7l3")))) + (base32 "0r36zwhl7fhmdng5pvl2a106gqbcqq184g2i2klz6ilna8pxjcml")))) (build-system cmake-build-system) (native-inputs `(("pkg-config" ,pkg-config) @@ -111,15 +110,6 @@ to remotely control a user's Windows desktop.") '("-DCMAKE_INSTALL_LIBDIR=lib" "-DWITH_PULSE=ON" "-DWITH_CUPS=ON") - #:phases - (modify-phases %standard-phases - (add-before 'configure 'patch-cmakelists - (lambda _ - ;; CMake would return an error on REMOVE_DUPLICATES because this - ;; list is empty. - (substitute* "channels/client/CMakeLists.txt" - (("list\\(REMOVE_DUPLICATES CHANNEL_STATIC_CLIENT_ENTRIES\\)") - ""))))) #:tests? #f)) ; no 'test' target (home-page "https://www.freerdp.com") (synopsis "Remote Desktop Protocol implementation") From 20f8d1dd78c67872a670bb98cf8e76cef74baa64 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 3 Aug 2017 21:55:20 +0200 Subject: [PATCH 128/162] gnu: sshfs-fuse: Update to 2.10. * gnu/packages/linux.scm (sshfs-fuse): Update to 2.10. --- gnu/packages/linux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index a189458ada..a7d24da7a1 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -1745,7 +1745,7 @@ UnionFS-FUSE additionally supports copy-on-write.") (define-public sshfs-fuse (package (name "sshfs-fuse") - (version "2.9") + (version "2.10") (source (origin (method url-fetch) (uri (string-append "https://github.com/libfuse/sshfs/releases/" @@ -1753,7 +1753,7 @@ UnionFS-FUSE additionally supports copy-on-write.") ".tar.gz")) (sha256 (base32 - "1pp5wsl1jx11apkv2fpp559miifqhi8ka400npy5awp9ghlf3la6")))) + "00fir2iykdx11g8nv5gijg0zjrp2g3ldypnv0yi6lq3h5pg5v13h")))) (build-system gnu-build-system) (inputs `(("fuse" ,fuse) From 0f08917df3f35ba5b54361c4b27255304102ced4 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 3 Aug 2017 22:14:54 +0200 Subject: [PATCH 129/162] =?UTF-8?q?gnu:=20zerofree:=20Use=20=E2=80=98modif?= =?UTF-8?q?y-phases=E2=80=99=20syntax.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/linux.scm (zerofree)[arguments]: Use ‘modify-phases’. --- gnu/packages/linux.scm | 28 +++++++++++++++------------- 1 file changed, 15 insertions(+), 13 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index a7d24da7a1..76f97f7e8a 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -833,19 +833,21 @@ ext3 or ext4 partition.") "1xncw3dn2cp922ly42m96p6fh7jv8ysg6bwqbk5xvw701f3dmkrs")))) (build-system gnu-build-system) (arguments - '(#:phases (alist-replace - 'install - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin"))) - (mkdir-p bin) - (copy-file "zerofree" - (string-append bin "/zerofree")) - (chmod (string-append bin "/zerofree") - #o555) - #t)) - (alist-delete 'configure %standard-phases)) - #:tests? #f)) ;no tests + '(#:phases + (modify-phases %standard-phases + (delete 'configure) ; no configure script + (replace 'install + ;; The Makefile lacks an ‘install’ target. + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) + (mkdir-p bin) + (copy-file "zerofree" + (string-append bin "/zerofree")) + (chmod (string-append bin "/zerofree") + #o555) + #t)))) + #:tests? #f)) ; no tests (inputs `(("libext2fs" ,e2fsprogs))) (synopsis "Zero non-allocated regions in ext2/ext3/ext4 file systems") (description From 7a068459ba9f1dd6f3dee12e39124a0c8b603ced Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 3 Aug 2017 22:22:43 +0200 Subject: [PATCH 130/162] =?UTF-8?q?gnu:=20zerofree:=20Use=20=E2=80=98insta?= =?UTF-8?q?ll-file=E2=80=99.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/linux.scm (zerofree)[arguments]: Simplify install phase, using ‘install-file’. --- gnu/packages/linux.scm | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 76f97f7e8a..481037066b 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -841,11 +841,8 @@ ext3 or ext4 partition.") (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) (bin (string-append out "/bin"))) - (mkdir-p bin) - (copy-file "zerofree" - (string-append bin "/zerofree")) - (chmod (string-append bin "/zerofree") - #o555) + (chmod "zerofree" #o555) + (install-file "zerofree" bin) #t)))) #:tests? #f)) ; no tests (inputs `(("libext2fs" ,e2fsprogs))) From 4de4a1cfccb981757765202a0fd2db4bf7479822 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 3 Aug 2017 22:26:36 +0200 Subject: [PATCH 131/162] gnu: zerofree: Expand description. * gnu/packages/linux.scm (zerofree)[description]: Expand. --- gnu/packages/linux.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 481037066b..843ee6dc45 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -848,9 +848,10 @@ ext3 or ext4 partition.") (inputs `(("libext2fs" ,e2fsprogs))) (synopsis "Zero non-allocated regions in ext2/ext3/ext4 file systems") (description - "The zerofree command scans the free blocks in an ext2 file system and -fills any non-zero blocks with zeroes. This is a useful way to make disk -images more compressible.") + "Zerofree finds the unallocated blocks with non-zero value content in an +ext2, ext3, or ext4 file system and fills them with zeroes (or another value). +This is a simple way to make disk images more compressible. +Zerofree requires the file system to be unmounted or mounted read-only.") (license license:gpl2))) (define-public strace From 30ac4cc7e6a1819d4d56c02e695020498d7653d3 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 3 Aug 2017 22:27:21 +0200 Subject: [PATCH 132/162] gnu: zerofree: Update to 1.1.0. * gnu/packages/linux.scm (zerofree): Update to 1.1.0. [home-page, source]: Update from old, inaccessible location. --- gnu/packages/linux.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 843ee6dc45..a103fd891a 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -822,15 +822,15 @@ ext3 or ext4 partition.") (define-public zerofree (package (name "zerofree") - (version "1.0.3") - (home-page "http://intgat.tigress.co.uk/rmy/uml/") + (version "1.1.0") + (home-page "https://frippery.org/uml/") (source (origin (method url-fetch) (uri (string-append home-page name "-" version ".tgz")) (sha256 (base32 - "1xncw3dn2cp922ly42m96p6fh7jv8ysg6bwqbk5xvw701f3dmkrs")))) + "059g29x5r1xj6wcj4xj85l8w6qrxyl86yqbybjqqz6nxz4falxzf")))) (build-system gnu-build-system) (arguments '(#:phases From 0a3ecfd29ccbac7f30e322d94854a526cc094883 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 4 Aug 2017 01:15:42 +0200 Subject: [PATCH 133/162] gnu: thefuck: Update to 3.19. * gnu/packages/admin.scm (thefuck): Update to 3.19. --- gnu/packages/admin.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 9729a30fc7..45f743199a 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -1718,7 +1718,7 @@ throughput (in the same interval).") (define-public thefuck (package (name "thefuck") - (version "3.18") + (version "3.19") (source (origin (method url-fetch) (uri (string-append "https://github.com/nvbn/thefuck/archive/" @@ -1726,7 +1726,7 @@ throughput (in the same interval).") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1xsvkqh89rgxq5w03mnlcfkn9y39nfwhb2pjabjspcc2mi2mq5y6")) + "191zbvkyc02h0wwd46xwj4zzg7jhlr8xv0ji6knqkgjnk0nvqq01")) (patches (search-patches "thefuck-test-environ.patch")))) (build-system python-build-system) (arguments From b55d15e795f55c521e3a3c22cc98138b47030e4c Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 4 Aug 2017 01:27:14 +0200 Subject: [PATCH 134/162] gnu: cmark: Update to 0.28.0. * gnu/packages/markup.scm (cmark): Update to 0.28.0. --- gnu/packages/markup.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/markup.scm b/gnu/packages/markup.scm index 4afe8c3c0e..121e6cdbf4 100644 --- a/gnu/packages/markup.scm +++ b/gnu/packages/markup.scm @@ -105,7 +105,7 @@ convert it to structurally valid XHTML (or HTML).") (define-public cmark (package (name "cmark") - (version "0.27.1") + (version "0.28.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/jgm/cmark/archive/" @@ -113,7 +113,7 @@ convert it to structurally valid XHTML (or HTML).") