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Ludovic Courtès 2019-10-07 17:06:13 +02:00
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13 changed files with 315 additions and 157 deletions
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1
gnu/local.mk
View file

@ -693,7 +693,6 @@ dist_patch_DATA = \
%D%/packages/patches/antlr3-3_1-fix-java8-compilation.patch \
%D%/packages/patches/antlr3-3_3-fix-java8-compilation.patch \
%D%/packages/patches/apr-skip-getservbyname-test.patch \
%D%/packages/patches/aria2-CVE-2019-3500.patch \
%D%/packages/patches/aspell-default-dict-dir.patch \
%D%/packages/patches/aspell-gcc-compat.patch \
%D%/packages/patches/ath9k-htc-firmware-binutils.patch \

42
gnu/packages/audio.scm
View file

@ -1536,7 +1536,7 @@ synchronous execution of all clients, and low latency operation.")
(define-public jack-2
(package (inherit jack-1)
(name "jack2")
(version "1.9.12")
(version "1.9.13")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/jackaudio/jack2/releases/"
@ -1545,40 +1545,38 @@ synchronous execution of all clients, and low latency operation.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"0crf4y9a5j9miw8r5ji4l3w5w0y2frrf7xyfsfdgacnw6vwy5vyy"))))
"1d1d403jn4366mqig6g8ghr8057b3rn7gs26b5p3rkal34j20qw2"))))
(build-system waf-build-system)
(arguments
`(#:python ,python-2
#:tests? #f ; no check target
`(#:tests? #f ; no check target
#:configure-flags '("--dbus"
"--alsa")
#:phases
(modify-phases %standard-phases
(add-before
'configure 'set-linkflags
(lambda _
;; Add $libdir to the RUNPATH of all the binaries.
(substitute* "wscript"
((".*CFLAGS.*-Wall.*" m)
(string-append m
" conf.env.append_unique('LINKFLAGS',"
"'-Wl,-rpath=" %output "/lib')\n")))
#t))
(add-before 'configure 'set-linkflags
(lambda _
;; Add $libdir to the RUNPATH of all the binaries.
(substitute* "wscript"
((".*CFLAGS.*-Wall.*" m)
(string-append m
" conf.env.append_unique('LINKFLAGS',"
"'-Wl,-rpath=" %output "/lib')\n")))
#t))
(add-after 'install 'wrap-python-scripts
(lambda* (#:key inputs outputs #:allow-other-keys)
;; Make sure 'jack_control' runs with the correct PYTHONPATH.
(let* ((out (assoc-ref outputs "out"))
(path (getenv "PYTHONPATH")))
(wrap-program (string-append out "/bin/jack_control")
`("PYTHONPATH" ":" prefix (,path))))
#t)))))
(lambda* (#:key inputs outputs #:allow-other-keys)
;; Make sure 'jack_control' runs with the correct PYTHONPATH.
(let* ((out (assoc-ref outputs "out"))
(path (getenv "PYTHONPATH")))
(wrap-program (string-append out "/bin/jack_control")
`("PYTHONPATH" ":" prefix (,path))))
#t)))))
(inputs
`(("alsa-lib" ,alsa-lib)
("dbus" ,dbus)
("expat" ,expat)
("libsamplerate" ,libsamplerate)
("opus" ,opus)
("python2-dbus" ,python2-dbus)
("python-dbus" ,python-dbus)
("readline" ,readline)))
(native-inputs
`(("pkg-config" ,pkg-config)))