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1da62ispca9aal2a36gaj87175rv5013pl7x740vk32y6lclr6v6")))) + "03pypf2mcacfa7lrwz66lh5hydsycc33arp1nx1lljbq98gikkv8")))) (build-system cmake-build-system) (arguments '(#:test-target "test")) From 9a7fd375a2caa6b0c7297ee1b9bc5c8c3fd0e31b Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 4 Aug 2017 02:06:39 +0200 Subject: [PATCH 135/162] gnu: xonsh: Update to 0.5.12. * gnu/packages/shells.scm (xonsh): Update to 0.5.12. --- gnu/packages/shells.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/shells.scm b/gnu/packages/shells.scm index 8d2a957eae..4603fd49b3 100644 --- a/gnu/packages/shells.scm +++ b/gnu/packages/shells.scm @@ -366,14 +366,14 @@ ksh, and tcsh.") (define-public xonsh (package (name "xonsh") - (version "0.5.9") + (version "0.5.12") (source (origin (method url-fetch) (uri (pypi-uri "xonsh" version)) (sha256 (base32 - "09s5k7fh4p0vkq0fha4ikwqlqsyv84vmlbqn8ggn0ymd47ajv38z")) + "1yz595hx5bni524m73cx8a08vcr6vfksfci14nx2ylz53igzva2c")) (modules '((guix build utils))) (snippet `(begin From 19dd5097d936aadf2a4da266c377ed8a4fb381c8 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 4 Aug 2017 02:11:37 +0200 Subject: [PATCH 136/162] gnu: certbot, python-acme: Update to 0.17.0. * gnu/packages/tls.scm (certbot, python-acme, python2-acme): Update to 0.17.0. --- gnu/packages/tls.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm index b39e06c8d9..6d71a9b809 100644 --- a/gnu/packages/tls.scm +++ b/gnu/packages/tls.scm @@ -502,13 +502,13 @@ netcat implementation that supports TLS.") (package (name "python-acme") ;; Remember to update the hash of certbot when updating python-acme. - (version "0.16.0") + (version "0.17.0") (source (origin (method url-fetch) (uri (pypi-uri "acme" version)) (sha256 (base32 - "1kg9bnwywsr18hgvqyhxqqi90l2qa7449f41q3fdq2y59h9nk2sk")))) + "0vmnv7qhdhl9qhq03v6zrcj1lsmpmpjb94s0xsc7piwqxfmf9jrw")))) (build-system python-build-system) (arguments `(#:phases @@ -559,7 +559,7 @@ netcat implementation that supports TLS.") (uri (pypi-uri name version)) (sha256 (base32 - "11p1vsps5rbpha3k5jnmf9i6rcp6299h9b34wdh21cq6dgyh2n3r")))) + "173619jkq4bg88f6i837z3pcjkrfabrvv8vrpyx18k9i7xnb5xa3")))) (build-system python-build-system) (arguments `(,@(substitute-keyword-arguments (package-arguments python-acme) From f58be417610e65f27b90452b78255f8d88ab1b4f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 4 Aug 2017 03:46:49 +0200 Subject: [PATCH 137/162] gnu: fabric: Update to 1.13.2. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/admin.scm (fabric): Update to 1.13.2. Remove outdated comments. [source]: Remove ‘patches’. * gnu/packages/patches/fabric-tests.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it. --- gnu/local.mk | 1 - gnu/packages/admin.scm | 18 ++++++------------ gnu/packages/patches/fabric-tests.patch | 15 --------------- 3 files changed, 6 insertions(+), 28 deletions(-) delete mode 100644 gnu/packages/patches/fabric-tests.patch diff --git a/gnu/local.mk b/gnu/local.mk index f4fef78f31..0491de6584 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -586,7 +586,6 @@ dist_patch_DATA = \ %D%/packages/patches/evilwm-lost-focus-bug.patch \ %D%/packages/patches/expat-CVE-2016-0718-fix-regression.patch \ %D%/packages/patches/exim-CVE-2017-1000369.patch \ - %D%/packages/patches/fabric-tests.patch \ %D%/packages/patches/fastcap-mulGlobal.patch \ %D%/packages/patches/fastcap-mulSetup.patch \ %D%/packages/patches/fasthenry-spAllocate.patch \ diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index 45f743199a..c4aa108f89 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -2105,28 +2105,22 @@ Intel DRM Driver.") (define-public fabric (package (name "fabric") - (version "1.13.1") + (version "1.13.2") (source (origin (method url-fetch) (uri (pypi-uri "Fabric" version)) (sha256 (base32 - "1z17hw0yiqp1blq217zxkg2jzkv8qd79saqhscgsw14mwlcqpwd0")) - (patches (search-patches "fabric-tests.patch")))) + "0k944dxr41whw7ib6380q9x15wyskx7fqni656icdn8rzshn9bwq")))) (build-system python-build-system) (arguments - `(#:python ,python-2)) ;Python 2 only + `(#:python ,python-2)) ; Python 2 only (native-inputs - `(("python2-fudge" ,python2-fudge) ; Requires < 1.0 - ("python2-jinja2" ,python2-jinja2) ; Requires < 3.0 - ("python2-nose" ,python2-nose))) ; Requires < 2.0 + `(("python2-fudge" ,python2-fudge) + ("python2-jinja2" ,python2-jinja2) + ("python2-nose" ,python2-nose))) (propagated-inputs - ;; Required upgrading python-paramiko 1.17.4 to fix an incompatibility - ;; between python-paramiko and newer python-pycrypto. Without this, the - ;; `fab` command fails with "ValueError: CTR mode needs counter - ;; parameter, not IV". See: - ;; https://github.com/paramiko/paramiko/pull/714#issuecomment-281191548. `(("python2-paramiko" ,python2-paramiko))) (home-page "http://fabfile.org") (synopsis "Simple Pythonic remote execution and deployment tool") diff --git a/gnu/packages/patches/fabric-tests.patch b/gnu/packages/patches/fabric-tests.patch deleted file mode 100644 index 4a0ca9f8f1..0000000000 --- a/gnu/packages/patches/fabric-tests.patch +++ /dev/null @@ -1,15 +0,0 @@ -The `fab` excecutable doesn't exist during the test phase as it is created -dynamically during installation. Refer to the equivalent Python module -directly. - ---- a/tests/test_utils.py -+++ b/tests/test_utils.py -@@ -93,7 +93,7 @@ - # perform when they are allowed to bubble all the way to the top. So, we - # invoke a subprocess and look at its stderr instead. - with quiet(): -- result = local("fab -f tests/support/aborts.py kaboom", capture=True) -+ result = local("python -m fabric -f tests/support/aborts.py kaboom", capture=True) - # When error in #1318 is present, this has an extra "It burns!" at end of - # stderr string. - eq_(result.stderr, "Fatal error: It burns!\n\nAborting.") \ No newline at end of file From 3b4018d6f212b19ab06a759118a025dfc8461f3a Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 4 Aug 2017 04:20:04 +0200 Subject: [PATCH 138/162] gnu: sshoot: Update to 1.2.6. * gnu/packages/vpn.scm (sshoot): Update to 1.2.6. [home-page]: Update to new project home. --- gnu/packages/vpn.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm index aec8c1807d..61ebf0d5fa 100644 --- a/gnu/packages/vpn.scm +++ b/gnu/packages/vpn.scm @@ -239,14 +239,14 @@ DNS domain name queries.") (define-public sshoot (package (name "sshoot") - (version "1.2.5") + (version "1.2.6") (source (origin (method url-fetch) (uri (pypi-uri name version)) (sha256 (base32 - "0a92lk8790dpp9j64vb6p4sazax0x3nby01lnfll7mxs1hx6n27q")))) + "1ccgh0hjyxrwkgy3hnxz3hgbjbs0lmfs25d5l5jam0xbpcpj63h0")))) (build-system python-build-system) (arguments '(#:phases @@ -265,7 +265,7 @@ DNS domain name queries.") `(("python-fixtures" ,python-fixtures) ("python-pbr" ,python-pbr) ("python-testtools" ,python-testtools))) - (home-page "https://bitbucket.org/ack/sshoot") + (home-page "https://github.com/albertodonato/sshoot") (synopsis "sshuttle VPN session manager") (description "sshoot provides a command-line interface to manage multiple @command{sshuttle} virtual private networks. It supports flexible profiles From 54360c917ee09a15c90d617ea164c40d9f6cb5a9 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 4 Aug 2017 04:30:11 +0200 Subject: [PATCH 139/162] gnu: diffoscope: Use HTTPS. * gnu/packages/package-management.scm (diffoscope)[home-page]: Use HTTPS. --- gnu/packages/package-management.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm index d9ba5f6ce1..1f65e21323 100644 --- a/gnu/packages/package-management.scm +++ b/gnu/packages/package-management.scm @@ -523,7 +523,7 @@ transactions from C or Python.") ;; Below are modules used for tests. ("python-pytest" ,python-pytest) ("python-chardet" ,python-chardet))) - (home-page "http://diffoscope.org/") + (home-page "https://diffoscope.org/") (synopsis "Compare files, archives, and directories in depth") (description "Diffoscope tries to get to the bottom of what makes files or directories From e9f6a935fbff9cfc1e5d8045aebe7230dbb5dbdf Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 4 Aug 2017 04:33:28 +0200 Subject: [PATCH 140/162] gnu: python-lz4: Update to 0.10.1. * gnu/packages/compression.scm (python-lz4): Update to 0.10.1. [native-inputs]: Add python-setuptools-scm. --- gnu/packages/compression.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index 92636de7fe..d2de0d3b8b 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -742,17 +742,18 @@ time for compression ratio.") (define-public python-lz4 (package (name "python-lz4") - (version "0.8.2") + (version "0.10.1") (source (origin (method url-fetch) (uri (pypi-uri "lz4" version)) (sha256 (base32 - "1irad4sq4hdr30fr53smvv3zzk4rddcf9b4jx19w8s9xsxhr1x3b")))) + "0ghv1xbaq693kgww1x9c22bplz479ls9szjsaa4ig778ls834hm0")))) (build-system python-build-system) (native-inputs - `(("python-nose" ,python-nose))) + `(("python-nose" ,python-nose) + ("python-setuptools-scm" ,python-setuptools-scm))) (home-page "https://github.com/python-lz4/python-lz4") (synopsis "LZ4 Bindings for Python") (description From b316caaa9cda8bf2a8b20d5ba87b5d306f3b39bd Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Fri, 4 Aug 2017 04:58:19 +0200 Subject: [PATCH 141/162] gnu: python-lz4: Fix typo in synopsis. * gnu/packages/compression.scm (python-lz4)[synopsis]: Fix typo. --- gnu/packages/compression.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/compression.scm b/gnu/packages/compression.scm index d2de0d3b8b..a732ca26de 100644 --- a/gnu/packages/compression.scm +++ b/gnu/packages/compression.scm @@ -755,7 +755,7 @@ time for compression ratio.") `(("python-nose" ,python-nose) ("python-setuptools-scm" ,python-setuptools-scm))) (home-page "https://github.com/python-lz4/python-lz4") - (synopsis "LZ4 Bindings for Python") + (synopsis "LZ4 bindings for Python") (description "This package provides python bindings for the lz4 compression library by Yann Collet. The project contains bindings for the LZ4 block format and From 88c8f247e594239807aafe80d5e8b084d07e32f6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 2 Aug 2017 22:49:30 +0200 Subject: [PATCH 142/162] build: Add minify build system. * guix/build-system/minify.scm: New file. * guix/build/minify-build-system: New file. * Makefile.am (MODULES): Add new files. * doc/guix.texi (Build Systems): Document minify-build-system. --- Makefile.am | 2 + doc/guix.texi | 15 ++++ guix/build-system/minify.scm | 127 +++++++++++++++++++++++++++++ guix/build/minify-build-system.scm | 73 +++++++++++++++++ 4 files changed, 217 insertions(+) create mode 100644 guix/build-system/minify.scm create mode 100644 guix/build/minify-build-system.scm diff --git a/Makefile.am b/Makefile.am index 0a7e375c29..91a9113d22 100644 --- a/Makefile.am +++ b/Makefile.am @@ -79,6 +79,7 @@ MODULES = \ guix/build-system/dub.scm \ guix/build-system/emacs.scm \ guix/build-system/font.scm \ + guix/build-system/minify.scm \ guix/build-system/asdf.scm \ guix/build-system/glib-or-gtk.scm \ guix/build-system/gnu.scm \ @@ -105,6 +106,7 @@ MODULES = \ guix/build/cmake-build-system.scm \ guix/build/dub-build-system.scm \ guix/build/emacs-build-system.scm \ + guix/build/minify-build-system.scm \ guix/build/font-build-system.scm \ guix/build/asdf-build-system.scm \ guix/build/git.scm \ diff --git a/doc/guix.texi b/doc/guix.texi index 2bb820b46c..88bf0bb621 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -3576,6 +3576,21 @@ specified with the @code{#:glib} parameter. Both phases are executed after the @code{install} phase. @end defvr +@defvr {Scheme Variable} minify-build-system +This variable is exported by @code{(guix build-system minify)}. It +implements a minification procedure for simple JavaScript packages. + +It adds @code{uglify-js} to the set of inputs and uses it to compress +all JavaScript files in the @file{src} directory. A different minifier +package can be specified with the @code{#:uglify-js} parameter, but it +is expected that the package writes the minified code to the standard +output. + +When the input JavaScript files are not all located in the @file{src} +directory, the parameter @code{#:javascript-files} can be used to +specify a list of file names to feed to the minifier. +@end defvr + @defvr {Scheme Variable} ocaml-build-system This variable is exported by @code{(guix build-system ocaml)}. It implements a build procedure for @uref{https://ocaml.org, OCaml} packages, which consists diff --git a/guix/build-system/minify.scm b/guix/build-system/minify.scm new file mode 100644 index 0000000000..af90a32f59 --- /dev/null +++ b/guix/build-system/minify.scm @@ -0,0 +1,127 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2017 Ricardo Wurmus +;;; +;;; This file is part of GNU Guix. +;;; +;;; GNU Guix is free software; you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation; either version 3 of the License, or (at +;;; your option) any later version. +;;; +;;; GNU Guix is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;; GNU General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with GNU Guix. If not, see . + +(define-module (guix build-system minify) + #:use-module (guix store) + #:use-module (guix utils) + #:use-module (guix packages) + #:use-module (guix derivations) + #:use-module (guix search-paths) + #:use-module (guix build-system) + #:use-module (guix build-system gnu) + #:use-module (ice-9 match) + #:use-module (srfi srfi-26) + #:export (%minify-build-system-modules + minify-build + minify-build-system)) + +;; Commentary: +;; +;; Standard minification procedure for JavaScript files. +;; +;; Code: + +(define %minify-build-system-modules + ;; Build-side modules imported by default. + `((guix build minify-build-system) + (ice-9 popen) + ,@%gnu-build-system-modules)) + +(define (default-uglify-js) + "Return the default package to minify JavaScript source files." + ;; Lazily resolve the binding to avoid a circular dependency. + (let ((lisp-mod (resolve-interface '(gnu packages lisp)))) + (module-ref lisp-mod 'uglify-js))) + +(define* (lower name + #:key source inputs native-inputs outputs system + (uglify-js (default-uglify-js)) + #:allow-other-keys + #:rest arguments) + "Return a bag for NAME." + (define private-keywords + '(#:source #:target #:inputs #:native-inputs)) + + (bag + (name name) + (system system) + (host-inputs `(,@(if source + `(("source" ,source)) + '()) + ,@inputs + ,@(standard-packages))) + (build-inputs `(("uglify-js" ,uglify-js) + ,@native-inputs)) + (outputs outputs) + (build minify-build) + (arguments (strip-keyword-arguments private-keywords arguments)))) + +(define* (minify-build store name inputs + #:key + (javascript-files #f) + (phases '(@ (guix build minify-build-system) + %standard-phases)) + (outputs '("out")) + (system (%current-system)) + search-paths + (guile #f) + (imported-modules %minify-build-system-modules) + (modules '((guix build minify-build-system) + (guix build utils)))) + "Build SOURCE with INPUTS." + (define builder + `(begin + (use-modules ,@modules) + (minify-build #:name ,name + #:source ,(match (assoc-ref inputs "source") + (((? derivation? source)) + (derivation->output-path source)) + ((source) + source) + (source + source)) + #:javascript-files ,javascript-files + #:phases ,phases + #:outputs %outputs + #:search-paths ',(map search-path-specification->sexp + search-paths) + #:inputs %build-inputs))) + + (define guile-for-build + (match guile + ((? package?) + (package-derivation store guile system #:graft? #f)) + (#f ; the default + (let* ((distro (resolve-interface '(gnu packages commencement))) + (guile (module-ref distro 'guile-final))) + (package-derivation store guile system #:graft? #f))))) + + (build-expression->derivation store name builder + #:inputs inputs + #:system system + #:modules imported-modules + #:outputs outputs + #:guile-for-build guile-for-build)) + +(define minify-build-system + (build-system + (name 'minify) + (description "The trivial JavaScript minification build system") + (lower lower))) + +;;; minify.scm ends here diff --git a/guix/build/minify-build-system.scm b/guix/build/minify-build-system.scm new file mode 100644 index 0000000000..3580deda07 --- /dev/null +++ b/guix/build/minify-build-system.scm @@ -0,0 +1,73 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2016 Ricardo Wurmus +;;; +;;; This file is part of GNU Guix. +;;; +;;; GNU Guix is free software; you can redistribute it and/or modify it +;;; under the terms of the GNU General Public License as published by +;;; the Free Software Foundation; either version 3 of the License, or (at +;;; your option) any later version. +;;; +;;; GNU Guix is distributed in the hope that it will be useful, but +;;; WITHOUT ANY WARRANTY; without even the implied warranty of +;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +;;; GNU General Public License for more details. +;;; +;;; You should have received a copy of the GNU General Public License +;;; along with GNU Guix. If not, see . + +(define-module (guix build minify-build-system) + #:use-module ((guix build gnu-build-system) #:prefix gnu:) + #:use-module ((guix build minify-build-system) #:prefix minify:) + #:use-module (guix build utils) + #:use-module (srfi srfi-1) + #:use-module (srfi srfi-26) + #:use-module (ice-9 popen) + #:export (%standard-phases + minify-build + minify)) + +;; Commentary: +;; +;; Builder-side code of the standard minification procedure for JavaScript +;; files. +;; +;; Code: + +(define* (minify file #:key target (directory "")) + (format #t "minifying ~a\n" file) + (let* ((base (basename file ".js")) + (installed (or target (string-append directory base ".min.js"))) + (minified (open-pipe* OPEN_READ "uglify-js" file))) + (call-with-output-file installed + (cut dump-port minified <>)) + #t)) + +(define* (build #:key javascript-files + #:allow-other-keys) + (let ((files (or javascript-files + (find-files "src" "\\.js$")))) + (mkdir-p "guix/build") + (every (cut minify <> #:directory "guix/build/") files))) + +(define* (install #:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (js (string-append out "/share/javascript/"))) + (mkdir-p js) + (for-each (cut install-file <> js) + (find-files "guix/build" "\\.min\\.js$"))) + #t) + +(define %standard-phases + (modify-phases gnu:%standard-phases + (delete 'configure) + (replace 'build build) + (delete 'check) + (replace 'install install))) + +(define* (minify-build #:key inputs (phases %standard-phases) + #:allow-other-keys #:rest args) + "Build the given JavaScript package, applying all of PHASES in order." + (apply gnu:gnu-build #:inputs inputs #:phases phases args)) + +;;; minify-build-system.scm ends here From ed69963b03d71928f8c926ed62e5d6f5e78d9b2a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 15:53:54 +0200 Subject: [PATCH 143/162] gnu: Add js-html5shiv. * gnu/packages/javascript.scm (js-html5shiv): New variable. --- gnu/packages/javascript.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/javascript.scm b/gnu/packages/javascript.scm index 43bc0bbf6d..8364651918 100644 --- a/gnu/packages/javascript.scm +++ b/gnu/packages/javascript.scm @@ -134,3 +134,28 @@ be able to view it naturally and easily."))) script to enable responsive web designs in browsers that don't support CSS3 Media Queries.") (license license:expat))) + +(define-public js-html5shiv + (package + (name "js-html5shiv") + (version "3.7.3") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/aFarkas/html5shiv/" + "archive/" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0inlbpxpqzdyi24lqagzf7l24zxg0y02xcpqs2h4npjscazzw7hg")))) + (build-system minify-build-system) + (home-page "https://github.com/aFarkas/html5shiv") + (synopsis "Enable HTML5 sectioning elements in legacy browsers") + (description "The HTML5 Shiv enables use of HTML5 sectioning elements in +legacy Internet Explorer and provides basic HTML5 styling for Internet +Explorer 6-9, Safari 4.x (and iPhone 3.x), and Firefox 3.x.") + ;; From the file "MIT and GPL2 licenses.md": + ;; + ;; This software is licensed under a dual license system (MIT or GPL + ;; version 2). This means you are free to choose with which of both + ;; licenses (MIT or GPL version 2) you want to use this library. + (license (list license:expat license:gpl2)))) From 68ffb6c586de4dfd4dd5c972d3481a4243ba8bde Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 15:54:16 +0200 Subject: [PATCH 144/162] gnu: Add js-json2. * gnu/packages/javascript.scm (js-json2): New variable. --- gnu/packages/javascript.scm | 49 ++++++++++++++++++++++++++++++++++++- 1 file changed, 48 insertions(+), 1 deletion(-) diff --git a/gnu/packages/javascript.scm b/gnu/packages/javascript.scm index 8364651918..a806cb0745 100644 --- a/gnu/packages/javascript.scm +++ b/gnu/packages/javascript.scm @@ -26,7 +26,9 @@ #:use-module (gnu packages lisp) #:use-module (guix packages) #:use-module (guix download) - #:use-module (guix build-system trivial)) + #:use-module (guix git-download) + #:use-module (guix build-system trivial) + #:use-module (guix build-system minify)) (define-public js-mathjax (package @@ -159,3 +161,48 @@ Explorer 6-9, Safari 4.x (and iPhone 3.x), and Firefox 3.x.") ;; version 2). This means you are free to choose with which of both ;; licenses (MIT or GPL version 2) you want to use this library. (license (list license:expat license:gpl2)))) + +(define-public js-json2 + (let ((commit "031b1d9e6971bd4c433ca85e216cc853f5a867bd") + (revision "1")) + (package + (name "js-json2") + (version (string-append "2016-10-28." revision "-" (string-take commit 7))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/douglascrockford/JSON-js.git") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "1fvb6b2y5sd3sqdgcj683sdxcbxdii34q0ysc9wg0dq1sy81l11v")))) + (build-system minify-build-system) + (arguments + `(#:javascript-files '("json2.js" + "json_parse.js" + "json_parse_state.js" + "cycle.js"))) + (home-page "https://github.com/douglascrockford/JSON-js") + (synopsis "JSON encoders and decoders") + (description "The files in this collection implement JSON +encoders/decoders in JavaScript. + +@code{json2.js}: This file creates a JSON property in the global object, if +there isn't already one, setting its value to an object containing a stringify +method and a parse method. The @code{parse} method uses the @code{eval} +method to do the parsing, guarding it with several regular expressions to +defend against accidental code execution hazards. On current browsers, this +file does nothing, preferring the built-in JSON object. + +@code{json_parse.js}: This file contains an alternative JSON @code{parse} +function that uses recursive descent instead of @code{eval}. + +@code{json_parse_state.js}: This files contains an alternative JSON +@code{parse} function that uses a state machine instead of @code{eval}. + +@code{cycle.js}: This file contains two functions, @code{JSON.decycle} and +@code{JSON.retrocycle}, which make it possible to encode cyclical structures +and DAGs in JSON, and to then recover them. This is a capability that is not +provided by ES5. @code{JSONPath} is used to represent the links.") + (license license:public-domain)))) From 3f48403aafc3cd6e50c178fb15b6251a40969c07 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 15:54:33 +0200 Subject: [PATCH 145/162] gnu: Add js-strftime. * gnu/packages/javascript.scm (js-strftime): New variable. --- gnu/packages/javascript.