13
gnu/packages/bioconductor.scm
View file

@ -1192,14 +1192,14 @@ the Human Protein Atlas project.")
(define-public r-regioner
(package
(name "r-regioner")
(version "1.16.4")
(version "1.16.5")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "regioneR" version))
(sha256
(base32
"0xzk057h6nkr3rvd412prxgnkpq625b90laj1kwb0i5q8j5ch760"))))
"12x7sh5d8y549hqz4qjb2j3ak22l79w9l0vdbv4gn0bwi5206k8h"))))
(properties `((upstream-name . "regioneR")))
(build-system r-build-system)
(propagated-inputs
@ -5343,14 +5343,14 @@ self-organizing map clustering and minimal spanning trees.")
(define-public r-mixomics
(package
(name "r-mixomics")
(version "6.8.4")
(version "6.8.5")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "mixOmics" version))
(sha256
(base32
"0lw4c9lxcm83xrvl4y120i1z710qjbdqginhrw738azpr1f82hcg"))))
"0s93ai5d7li8pnxd87n12j9gypvac5zfahsk68j7zjv68dglj8s7"))))
(properties `((upstream-name . "mixOmics")))
(build-system r-build-system)
(propagated-inputs
@ -6010,19 +6010,20 @@ arrays based on fast wavelet-based functional models.")
(define-public r-variancepartition
(package
(name "r-variancepartition")
(version "1.14.0")
(version "1.14.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "variancePartition" version))
(sha256
(base32
"1ycapwb2mq57xibrzzjz9zwxqz4nwz9f3n5gskhlr5vcs7irkjd6"))))
"0w4kri2389x1082xppx7l6xl1a5g74fyp02iwb4938x3gzwqwbjd"))))
(properties
`((upstream-name . "variancePartition")))
(build-system r-build-system)
(propagated-inputs
`(("r-biobase" ,r-biobase)
("r-biocparallel" ,r-biocparallel)
("r-colorramps" ,r-colorramps)
("r-doparallel" ,r-doparallel)
("r-foreach" ,r-foreach)

13
gnu/packages/bioinformatics.scm
View file

@ -7647,13 +7647,13 @@ annotation data packages using SQLite data storage.")
(define-public r-biomart
(package
(name "r-biomart")
(version "2.40.4")
(version "2.40.5")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biomaRt" version))
(sha256
(base32
"0dj51qkxm7bh24b3bs1di7lic6zgi7g5gf9iqkqhrwkbm7sqvn0v"))))
"1kjvxnkpsx3j2hji3cg3ka2gv8a9mg117lzzxyqjb7qa4zw7dipx"))))
(properties
`((upstream-name . "biomaRt")))
(build-system r-build-system)
@ -7731,13 +7731,13 @@ biological sequences or sets of sequences.")
(define-public r-rsamtools
(package
(name "r-rsamtools")
(version "2.0.1")
(version "2.0.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Rsamtools" version))
(sha256
(base32
"0wzp5vsmqs7h44r7lcw8fnz5x9bcdcfiqq8d3h62wwibyk2lg0w1"))))
"188k5g40lbli7dxr96hldyvg9r9hmlbh2fp0qs5nnd12b8zbf338"))))
(properties
`((upstream-name . "Rsamtools")))
(build-system r-build-system)
@ -9454,13 +9454,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
(define-public r-seurat
(package
(name "r-seurat")
(version "3.1.0")
(version "3.1.1")
(source (origin
(method url-fetch)
(uri (cran-uri "Seurat" version))
(sha256
(base32
"0icxndnnkkmmr9hhd01dv3w8pih7x9r0rlp3fq9pk3qajp9gmlyq"))))
"084lr2fjdksshsmv1ww82bgn3a9mml7kswsidjrs89snabgvn360"))))
(properties `((upstream-name . "Seurat")))
(build-system r-build-system)
(propagated-inputs
@ -9473,6 +9473,7 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.")
("r-ggplot2" ,r-ggplot2)
("r-ggrepel" ,r-ggrepel)
("r-ggridges" ,r-ggridges)
("r-httr" ,r-httr)
("r-ica" ,r-ica)
("r-igraph" ,r-igraph)
("r-irlba" ,r-irlba)

13
gnu/packages/bittorrent.scm
View file

@ -2,7 +2,7 @@
;;; Copyright © 2014 Taylan Ulrich Bayirli/Kammer <taylanbayirli@gmail.com>
;;; Copyright © 2014, 2015, 2016 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016, 2017, 2018, 2019 Leo Famulari <leo@famulari.name>
;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016 Tomáš Čech <sleep_walker@gnu.org>
;;; Copyright © 2016, 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017 Jelle Licht <jlicht@fsfe.org>
@ -262,16 +262,15 @@ maintained upstream.")
(define-public aria2
(package
(name "aria2")
(version "1.34.0")
(version "1.35.0")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/tatsuhiro-t/aria2/"
"releases/download/release-" version "/"
name "-" version ".tar.xz"))
(patches (search-patches "aria2-CVE-2019-3500.patch"))
(uri (string-append "https://github.com/aria2/aria2/releases/"
"download/release-" version
"/aria2-" version ".tar.xz"))
(sha256
(base32
"18vpgr430vxlwbcc3598rr1srfmwypls6wp1m4wf21hncc1ahi1s"))))
"1zbxc517d97lb96f15xcy4l7b66grxrp3h2ids2jiwkaip87yaqy"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags (list "--enable-libaria2"