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/javascript.scm b/gnu/packages/javascript.scm index a806cb0745..fdf5224746 100644 --- a/gnu/packages/javascript.scm +++ b/gnu/packages/javascript.scm @@ -206,3 +206,26 @@ function that uses recursive descent instead of @code{eval}. and DAGs in JSON, and to then recover them. This is a capability that is not provided by ES5. @code{JSONPath} is used to represent the links.") (license license:public-domain)))) + +(define-public js-strftime + (package + (name "js-strftime") + (version "0.10.0") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/samsonjs/strftime/" + "archive/v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1iya43w7y26y2dp9l4d40bhjc4scb5a9mng5ng5c8hsqr82f1375")))) + (build-system minify-build-system) + (arguments + `(#:javascript-files '("strftime.js"))) + (home-page "https://github.com/samsonjs/strftime") + (synopsis "Implementation of strftime to JavaScript") + (description "This is an implementation of the @code{strftime} procedure +for JavaScript. It works in (at least) node.js and browsers. It supports +localization and timezones. Most standard specifiers from C are supported as +well as some other extensions from Ruby.") + (license license:expat))) From a6bbb2a0d864c68356baa7dc94b801cbb769a117 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 15:54:51 +0200 Subject: [PATCH 146/162] gnu: Add js-highlight. * gnu/packages/javascript.scm (js-highlight): New variable. --- gnu/packages/javascript.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/javascript.scm b/gnu/packages/javascript.scm index fdf5224746..533e7365ac 100644 --- a/gnu/packages/javascript.scm +++ b/gnu/packages/javascript.scm @@ -229,3 +229,26 @@ for JavaScript. It works in (at least) node.js and browsers. It supports localization and timezones. Most standard specifiers from C are supported as well as some other extensions from Ruby.") (license license:expat))) + +(define-public js-highlight + (package + (name "js-highlight") + (version "9.12.0") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/isagalaev/highlight.js/" + "archive/" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1jjn9mj7fwq4zpr6is438bscf03b3q8jkj0k5c3fc6pkmjnhw939")))) + (build-system minify-build-system) + (arguments + `(#:javascript-files '("src/highlight.js"))) + (home-page "https://github.com/isagalaev/highlight.js") + (synopsis "Syntax highlighting for JavaScript") + (description "Highlight.js is a syntax highlighter written in JavaScript. +It works in the browser as well as on the server. It works with pretty much +any markup, doesn’t depend on any framework and has automatic language +detection.") + (license license:bsd-3))) From c4abc94d2b3106e336573ec4644fb09e2b6c6368 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 15:55:05 +0200 Subject: [PATCH 147/162] gnu: Add js-datatables. * gnu/packages/javascript.scm (js-datatables): New variable. --- gnu/packages/javascript.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/javascript.scm b/gnu/packages/javascript.scm index 533e7365ac..ff964aee94 100644 --- a/gnu/packages/javascript.scm +++ b/gnu/packages/javascript.scm @@ -252,3 +252,27 @@ It works in the browser as well as on the server. It works with pretty much any markup, doesn’t depend on any framework and has automatic language detection.") (license license:bsd-3))) + +(define-public js-datatables + (package + (name "js-datatables") + (version "1.10.15") + (source (origin + (method url-fetch) + (uri (string-append "https://datatables.net/releases/DataTables-" + version ".zip")) + (sha256 + (base32 + "1y9xqyqyz7x1ls3ska71pshl2hpiy3qnw1f7wygyslbhy4ssgf57")))) + (build-system minify-build-system) + (arguments + `(#:javascript-files '("media/js/dataTables.bootstrap.js" + "media/js/jquery.dataTables.js"))) + (native-inputs + `(("unzip" ,unzip))) + (home-page "https://datatables.net") + (synopsis "DataTables plug-in for jQuery") + (description "DataTables is a table enhancing plug-in for the jQuery +Javascript library, adding sorting, paging and filtering abilities to plain +HTML tables with minimal effort.") + (license license:expat))) From 4f65067bde7e886c42a9549eb0e16706b43f8af7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 15:55:22 +0200 Subject: [PATCH 148/162] gnu: Add js-selectize. * gnu/packages/javascript.scm (js-selectize): New variable. --- gnu/packages/javascript.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/javascript.scm b/gnu/packages/javascript.scm index ff964aee94..19021ac5a4 100644 --- a/gnu/packages/javascript.scm +++ b/gnu/packages/javascript.scm @@ -276,3 +276,24 @@ detection.") Javascript library, adding sorting, paging and filtering abilities to plain HTML tables with minimal effort.") (license license:expat))) + +(define-public js-selectize + (package + (name "js-selectize") + (version "0.12.4") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/selectize/selectize.js/" + "archive/v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0756p49aaz34mw2dx8k1gxf210mngfrri25vkba0j7wihd2af8gn")))) + (build-system minify-build-system) + (arguments `(#:javascript-files '("src/selectize.js"))) + (home-page "http://selectize.github.io/selectize.js/") + (synopsis "Hybrid widget between a textbox and } +box. It's jQuery based and it has autocomplete and native-feeling keyboard +navigation; it is useful for tagging, contact lists, etc.") + (license license:asl2.0))) From 0b0aa76fa84b421e6c7c127984a24211439f6146 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 15:55:39 +0200 Subject: [PATCH 149/162] gnu: Add js-es5-shim. * gnu/packages/javascript.scm (js-es5-shim): New variable. --- gnu/packages/javascript.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/javascript.scm b/gnu/packages/javascript.scm index 19021ac5a4..12f12bf8f1 100644 --- a/gnu/packages/javascript.scm +++ b/gnu/packages/javascript.scm @@ -297,3 +297,29 @@ HTML tables with minimal effort.") box. It's jQuery based and it has autocomplete and native-feeling keyboard navigation; it is useful for tagging, contact lists, etc.") (license license:asl2.0))) + +(define-public js-es5-shim + (package + (name "js-es5-shim") + (version "4.5.9") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/es-shims/es5-shim/" + "archive/v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0yfndyijz0ykddzprpvfjb2453gzpn528klmwycwbqc1bqd3m1hl")))) + (build-system minify-build-system) + (arguments `(#:javascript-files + '("es5-sham.js" + "es5-shim.js"))) + (home-page "https://github.com/es-shims/es5-shim") + (synopsis "ECMAScript 5 compatibility shims for legacy JavaScript engines") + (description "@code{es5-shim.js} patches a JavaScript context to contain +all ECMAScript 5 methods that can be faithfully emulated with a legacy +JavaScript engine. @code{es5-sham.js} patches other ES5 methods as closely as +possible. Many of these shams are intended only to allow code to be written +to ES5 without causing run-time errors in older engines. In many cases, this +means that these shams cause many ES5 methods to silently fail.") + (license license:expat))) From a3cd23b6393e34a6b106ad273d1705adb7685bed Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 16:04:24 +0200 Subject: [PATCH 150/162] gnu: Add r-shiny. * gnu/packages/web.scm (r-shiny): New variable. --- gnu/packages/web.scm | 104 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 104 insertions(+) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 972f1bdbce..86a7dc1868 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -73,6 +73,7 @@ #:use-module (gnu packages gnuzilla) #:use-module (gnu packages gperf) #:use-module (gnu packages gtk) + #:use-module (gnu packages javascript) #:use-module (gnu packages image) #:use-module (gnu packages libidn) #:use-module (gnu packages libunistring) @@ -4748,3 +4749,106 @@ internetarchive python module for programatic access to archive.org.") (define-public python2-internetarchive (package-with-python2 (strip-python2-variant python-internetarchive))) + +(define-public r-shiny + (package + (name "r-shiny") + (version "1.0.3") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/rstudio/shiny/" + "archive/v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0z2v2s4hd44mvzjn7r70549kdzkrrch9nxhp27r6x2cy6micizm3")))) + (build-system