49
gnu/packages/cran.scm
View file

@ -525,31 +525,18 @@ directory.")
(define-public r-htmltools
(package
(name "r-htmltools")
(version "0.3.6")
(version "0.4.0")
(source (origin
(method url-fetch)
(uri (cran-uri "htmltools" version))
(sha256
(base32
"18k8r1s8sz1jy7dkz35n69wj20xhmllr53xmwb4pdzf2z61gpbs4"))))
"06l17d8jkf438yk2mchpsp4j90bynnapz3nabh5vkcc324p5a62v"))))
(build-system r-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
;; See https://github.com/rstudio/htmltools/pull/68
;; The resource files are in the store and have mode 444. After
;; copying the files R fails to remove them again because it doesn't
;; have write access to them.
(add-after 'unpack 'copy-files-without-mode
(lambda _
(substitute* "R/html_dependency.R"
(("file.copy\\(from, to, " prefix)
(string-append prefix
"copy.mode = FALSE, ")))
#t)))))
(propagated-inputs
`(("r-digest" ,r-digest)
("r-rcpp" ,r-rcpp)))
("r-rcpp" ,r-rcpp)
("r-rlang" ,r-rlang)))
(home-page "https://cran.r-project.org/web/packages/htmltools")
(synopsis "R tools for HTML")
(description
@ -559,13 +546,13 @@ directory.")
(define-public r-htmlwidgets
(package
(name "r-htmlwidgets")
(version "1.3")
(version "1.5")
(source (origin
(method url-fetch)
(uri (cran-uri "htmlwidgets" version))
(sha256
(base32
"04jsdh14l2zifbjpbbh23w7bxz1wpsas0zb2gy2zwv4yqamzzr7i"))))
"1h2sj5h9vcssb73nz63gmw5bajs73m9q807fsypvr621gb1s124i"))))
(build-system r-build-system)
(propagated-inputs
`(("r-htmltools" ,r-htmltools)
@ -5339,14 +5326,14 @@ simple method for converting between file types.")
(define-public r-maptools
(package
(name "r-maptools")
(version "0.9-5")
(version "0.9-8")
(source
(origin
(method url-fetch)
(uri (cran-uri "maptools" version))
(sha256
(base32
"1pbvcn9xfx0hxq1ppbfg9xm5j04q4c15nj983yjmg7dlkzq135ax"))))
"1ix3cg74w0w6cj8nwi0r9n3y5q9ljc21hm8xq6yqqngs57prvn2x"))))
(build-system r-build-system)
(propagated-inputs
`(("r-foreign" ,r-foreign)
@ -5367,14 +5354,14 @@ exchanging spatial objects with other R packages.")
(define-public r-later
(package
(name "r-later")
(version "0.8.0")
(version "1.0.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "later" version))
(sha256
(base32
"08g503xjxrfxvrzj0cavsrz4m8ykbha64344j1w2r6v17js2hakb"))))
"11xjavj7siz0xv2ffq1ld4bwl35jyrcfpvvs4p3ilpifxx49hyr7"))))
(build-system r-build-system)
(propagated-inputs
`(("r-bh" ,r-bh)
@ -5390,14 +5377,14 @@ time after the current time, after the R execution stack has emptied.")
(define-public r-promises
(package
(name "r-promises")
(version "1.0.1")
(version "1.1.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "promises" version))
(sha256
(base32
"0n2mlv6bvfb4yhgcml696l9vkbw21pz0smqylivr606z99rwgny2"))))
"01l0ydjvvy6afcg5d6pzvk1ikd3djq8n2flv8c831ksn68z0zsn8"))))
(build-system r-build-system)
(propagated-inputs
`(("r-later" ,r-later)
@ -5860,14 +5847,14 @@ results to the user.")
(define-public r-hdf5r
(package
(name "r-hdf5r")
(version "1.2.0")
(version "1.3.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "hdf5r" version))
(sha256
(base32
"10gynjwaaxks8y9c2fl8k040j0nbwn372nil70009yfk9wrkx0aq"))))
"1pq12vkfqxvcaznwaxvjdg3acimk5a20m8h18sixvxc34vnqxw8f"))))
(build-system r-build-system)
(inputs
`(("hdf5" ,hdf5)
@ -8960,14 +8947,14 @@ package provides a minimal R interface by relying on the Rcpp package.")
(define-public r-rcppparallel
(package
(name "r-rcppparallel")
(version "4.4.3")
(version "4.4.4")
(source
(origin
(method url-fetch)
(uri (cran-uri "RcppParallel" version))
(sha256
(base32
"1ym0bzs9g6bsg2lz24fisxxa3gypr6xcvrczn304czmrrag9413s"))))
"0p13f2mywjr7gmskf8ri4y8p5yr1bvr4xrpw2w11vdvafwz1vcia"))))
(properties `((upstream-name . "RcppParallel")))
(build-system r-build-system)
(home-page "http://rcppcore.github.io/RcppParallel")
@ -10317,14 +10304,14 @@ and manipulating sets of ontological terms.")
(define-public r-gargle
(package
(name "r-gargle")
(version "0.3.1")
(version "0.4.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "gargle" version))
(sha256
(base32
"0vqgp4w03sdyj0q96gxkybqflzzbaw84zifsbi7pxk5y08fimj2v"))))
"08zhfk2sl342w35i5n2c93ayypg3z0kbl0020l3y9adqka1vazgx"))))
(build-system r-build-system)
(propagated-inputs
`(("r-fs" ,r-fs)