r-build-system) + (arguments + `(#:modules ((guix build r-build-system) + (guix build minify-build-system) + (guix build utils) + (ice-9 match)) + #:imported-modules (,@%r-build-system-modules + (guix build minify-build-system)) + #:phases + (modify-phases (@ (guix build r-build-system) %standard-phases) + (add-after 'unpack 'replace-bundled-minified-JavaScript + (lambda* (#:key inputs #:allow-other-keys) + (let ((replace-file (lambda (old new) + (format #t "replacing ~a with ~a\n" old new) + (delete-file old) + (symlink new old)))) + ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/ + ;; contain just data. They are not minified code, so we don't + ;; replace them. + (with-directory-excursion "inst/www/shared" + (replace-file "bootstrap/shim/respond.min.js" + (string-append (assoc-ref inputs "js-respond") + "/share/javascript/respond.min.js")) + (replace-file "bootstrap/shim/html5shiv.min.js" + (string-append (assoc-ref inputs "js-html5shiv") + "/share/javascript/html5shiv.min.js")) + (replace-file "json2-min.js" + (string-append (assoc-ref inputs "js-json2") + "/share/javascript/json2.min.js")) + (replace-file "strftime/strftime-min.js" + (string-append (assoc-ref inputs "js-strftime") + "/share/javascript/strftime.min.js")) + (replace-file "highlight/highlight.pack.js" + (string-append (assoc-ref inputs "js-highlight") + "/share/javascript/highlight.min.js")) + (replace-file "datatables/js/jquery.dataTables.min.js" + (string-append (assoc-ref inputs "js-datatables") + "/share/javascript/jquery.dataTables.min.js")) + (replace-file "selectize/js/selectize.min.js" + (string-append (assoc-ref inputs "js-selectize") + "/share/javascript/selectize.min.js")) + (replace-file "selectize/js/es5-shim.min.js" + (string-append (assoc-ref inputs "js-es5-shim") + "/share/javascript/es5-shim.min.js")) + (for-each (match-lambda + ((source . target) + (delete-file target) + (minify source #:target target))) + '(("jqueryui/jquery-ui.js" . + "jqueryui/jquery-ui.min.js") + ("showdown/src/showdown.js" . + "showdown/compressed/showdown.js") + ("datepicker/js/bootstrap-datepicker.js" . + "datepicker/js/bootstrap-datepicker.min.js") + ("ionrangeslider/js/ion.rangeSlider.js" . + "ionrangeslider/js/ion.rangeSlider.min.js") + ("bootstrap/js/bootstrap.js" . + "bootstrap/js/bootstrap.min.js") + ("shiny.js" . + "shiny.min.js") + ("jquery.js" . + "jquery.min.js"))))) + #t))))) + (propagated-inputs + `(("r-httpuv" ,r-httpuv) + ("r-mime" ,r-mime) + ("r-jsonlite" ,r-jsonlite) + ("r-xtable" ,r-xtable) + ("r-digest" ,r-digest) + ("r-htmltools" ,r-htmltools) + ("r-r6" ,r-r6) + ("r-sourcetools" ,r-sourcetools))) + (inputs + `(("js-datatables" ,js-datatables) + ("js-html5shiv" ,js-html5shiv) + ("js-json2" ,js-json2) + ("js-respond" ,js-respond) + ("js-selectize" ,js-selectize) + ("js-strftime" ,js-strftime) + ("js-highlight" ,js-highlight) + ("js-es5-shim" ,js-es5-shim))) + (home-page "http://shiny.rstudio.com") + (synopsis "Easy interactive web applications with R") + (description + "Makes it incredibly easy to build interactive web applications +with R. Automatic \"reactive\" binding between inputs and outputs and +extensive prebuilt widgets make it possible to build beautiful, +responsive, and powerful applications with minimal effort.") + (license l:artistic2.0))) From 8d6c845d68211005a873811f0aa2dbc369bddbb5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 4 Aug 2017 11:22:19 +0200 Subject: [PATCH 151/162] gnu: Add r-crosstalk. * gnu/packages/web.scm (r-crosstalk): New variable. --- gnu/packages/web.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 86a7dc1868..5459a3051d 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -4852,3 +4852,30 @@ with R. Automatic \"reactive\" binding between inputs and outputs and extensive prebuilt widgets make it possible to build beautiful, responsive, and powerful applications with minimal effort.") (license l:artistic2.0))) + +(define-public r-crosstalk + (package + (name "r-crosstalk") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "crosstalk" version)) + (sha256 + (base32 + "0lfa89vhrzi7a1rghmygcjr8gzddw35sinb3jx6g49mc9jias7mk")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-htmltools" ,r-htmltools) + ("r-jsonlite" ,r-jsonlite) + ("r-lazyeval" ,r-lazyeval) + ("r-r6" ,r-r6) + ("r-shiny" ,r-shiny))) + (home-page "https://rstudio.github.io/crosstalk/") + (synopsis "Inter-widget interactivity for HTML widgets") + (description + "This package provides building blocks for allowing HTML widgets to +communicate with each other, with Shiny or without (i.e. static @code{.html} +files). It currently supports linked brushing and filtering.") + (license l:expat))) From 1cec3462323717e063c98b6404e9c5c5ef037bdd Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Thu, 3 Aug 2017 20:14:56 +0200 Subject: [PATCH 152/162] gnu: php: Update to 7.1.8. * gnu/packages/patches/gd-CVE-2017-7890.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it * gnu/packages/php.scm (php): Update to 7.1.8. --- gnu/local.mk | 1 + gnu/packages/patches/gd-CVE-2017-7890.patch | 30 +++++++++++++++++++++ gnu/packages/php.scm | 17 +++++++++--- 3 files changed, 45 insertions(+), 3 deletions(-) create mode 100644 gnu/packages/patches/gd-CVE-2017-7890.patch diff --git a/gnu/local.mk b/gnu/local.mk index 0491de6584..1bece24418 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -625,6 +625,7 @@ dist_patch_DATA = \ %D%/packages/patches/gcr-disable-failing-tests.patch \ %D%/packages/patches/gcr-fix-collection-tests-to-work-with-gpg-21.patch \ %D%/packages/patches/gdk-pixbuf-list-dir.patch \ + %D%/packages/patches/gd-CVE-2017-7890.patch \ %D%/packages/patches/gd-fix-gd2-read-test.patch \ %D%/packages/patches/gd-fix-tests-on-i686.patch \ %D%/packages/patches/gd-freetype-test-failure.patch \ diff --git a/gnu/packages/patches/gd-CVE-2017-7890.patch b/gnu/packages/patches/gd-CVE-2017-7890.patch new file mode 100644 index 0000000000..66034c5703 --- /dev/null +++ b/gnu/packages/patches/gd-CVE-2017-7890.patch @@ -0,0 +1,30 @@ +From 99ba5c353373ed198f54af66fe4e355ebb96e363 Mon Sep 17 00:00:00 2001 +From: LEPILLER Julien +Date: Thu, 3 Aug 2017 17:04:17 +0200 +Subject: [PATCH] Fix #399: Buffer over-read into uninitialized memory. + +The stack allocated color map buffers were not zeroed before usage, and +so undefined palette indexes could cause information leakage. + +This is CVE-2017-7890. +--- + src/gd_gif_in.c | 3 +++ + 1 file changed, 3 insertions(+) + +diff --git a/src/gd_gif_in.c b/src/gd_gif_in.c +index 008d1ec..c195448 100644 +--- a/src/gd_gif_in.c ++++ b/src/gd_gif_in.c +@@ -216,6 +216,9 @@ BGD_DECLARE(gdImagePtr) gdImageCreateFromGifCtx(gdIOCtxPtr fd) + + gdImagePtr im = 0; + ++ memset(ColorMap, 0, 3 * MAXCOLORMAPSIZE); ++ memset(localColorMap, 0, 3 * MAXCOLORMAPSIZE); ++ + if(!ReadOK(fd, buf, 6)) { + return 0; + } +-- +2.13.3 + diff --git a/gnu/packages/php.scm b/gnu/packages/php.scm index 7d569eef3e..d0afab0931 100644 --- a/gnu/packages/php.scm +++ b/gnu/packages/php.scm @@ -49,10 +49,21 @@ #:use-module (guix build-system gnu) #:use-module ((guix licenses) #:prefix license:)) +(define gd-for-php + (package + (inherit gd) + (source (origin + (inherit (package-source gd)) + (patches + (append + (origin-patches (package-source gd)) + (search-patches "gd-CVE-2017-7890.patch"))))))) + + (define-public php (package (name "php") - (version "7.1.6") + (version "7.1.8") (home-page "https://secure.php.net/") (source (origin (method url-fetch) @@ -60,7 +71,7 @@ name "-" version ".tar.xz")) (sha256 (base32 - "0nr49gqhk4pv8kcdc60cl1mgwlinawpraq9ba15whzmb472lsn01")) + "1aramb6dm57pr2iz61id9vzfy7h5qkb6bf7dxhrwnjk0723qahw9")) (modules '((guix build utils))) (snippet '(with-directory-excursion "ext" @@ -282,7 +293,7 @@ ("curl" ,curl) ("cyrus-sasl" ,cyrus-sasl) ("freetype" ,freetype) - ("gd" ,gd) + ("gd" ,gd-for-php) ("gdbm" ,gdbm) ("glibc" ,glibc) ("gmp" ,gmp) From 