75
gnu/packages/emacs-xyz.scm
View file

@ -6621,7 +6621,7 @@ ack, ag, helm and pt.")
(define-public emacs-helm
(package
(name "emacs-helm")
(version "3.3")
(version "3.5.0")
(source
(origin
(method git-fetch)
@ -6630,7 +6630,7 @@ ack, ag, helm and pt.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0fqhw7r9fcsja5d3pgbipw7pkw9nj534faav6hi45413hc3gyv92"))))
(base32 "07bijcnfkv60l3swasxv53x32l6glds05mxnbb3xbnmkgm1pm9if"))))
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-async" ,emacs-async)
@ -6647,6 +6647,31 @@ considered to be its successor. Helm sets out to clean up the legacy code in
not tied in the trap of backward compatibility.")
(license license:gpl3+)))
(define-public emacs-helm-org
(let ((commit "542dda7bc9a3b9dfb439e4f8a1e5f60cfb6cc256")
(revision "1"))
(package
(name "emacs-helm-org")
(version (git-version "1.0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/emacs-helm/helm-org.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "1xa32w80icrykpyfb89fhb0s4l7ysi0sc7f7lfwqz5najwbgqipl"))))
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-helm" ,emacs-helm)))
(home-page "https://github.com/emacs-helm/helm-org")
(synopsis "Helm interface to the Silver Searcher")
(description
"This package provides a frontend for grepping tools like ag and ack,
as well as features for editing search results.")
(license license:gpl3+))))
(define-public emacs-helm-swoop
(package
(name "emacs-helm-swoop")
@ -6675,7 +6700,7 @@ for search-based navigation of buffers.")
(revision "1"))
(package
(name "emacs-helm-ag")
(version "0.58")
(version (git-version "0.58" revision commit))
(source
(origin
(method git-fetch)
@ -7267,7 +7292,7 @@ pasting into and from @code{tmux} paste buffers.")
(define-public emacs-evil-nerd-commenter
(package
(name "emacs-evil-nerd-commenter")
(version "3.3.7")
(version "3.3.8")
(source
(origin
(method git-fetch)
@ -7277,7 +7302,7 @@ pasting into and from @code{tmux} paste buffers.")
(file-name (git-file-name name version))
(sha256
(base32
"1r8shfdddys9vqvrxf7s6z83ydqx9xhqs9sa7klbsajryqcp50b7"))))
"0qd5a89mzvdyhd8lm13iwp220vzpd6dajwx54frlc5bzsxdmg6vc"))))
(build-system emacs-build-system)
(propagated-inputs `(("emacs-evil" ,emacs-evil)))
(arguments
@ -11690,6 +11715,26 @@ tables of contents.")
timestamps by providing a @code{ts} struct.")
(license license:gpl3+))))
(define-public emacs-peg
(package
(name "emacs-peg")
(version "0.6")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/emacsmirror/peg")
(commit version)))
(sha256
(base32
"0kjz7ch4bn0m4v9zgqyqcrsasnqc5c5drv2hp22j7rnbb7ny0q3n"))
(file-name (git-file-name name version))))
(build-system emacs-build-system)
(home-page "https://github.com/emacsmirror/peg/")
(synopsis "Parsing Expression Grammars in Elisp")
(description "This package provides a macro that parses the current buffer
according to a parsing expression grammar.")
(license license:gpl3+)))
(define-public emacs-org-ql
(package
(name "emacs-org-ql")
@ -12609,8 +12654,8 @@ key again.")
(license license:gpl3+)))