7656739771b0e07e467af709c730fee85bf65821 Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Sat, 5 Aug 2017 01:57:25 -0400 Subject: [PATCH 153/162] Revert "daemon: Ensure proper alignment on the stack." This reverts commit ab4ccc8fcfaf2215d4b33b1376147e4c2c70426a. --- nix/libstore/build.cc | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/nix/libstore/build.cc b/nix/libstore/build.cc index a93095dd1e..c6615865be 100644 --- a/nix/libstore/build.cc +++ b/nix/libstore/build.cc @@ -26,7 +26,6 @@ #include #include #include -#include #include #include @@ -2009,11 +2008,7 @@ void DerivationGoal::startBuilder() char stack[32 * 1024]; int flags = CLONE_NEWPID | CLONE_NEWNS | CLONE_NEWIPC | CLONE_NEWUTS | SIGCHLD; if (!fixedOutput) flags |= CLONE_NEWNET; - - /* Ensure proper alignment on the stack. On aarch64, it has to be 16 - bytes. */ - pid = clone(childEntry, (char *)(((uintptr_t)stack + 16) & ~0xf), - flags, this); + pid = clone(childEntry, stack + sizeof(stack) - 8, flags, this); if (pid == -1) throw SysError("cloning builder process"); } else From 3d5d87a3ae4a3320bb909265ac4d2739e206dfdd Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sun, 30 Jul 2017 10:23:08 +0200 Subject: [PATCH 154/162] gnu: Add cubicle. * gnu/packages/maths.scm (cubicle): New variable. --- gnu/packages/maths.scm | 43 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 00732a5756..e19c8edc82 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -3197,3 +3197,46 @@ as equations, scalars, vectors, and matrices.") theories} (SMT) solver. It provides a C/C++ API.") (home-page "https://github.com/Z3Prover/z3") (license license:expat))) + +(define-public cubicle + (package + (name "cubicle") + (version "1.1.1") + (source (origin + (method url-fetch) + (uri (string-append "http://cubicle.lri.fr/cubicle-" + version ".tar.gz")) + (sha256 + (base32 + "1sny9c4fm14k014pk62ibpwbrjjirkx8xmhs9jg7q1hk7y7x3q2h")))) + (build-system gnu-build-system) + (native-inputs + `(("ocaml" ,ocaml) + ("which" ,which))) + (propagated-inputs + `(("z3" ,z3))) + (arguments + `(#:configure-flags (list "--with-z3") + #:tests? #f + #:phases + (modify-phases %standard-phases + (add-before 'configure 'configure-for-release + (lambda _ + (substitute* "Makefile.in" + (("SVNREV=") "#SVNREV=")))) + (add-before 'configure 'fix-/bin/sh + (lambda _ + (substitute* "configure" + (("/bin/sh") (which "sh"))))) + (add-before 'configure 'fix-smt-z3wrapper.ml + (lambda _ + (substitute* "Makefile.in" + (("\\\\n") ""))))))) + (home-page "http://cubicle.lri.fr/") + (synopsis "Model checker for array-based systems") + (description "Cubicle is an open source model checker for verifying safety +properties of array-based systems. This is a syntactically restricted class of +parametrized transition systems with states represented as arrays indexed by an +arbitrary number of processes. Cache coherence protocols and mutual exclusion +algorithms are typical examples of such systems.") + (license license:asl2.0))) From eedcfa704e650e203ecd8b4c448a5e69340cbfdf Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 5 Aug 2017 13:44:03 +0200 Subject: [PATCH 155/162] gnu: lftp: Update to 4.7.8. * gnu/packages/ftp.scm (lftp): Update to 4.7.8. --- gnu/packages/ftp.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/ftp.scm b/gnu/packages/ftp.scm index 49e7214991..eb108491a4 100644 --- a/gnu/packages/ftp.scm +++ b/gnu/packages/ftp.scm @@ -46,7 +46,7 @@ (define-public lftp (package (name "lftp") - (version "4.7.5") + (version "4.7.8") (source (origin (method url-fetch) ;; See https://lftp.tech/get.html for mirrors. @@ -58,7 +58,7 @@ "ftp/lftp/lftp-" version ".tar.xz"))) (sha256 (base32 - "1n6h3y5jz1rxlx7ap46vykgm0q2rvzr7c5s5ry5l32z3lbmwbdak")))) + "19ijsmbb5589vg5ga355ys3075z6s2x2h0bdbga343hfqmnid2pi")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) From 7f171fdaadb15bb1b313b25e9be3d1988b0f650f Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Sat, 5 Aug 2017 14:07:12 +0200 Subject: [PATCH 156/162] gnu: git: Update to 2.14.0. * gnu/packages/version-control.scm (git): Update to 2.14.0. --- gnu/packages/version-control.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/version-control.scm b/gnu/packages/version-control.scm index 08a6f3aae8..729746aed3 100644 --- a/gnu/packages/version-control.scm +++ b/gnu/packages/version-control.scm @@ -121,14 +121,14 @@ as well as the classic centralized workflow.") (define-public git (package (name "git") - (version "2.13.4") + (version "2.14.0") (source (origin (method url-fetch) (uri (string-append "mirror://kernel.org/software/scm/git/git-" version ".tar.xz")) (sha256 (base32 - "1nmg0n9l5ix876iqhcyhdnmiy7ihv0ybdijf1lssch6ja8m5j6ip")))) + "0xarcp0m7jbncic0g3ahz8l2d6b27h0g9ndgrhy9abkx61m6wgpr")))) (build-system gnu-build-system) (native-inputs `(("native-perl" ,perl) @@ -141,7 +141,7 @@ as well as the classic centralized workflow.") version ".tar.xz")) (sha256 (base32 - "0ljxkfi7ski9bgpdb8xpikl1xgjjk7bdzmzzkbj93jybk6iajkv7")))))) + "0kc2n6b1lrbr0wc8lk3xnrljn4fgzgab82icv658gdvyl9l3qrbx")))))) (inputs `(("curl" ,curl) ("expat" ,expat) From e78e38a4bb341b33f91afa7a8efa421be2d74905 Mon Sep 17 00:00:00 2001 From: Feng Shu Date: Thu, 3 Aug 2017 21:03:41 +0800 Subject: [PATCH 157/162] gnu: emacs-exwm: Update to 0.15. * gnu/packages/emacs.scm (emacs-exwm): Update to 0.15. Signed-off-by: Arun Isaac --- gnu/packages/emacs.scm | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 917c511f32..9beb7ae62e 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -4631,7 +4631,7 @@ It should enable you to implement low-level X11 applications.") (define-public emacs-exwm (package (name "emacs-exwm") - (version "0.14") + (version "0.15") (synopsis "Emacs X window manager") (source (origin (method url-fetch) @@ -4639,7 +4639,7 @@ It should enable you to implement low-level X11 applications.") version ".tar")) (sha256 (base32 - "14hjjpbasm84p54fxy73fg7g1fdwqkvisdw8dwwgzkflmd647mkx")))) + "1y7nqry9y0a99bsdqkk9f554vczfw4sz6raadw3138835qy697jg")))) (build-system emacs-build-system) (propagated-inputs `(("emacs-xelb" ,emacs-xelb))) @@ -4673,12 +4673,9 @@ It should enable you to implement low-level X11 applications.") TryExec=~@*~a~@ Type=Application~%" ,name ,synopsis exwm-executable))) ;; Add a shell wrapper to bin - ;; Set DISPLAY variable to work around - ;; https://github.com/ch11ng/exwm/issues/213 (with-output-to-file exwm-executable (lambda _ (format #t "#!~a ~@ - export DISPLAY=:0 ~@ ~a +SI:localuser:$USER ~@ exec ~a --exit-with-session ~a \"$@\" --eval '~s' ~%" (string-append (assoc-ref inputs "bash") "/bin/sh") From 91d94e28ec30d72e1e6a7d0ff8af49656c3f1d7e Mon Sep 17 00:00:00 2001 From: Feng Shu Date: Fri, 4 Aug 2017 20:52:16 +0800 Subject: [PATCH 158/162] gnu: emacs-exwm-x: Do not set DISPLAY. * gnu/packages/emacs.scm (emacs-exwm-x): Do not set DISPLAY. The issue has been fixed upstream in exwm-0.15. Signed-off-by: Arun Isaac --- gnu/packages/emacs.scm | 3 --- 1 file changed, 3 deletions(-) diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 9beb7ae62e..4aa713346f 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -4767,12 +4767,9 @@ other operations.") TryExec=~@*~a~@ Type=Application~%" ,name ,synopsis exwm-executable))) ;; Add a shell wrapper to bin - ;; Set DISPLAY variable to work around - ;; https://github.com/ch11ng/exwm/issues/213 (with-output-to-file exwm-executable (lambda _ (format #t "#!