(define-public emacs-mbsync
(let ((commit "8f80c267cab1acb0d5bdd5b0059f5d1790d499ff")
(revision "3"))
(let ((commit "b62491c0e0d89eb9c66261a16d7ac81231c9c453")
(revision "4"))
(package
(name "emacs-mbsync")
(version (git-version "0.1.2" revision commit))
@ -12623,7 +12668,7 @@ key again.")
(file-name (git-file-name name version))
(sha256
(base32
"1dwlpcczsa6b7bwv5149by0qmk8v2y7bjad02k4fy25yxznqzci9"))))
"1zlih37mkqjn2czl12zn7lgxxljvrwhqqpbksj9c91zn0f0rm3mz"))))
(build-system emacs-build-system)
(home-page "https://github.com/dimitri/mbsync-el")
(synopsis "Interface to mbsync for Emacs")
@ -15082,10 +15127,8 @@ accept and reject GitHub pull requests.")
(license license:gpl3+))))
(define-public emacs-deadgrep
;; We prefer a newer commit (four commits newer than release) because of a
;; bugfix for globbing.
(let ((commit "329119c65126f7917d3910bc584f4191ba8f21ac")
(revision "1"))
(let ((commit "3fc7ca1f58e190f0c80da455a0e40187e673020e")
(revision "2"))
(package
(name "emacs-deadgrep")
(version (git-version "0.8" revision commit))
@ -15098,7 +15141,7 @@ accept and reject GitHub pull requests.")
(file-name (git-file-name name version))
(sha256
(base32
"0fxf7gq9sjfkgpdfqx10w3l3nd4rwa8kv9plyxk1fqacb3s5m6ai"))))
"016gwqxd9aqzjw3hqv3vdf8cs6la8r65g6azg5rlmjqwfx3vsaha"))))
(build-system emacs-build-system)
(inputs
`(("emacs-dash" ,emacs-dash)
@ -18161,8 +18204,8 @@ corresponding Evil keys.")
(license license:expat))))
(define-public emacs-evil-traces
(let ((commit "b41b7432b8110378c199a3d25af464083777f453")
(revision "1"))
(let ((commit "1931e3ea2c64b4aec393a9c25063c330deff55e3")
(revision "2"))
(package
(name "emacs-evil-traces")
(version (git-version "0.0.1" revision commit))
@ -18174,7 +18217,7 @@ corresponding Evil keys.")
(file-name (git-file-name name version))
(sha256
(base32
"0a15f2saynz9fws1h5s7py3cshsk4xs1kwgwj1m5rsin36g0j6hc"))))
"12p9lfxscs182vbd4dy0m5gacs3d4kyprbz5yndpwvl8g2qsqplz"))))
(build-system emacs-build-system)
(propagated-inputs
`(("emacs-evil" ,emacs-evil)))

15
gnu/packages/java.scm
View file

@ -1406,12 +1406,17 @@ bootstrapping purposes.")
(add-after 'install 'install-libjvm
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((lib-path (string-append (assoc-ref outputs "out")
"/lib/"
;; See 'INSTALL_ARCH_DIR' in
;; 'configure'.
,(match (%current-system)
("i686-linux"
"i386")
"/lib/i386")
("x86_64-linux"
"amd64")))))
"/lib/amd64")
("armhf-linux"
"/lib/arm")
("aarch64-linux"
"/lib/aarch64")))))
(symlink (string-append lib-path "/server/libjvm.so")
(string-append lib-path "/libjvm.so")))
#t))
@ -1559,6 +1564,10 @@ bootstrapping purposes.")
(description
"This package provides the Java development kit OpenJDK built with the
IcedTea build harness.")
;; 'configure' lists "mips" and "mipsel", but not "mips64el'.
(supported-systems (delete "mips64el-linux" %supported-systems))
;; IcedTea is released under the GPL2 + Classpath exception, which is the
;; same license as both GNU Classpath and OpenJDK.
(license license:gpl2+))))

8
gnu/packages/linux.scm
View file

@ -183,9 +183,9 @@ defconfig. Return the appropriate make target if applicable, otherwise return
(define deblob-scripts-5.3
(linux-libre-deblob-scripts
"5.3.1"
"5.3.4"
(base32 "15n09zq38d69y1wl28s3nasf3377qp2yil5b887zpqrm00dif7i4")
(base32 "1av9ykv714cnl0clls8rhwa8rwflz6ivg17gharj1x650qp6vnw3")))
(base32 "0nrimraf46nf6y1hwkg29fyl0a83wnj0mwq54ggxvffn9gk5h9pa")))
(define deblob-scripts-5.2
(linux-libre-deblob-scripts
@ -357,10 +357,10 @@ corresponding UPSTREAM-SOURCE (an origin), using the given DEBLOB-SCRIPTS."
"linux-" version ".tar.xz"))
(sha256 hash)))
(define-public linux-libre-5.3-version "5.3.2")
(define-public linux-libre-5.3-version "5.3.4")
(define-public linux-libre-5.3-pristine-source
(let ((version linux-libre-5.3-version)
(hash (base32 "0szw21mpp94gp3zn2fgllbv6fdjjf20njgrcjay7vjmm7farq7rn")))
(hash (base32 "0vi4bgcr921z5l6fbcrcgmhaji5gl2avpmp7njna6v0f7sxism0r")))
(make-linux-libre-source version
(%upstream-linux-source version hash)
deblob-scripts-5.3)))