~a ~@ - export DISPLAY=:0 ~@ ~a +SI:localuser:$USER ~@ exec ~a --exit-with-session ~a \"$@\" --eval '~s' ~%" (string-append (assoc-ref inputs "bash") "/bin/sh") From 9833bcfc08ef009b9e8b4398baa481ef65c80ad7 Mon Sep 17 00:00:00 2001 From: Danny Milosavljevic Date: Fri, 21 Jul 2017 01:06:46 +0200 Subject: [PATCH 159/162] build: Allow mounting of entire disks. * gnu/build/file-systems.scm (disk-partitions): Also return entire drives. --- gnu/build/file-systems.scm | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/gnu/build/file-systems.scm b/gnu/build/file-systems.scm index b6930497d6..203fbdfffb 100644 --- a/gnu/build/file-systems.scm +++ b/gnu/build/file-systems.scm @@ -373,15 +373,16 @@ not valid header was found." (define (disk-partitions) "Return the list of device names corresponding to valid disk partitions." - (define (last-character str) - (string-ref str (- (string-length str) 1))) - (define (partition? name major minor) - ;; Select device names that end in a digit, like libblkid's 'probe_all' - ;; function does. Checking for "/sys/dev/block/MAJOR:MINOR/partition" - ;; doesn't work for partitions coming from mapped devices. - (and (char-set-contains? char-set:digit (last-character name)) - (> major 2))) ;ignore RAM disks and floppy disks + ;; grub-mkrescue does some funny things for EFI support which + ;; makes it a lot more difficult than one would expect to support + ;; booting an ISO-9660 image from an USB flash drive. + ;; For example there's a buggy (too small) hidden partition in it + ;; which Linux mounts and then proceeds to fail while trying to + ;; fall off the edge. + ;; In any case, partition tables are supposed to be optional so + ;; here we allow checking entire disks for file systems, too. + (> major 2)) ;ignore RAM disks and floppy disks (call-with-input-file "/proc/partitions" (lambda (port) From 31ed845b7057b6f07450f15eaa877d5a1ae12ce1 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Sat, 5 Aug 2017 22:36:10 +0300 Subject: [PATCH 160/162] daemon: On aarch64, use increments of 16 on the stack. * nix/libstore/build.cc (DerivationGoal::startBuilder): When on aarch64, when calling clone(), increment the stack by 16. --- nix/libstore/build.cc | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/nix/libstore/build.cc b/nix/libstore/build.cc index c6615865be..693fa70c8d 100644 --- a/nix/libstore/build.cc +++ b/nix/libstore/build.cc @@ -2008,7 +2008,11 @@ void DerivationGoal::startBuilder() char stack[32 * 1024]; int flags = CLONE_NEWPID | CLONE_NEWNS | CLONE_NEWIPC | CLONE_NEWUTS | SIGCHLD; if (!fixedOutput) flags |= CLONE_NEWNET; - pid = clone(childEntry, stack + sizeof(stack) - 8, flags, this); +#ifdef __aarch64__ + pid = clone(childEntry, stack + sizeof(stack) - 16, flags, this); +#else + pid = clone(childEntry, stack + sizeof(stack) - 8, flags, this); +#endif if (pid == -1) throw SysError("cloning builder process"); } else From 6a4364335c967f841b53ed35c22f90445437e4b0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Sat, 5 Aug 2017 23:08:44 +0200 Subject: [PATCH 161/162] doc: Suggest running guix-daemon with 'sudo -E'. Suggested by Martin H. . * doc/contributing.texi (Running Guix Before It Is Installed): Suggest 'sudo -E'. --- doc/contributing.texi | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/doc/contributing.texi b/doc/contributing.texi index 00edd47710..98971a9bbc 100644 --- a/doc/contributing.texi +++ b/doc/contributing.texi @@ -110,10 +110,13 @@ actually installing them. So that you can distinguish between your To that end, all the command-line tools can be used even if you have not run @code{make install}. To do that, prefix each command with @command{./pre-inst-env} (the @file{pre-inst-env} script lives in the -top build tree of Guix), as in: +top build tree of Guix), as in@footnote{The @option{-E} flag to +@command{sudo} guarantees that @code{GUILE_LOAD_PATH} is correctly set +such that @command{guix-daemon} and the tools it uses can find the Guile +modules they need.}: @example -$ sudo ./pre-inst-env guix-daemon --build-users-group=guixbuild +$ sudo -E ./pre-inst-env guix-daemon --build-users-group=guixbuild $ ./pre-inst-env guix build hello @end example From 01a61d7040b1794f36547b107abce6e967d59f21 Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Tue, 25 Jul 2017 15:04:57 -0400 Subject: [PATCH 162/162] gnu: libtasn1: Fix CVE-2017-10790. * gnu/packages/patches/libtasn1-CVE-2017-10790.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/tls.scm (libtasn1/fixed)[source]: Use it. --- gnu/local.mk | 1 + .../patches/libtasn1-CVE-2017-10790.patch | 63 +++++++++++++++++++ gnu/packages/tls.scm | 3 +- 3 files changed, 66 insertions(+), 1 deletion(-) create mode 100644 gnu/packages/patches/libtasn1-CVE-2017-10790.patch diff --git a/gnu/local.mk b/gnu/local.mk index 1bece24418..9482d4bb53 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -775,6 +775,7 @@ dist_patch_DATA = \ %D%/packages/patches/libssh2-fix-build-failure-with-gcrypt.patch \ %D%/packages/patches/libtar-CVE-2013-4420.patch \ %D%/packages/patches/libtasn1-CVE-2017-6891.patch \ + %D%/packages/patches/libtasn1-CVE-2017-10790.patch \ %D%/packages/patches/libtheora-config-guess.patch \ %D%/packages/patches/libtiff-CVE-2016-10092.patch \ %D%/packages/patches/libtiff-CVE-2016-10093.patch \ diff --git a/gnu/packages/patches/libtasn1-CVE-2017-10790.patch b/gnu/packages/patches/libtasn1-CVE-2017-10790.patch new file mode 100644 index 0000000000..6cec0c8030 --- /dev/null +++ b/gnu/packages/patches/libtasn1-CVE-2017-10790.patch @@ -0,0 +1,63 @@ +Fix CVE-2017-10790: + +https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2017-10790 + +Patch copied from upstream source repository: + +https://git.savannah.nongnu.org/cgit/libtasn1.git/commit/?id=d8d805e1f2e6799bb2dff4871a8598dc83088a39 + +From d8d805e1f2e6799bb2dff4871a8598dc83088a39 Mon Sep 17 00:00:00 2001 +From: Nikos Mavrogiannopoulos +Date: Thu, 22 Jun 2017 16:31:37 +0200 +Subject: [PATCH] _asn1_check_identifier: safer access to values read + +Signed-off-by: Nikos Mavrogiannopoulos +--- + lib/parser_aux.c | 17 ++++++++++++----- + 1 file changed, 12 insertions(+), 5 deletions(-) + +diff --git a/lib/parser_aux.c b/lib/parser_aux.c +index 976ab38..786ea64 100644 +--- a/lib/parser_aux.c ++++ b/lib/parser_aux.c +@@ -955,7 +955,7 @@ _asn1_check_identifier (asn1_node node) + if (p2 == NULL) + { + if (p->value) +- _asn1_strcpy (_asn1_identifierMissing, p->value); ++ _asn1_str_cpy (_asn1_identifierMissing, sizeof(_asn1_identifierMissing), (char*)p->value); + else + _asn1_strcpy (_asn1_identifierMissing, "(null)"); + return ASN1_IDENTIFIER_NOT_FOUND; +@@ -968,9 +968,15 @@ _asn1_check_identifier (asn1_node node) + if (p2 && (type_field (p2->type) == ASN1_ETYPE_DEFAULT)) + { + _asn1_str_cpy (name2, sizeof (name2), node->name); +- _asn1_str_cat (name2, sizeof (name2), "."); +- _asn1_str_cat (name2, sizeof (name2), (char *) p2->value); +- _asn1_strcpy (_asn1_identifierMissing, p2->value); ++ if (p2->value) ++ { ++ _asn1_str_cat (name2, sizeof (name2), "."); ++ _asn1_str_cat (name2, sizeof (name2), (char *) p2->value); ++ _asn1_str_cpy (_asn1_identifierMissing, sizeof(_asn1_identifierMissing), (char*)p2->value); ++ } ++ else ++ _asn1_strcpy (_asn1_identifierMissing, "(null)"); ++ + p2 = asn1_find_node (node, name2); + if (!p2 || (type_field (p2->type) != ASN1_ETYPE_OBJECT_ID) || + !(p2->type & CONST_ASSIGN)) +@@ -990,7 +996,8 @@ _asn1_check_identifier (asn1_node node) + _asn1_str_cpy (name2, sizeof (name2), node->name); + _asn1_str_cat (name2, sizeof (name2), "."); + _asn1_str_cat (name2, sizeof (name2), (char *) p2->value); +- _asn1_strcpy (_asn1_identifierMissing, p2->value); ++ _asn1_str_cpy (_asn1_identifierMissing, sizeof(_asn1_identifierMissing), (char*)p2->value); ++ + p2 = asn1_find_node (node, name2); + if (!p2 || (type_field (p2->type) != ASN1_ETYPE_OBJECT_ID) + || !(p2->type & CONST_ASSIGN)) +-- +2.13.3 + diff --git a/gnu/packages/tls.scm b/gnu/packages/tls.scm index 6d71a9b809..58ec9ff5ec 100644 --- a/gnu/packages/tls.scm +++ b/gnu/packages/tls.scm @@ -81,7 +81,8 @@ specifications.") (origin (inherit (package-source libtasn1)) (patches - (search-patches "libtasn1-CVE-2017-6891.patch")))))) + (search-patches "libtasn1-CVE-2017-6891.patch" + "libtasn1-CVE-2017-10790.patch")))))) (define-public asn1c (package