178
gnu/packages/lisp.scm
View file

@ -6388,7 +6388,7 @@ the return type of a function.")
(package
(name "sbcl-optima")
(build-system asdf-build-system/sbcl)
(version (git-version "0.1" revision commit))
(version (git-version "1.0" revision commit))
(home-page "https://github.com/m2ym/optima")
(source
(origin
@ -6451,6 +6451,29 @@ quasiquote is enable matching of quasiquoted patterns, using Optima or
Trivia.")
(license license:expat)))
(define-public cl-fare-quasiquote
(sbcl-package->cl-source-package sbcl-fare-quasiquote))
(define-public sbcl-fare-quasiquote-optima
(package
(inherit sbcl-fare-quasiquote)
(name "sbcl-fare-quasiquote-optima")
(inputs
`(("optima" ,sbcl-optima)
("fare-quasiquote" ,sbcl-fare-quasiquote)))
(arguments
'(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'patch-requirement
(lambda _
(substitute* "fare-quasiquote-optima.asd"
(("\\(:version \"optima\" \"1\\.0\"\\)")
"\"optima\""))
#t)))))))
(define-public cl-fare-quasiquote-optima
(sbcl-package->cl-source-package sbcl-fare-quasiquote-optima))
(define-public sbcl-fare-quasiquote-readtable
(package
(inherit sbcl-fare-quasiquote)
@ -6464,6 +6487,22 @@ Trivia.
This package uses fare-quasiquote with named-readtable.")))
(define-public cl-fare-quasiquote-readtable
(sbcl-package->cl-source-package sbcl-fare-quasiquote-readtable))
;; TODO: Add support for component-less system in asdf-build-system/sbcl.
(define-public cl-fare-quasiquote-extras
(package
(inherit cl-fare-quasiquote)
(name "cl-fare-quasiquote-extras")
(build-system asdf-build-system/source)
(propagated-inputs
`(("fare-quasiquote" ,cl-fare-quasiquote)
("fare-quasiquote-optima" ,cl-fare-quasiquote-optima)
("fare-quasiquote-readtable" ,cl-fare-quasiquote-readtable)))
(description "This library combines @code{fare-quasiquote-readtable} and
@code{fare-quasiquote-optima}.")))
(define-public sbcl-trivia.level0
(let ((commit "902e0c65602bbfe96ae82e679330b3771ddc7603")
(revision "1"))
@ -7488,3 +7527,140 @@ of C+GObject libraries without the need of writing dedicated bindings.")
(define-public cl-gobject-introspection
(sbcl-package->cl-source-package sbcl-cl-gobject-introspection))
(define-public sbcl-string-case
(let ((commit "718c761e33749e297cd2809c7ba3ade1985c49f7")
(revision "0"))
(package
(name "sbcl-string-case")
(version (git-version "0.0.2" revision commit))
(home-page "https://github.com/pkhuong/string-case")
(source
(origin
(method git-fetch)
(uri (git-reference
(url home-page)
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"1n5i3yh0h5s636rcnwn7jwqy3rjflikra04lymimhpcshhjsk0md"))))
(build-system asdf-build-system/sbcl)
(synopsis "Efficient string= case in Common Lisp")
(description
"@code{string-case} is a Common Lisp macro that generates specialised decision
trees to dispatch on string equality.")
(license license:bsd-3))))
(define-public cl-string-case
(sbcl-package->cl-source-package sbcl-string-case))
(define-public ecl-string-case
(sbcl-package->ecl-package sbcl-string-case))
(define-public sbcl-global-vars
(let ((commit "c749f32c9b606a1457daa47d59630708ac0c266e")
(revision "0"))
(package
(name "sbcl-global-vars")
(version (git-version "1.0.0" revision commit))
(home-page "https://github.com/lmj/global-vars")
(source
(origin
(method git-fetch)
(uri (git-reference
(url home-page)
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"06m3xc8l3pgsapl8fvsi9wf6y46zs75cp9zn7zh6dc65v4s5wz3d"))))
(build-system asdf-build-system/sbcl)
(synopsis "Efficient global variables in Common Lisp")
(description
"In Common Lisp, a special variable that is never dynamically bound
typically serves as a stand-in for a global variable. The @code{global-vars}
library provides true global variables that are implemented by some compilers.
An attempt to rebind a global variable properly results in a compiler error.
That is, a global variable cannot be dynamically bound.
Global variables therefore allow us to communicate an intended usage that
differs from special variables. Global variables are also more efficient than
special variables, especially in the presence of threads.")
(license license:expat))))
(define-public cl-global-vars
(sbcl-package->cl-source-package sbcl-global-vars))
(define-public ecl-global-vars
(sbcl-package->ecl-package sbcl-global-vars))
(define-public sbcl-trivial-file-size
(let ((commit "1c1d672a01a446ba0391dbb4ffc40be3b0476f23")
(revision "0"))
(package
(name "sbcl-trivial-file-size")
(version (git-version "0.0.0" revision commit))
(home-page "https://github.com/ruricolist/trivial-file-size")
(source
(origin
(method git-fetch)
(uri (git-reference
(url home-page)
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"17pp86c9zs4y7i1sh7q9gbfw9iqv6655k7fz8qbj9ly1ypgxp4qs"))))
(build-system asdf-build-system/sbcl)
(native-inputs
`(("fiveam" ,sbcl-fiveam)))
(synopsis "Size of a file in bytes in Common Lisp")
(description
"The canonical way to determine the size of a file in bytes, using Common Lisp,
is to open the file with an element type of (unsigned-byte 8) and then
calculate the length of the stream. This is less than ideal. In most cases
it is better to get the size of the file from its metadata, using a system
call.
This library exports a single function, file-size-in-octets. It returns the
size of a file in bytes, using system calls when possible.")
(license license:expat))))
(define-public cl-trivial-file-size
(sbcl-package->cl-source-package sbcl-trivial-file-size))
(define-public ecl-trivial-file-size
(sbcl-package->ecl-package sbcl-trivial-file-size))
(define-public sbcl-trivial-macroexpand-all
(let ((commit "933270ac7107477de1bc92c1fd641fe646a7a8a9")
(revision "0"))
(package
(name "sbcl-trivial-macroexpand-all")
(version (git-version "0.0.0" revision commit))
(home-page "https://github.com/cbaggers/trivial-macroexpand-all")
(source
(origin
(method git-fetch)
(uri (git-reference
(url home-page)
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"191hnn4b5j4i3crydmlzbm231kj0h7l8zj6mzj69r1npbzkas4bd"))))
(build-system asdf-build-system/sbcl)
(native-inputs
`(("fiveam" ,sbcl-fiveam)))
(synopsis "Portable macroexpand-all for Common Lisp")
(description
"This library provides a macroexpand-all function that calls the
implementation specific equivalent.")
(license license:unlicense))))
(define-public cl-trivial-macroexpand-all
(sbcl-package->cl-source-package sbcl-trivial-macroexpand-all))
(define-public ecl-trivial-macroexpand-all
(sbcl-package->ecl-package sbcl-trivial-macroexpand-all))

6
gnu/packages/openldap.scm
View file

@ -112,14 +112,14 @@
(define-public nss-pam-ldapd
(package
(name "nss-pam-ldapd")
(version "0.9.10")
(version "0.9.11")
(source (origin
(method url-fetch)
(uri (string-append "https://arthurdejong.org/nss-pam-ldapd/"
"nss-pam-ldapd-" version ".tar.gz"))
(sha256
(base32
"1cqamcr6qpgwxijlr6kg7jspjamjra8w0haan0qssn0yxn95d7c0"))))
"1dna3r0q6sjhhlkhcp8x2zkslrd4y7701kk6fl5r940sdph1pmyh"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags
@ -146,7 +146,7 @@
`(("linux-pam" ,linux-pam)
("openldap" ,openldap)
("mit-krb5" ,mit-krb5)
("python" ,python-2)))
("python" ,python)))
(home-page "https://arthurdejong.org/nss-pam-ldapd")
(synopsis "NSS and PAM modules for LDAP")
(description "nss-pam-ldapd provides a @dfn{Name Service Switch} (NSS)

55
gnu/packages/patches/aria2-CVE-2019-3500.patch
View file

@ -1,55 +0,0 @@
Fix CVE-2019-3500:
https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2019-3500
https://github.com/aria2/aria2/issues/1329
Patch copied from upstream source repository:
https://github.com/aria2/aria2/commit/37368130ca7de5491a75fd18a20c5c5cc641824a
From 37368130ca7de5491a75fd18a20c5c5cc641824a Mon Sep 17 00:00:00 2001
From: Tatsuhiro Tsujikawa <tatsuhiro.t@gmail.com>
Date: Sat, 5 Jan 2019 09:32:40 +0900
Subject: [PATCH] Mask headers
---
src/HttpConnection.cc | 18 ++++++++++++------
1 file changed, 12 insertions(+), 6 deletions(-)
diff --git a/src/HttpConnection.cc b/src/HttpConnection.cc
index 77cb9d27a..be5b97723 100644
--- a/src/HttpConnection.cc
+++ b/src/HttpConnection.cc
@@ -102,11 +102,17 @@ std::string HttpConnection::eraseConfidentialInfo(const std::string& request)
std::string result;
std::string line;
while (getline(istr, line)) {
- if (util::startsWith(line, "Authorization: Basic")) {
- result += "Authorization: Basic ********\n";
+ if (util::istartsWith(line, "Authorization: ")) {
+ result += "Authorization: <snip>\n";
}
- else if (util::startsWith(line, "Proxy-Authorization: Basic")) {
- result += "Proxy-Authorization: Basic ********\n";
+ else if (util::istartsWith(line, "Proxy-Authorization: ")) {
+ result += "Proxy-Authorization: <snip>\n";
+ }
+ else if (util::istartsWith(line, "Cookie: ")) {
+ result += "Cookie: <snip>\n";
+ }
+ else if (util::istartsWith(line, "Set-Cookie: ")) {
+ result += "Set-Cookie: <snip>\n";
}
else {
result += line;
@@ -154,8 +160,8 @@ std::unique_ptr<HttpResponse> HttpConnection::receiveResponse()
const auto& proc = outstandingHttpRequests_.front()->getHttpHeaderProcessor();
if (proc->parse(socketRecvBuffer_->getBuffer(),
socketRecvBuffer_->getBufferLength())) {
- A2_LOG_INFO(
- fmt(MSG_RECEIVE_RESPONSE, cuid_, proc->getHeaderString().c_str()));
+ A2_LOG_INFO(fmt(MSG_RECEIVE_RESPONSE, cuid_,
+ eraseConfidentialInfo(proc->getHeaderString()).c_str()));
auto result = proc->getResult();
if (result->getStatusCode() / 100 == 1) {
socketRecvBuffer_->drain(proc->getLastBytesProcessed());

4
gnu/packages/statistics.scm
View file

@ -2119,14 +2119,14 @@ limited to R.")
(define-public r-backports
(package
(name "r-backports")
(version "1.1.4")
(version "1.1.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "backports" version))
(sha256
(base32
"00zz969vc2gfi5p9q65pzghq2bxm3p9zqgwqswkyz9rgybz5wjzf"))))
"0k19w68b2aihyj5mflw3732gkkzs78sssqdns960pdw3yfnkiv33"))))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/backports")
(synopsis "Reimplementations of functions introduced since R 3.0.0")