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61927 Commits (f71791c501a13ae34fd61e9be0590538a88be1b4)

Author SHA1 Message Date
Ricardo Wurmus 8637b77a9f
gnu: r-rcpparmadillo: Update to 0.9.900.1.0.
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.9.900.1.0.
2020-06-11 17:03:41 +02:00
Ricardo Wurmus 17788c8c2f
gnu: r-backports: Update to 1.1.7.
* gnu/packages/statistics.scm (r-backports): Update to 1.1.7.
2020-06-11 17:03:41 +02:00
Ricardo Wurmus 91428c3611
gnu: r-dbplyr: Update to 1.4.4.
* gnu/packages/statistics.scm (r-dbplyr): Update to 1.4.4.
[propagated-inputs]: Add r-blob and r-magrittr.
2020-06-11 17:03:41 +02:00
Ricardo Wurmus b2c2982755
gnu: r-dplyr: Update to 1.0.0.
* gnu/packages/statistics.scm (r-dplyr): Update to 1.0.0.
[propagated-inputs]: Remove r-assertthat, r-bh, r-pkgconfig, r-plogr, and
r-rcpp; add r-generics, r-lifecycle, and r-vctrs.
2020-06-11 17:03:41 +02:00
Ricardo Wurmus 015a7455a8
gnu: r-ggplot2: Update to 3.3.1.
* gnu/packages/statistics.scm (r-ggplot2): Update to 3.3.1.
[native-inputs]: Add r-knitr.
2020-06-11 17:03:41 +02:00
Ricardo Wurmus 06dfe35322
gnu: r-nlme: Update to 3.1-148.
* gnu/packages/statistics.scm (r-nlme): Update to 3.1-148.
2020-06-11 17:03:41 +02:00
Ricardo Wurmus 0b684d087d
gnu: r-foreign: Update to 0.8-80.
* gnu/packages/statistics.scm (r-foreign): Update to 0.8-80.
2020-06-11 17:03:41 +02:00
Julien Lepiller 82b9ed4eae
gnu: php: Update to 7.4.7.
* gnu/packages/php.scm (php): Update to 7.4.7.
2020-06-11 15:45:05 +02:00
Jakub Kądziołka f65adfa445
gnu: sameboy: Update to 0.13.2.
* gnu/packages/emulators.scm (sameboy): Update to 0.13.2.
  [arguments]: Specify NATIVE_CC to avoid requiring the `cc' program.
2020-06-11 14:08:07 +02:00
Efraim Flashner bb0d840b7d
gnu: java-jakarta-oro: Use a mirror URL.
* gnu/packages/java.scm (java-jakarta-oro)[source]: Download using an
apache mirror:// URL.
2020-06-11 11:54:31 +03:00
Efraim Flashner 894d6a085d
gnu: java-commons-httpclient: Use a mirror URL.
* gnu/packages/java.scm (java-commons-httpclient)[source]: Use an apache
mirror:// URL.
2020-06-11 11:53:39 +03:00
Efraim Flashner f4bb881abd
gnu: ant-bootstrap: Use a mirror URL.
* gnu/packages/java.scm (ant-bootstrap)[source]: Use an apache mirror://
URL.
2020-06-11 11:52:18 +03:00
Efraim Flashner 21d3307875
gnu: maven-artifact: Use a mirror URL.
* gnu/packages/maven.scm (maven-artifact)[source]: Use an apache
mirror:// URL.
2020-06-11 11:50:29 +03:00
Efraim Flashner 67b1257775
gnu: maven-wagon-provider-api: Use a mirror URL.
* gnu/packages/maven.scm (maven-wagon-provider-api)[source]: Use an
apache mirror:// URL.
2020-06-11 11:49:41 +03:00
Efraim Flashner 623aa56402
gnu: maven-plugin-annotations: Use a mirror URL.
* gnu/packages/maven.scm (maven-plugin-annotations)[source]: Use an
apache mirror:// URL.
2020-06-11 11:48:58 +03:00
Efraim Flashner a00687427d
gnu: maven-shared-utils: Use a mirror URL.
* gnu/packages/maven.scm (maven-shared-utils)[source]: Use an apache
mirror:// URL.
2020-06-11 11:48:08 +03:00
Efraim Flashner 1c32eb95af
gnu: serf: Use a mirror URL.
* gnu/packages/web.scm (serf)[source]: Use an apache mirror:// URL.
2020-06-11 11:46:51 +03:00
Efraim Flashner 3d79fd59fe
gnu: subversion: Use a mirror URL.
* gnu/packages/version-control.scm (subversion)[source]: Use an apache
mirror:// URL.
2020-06-11 11:34:59 +03:00
Efraim Flashner e192b9e02d
gnu: lyx: Use qt-build-system.
* gnu/packages/tex.scm (lyx)[build-system]: Switch to qt-build-system.
[arguments]: Remove imported modules. Remove custom 'wrap-qt phase.
2020-06-11 09:56:30 +03:00
Efraim Flashner dadf97952d
gnu: lyx: Don't install to custom directory.
* gnu/packages/tex.scm (lyx)[arguments]: Adjust configure-flags to not
add the version to the binary's suffix. Remove custom
'patch-desktop-file, 'setenv-check and 'install-symlink phases.
2020-06-11 09:56:30 +03:00
Efraim Flashner 03a7b67b31
gnu: lyx: Update to 2.3.5.1.
* gnu/packages/tex.scm (lyx): Update to 2.3.5.1.
[arguments]: Remove 'fix-compilation-with-boost-1.69 phase. In
'patch-python phase patch more files, substitute with python3. Split
'setenv-check and create empty file after 'unpack.
2020-06-11 09:56:30 +03:00
Efraim Flashner 7a7a29445c
gnu: lyx: Wrap binary.
Fixes <https://bugs.gnu.org/37147>.

* gnu/packages/tex.scm (lyx)[arguments]: Import qt-utils. Add phase to
wrap the lyx2.3 binary.
2020-06-11 09:56:15 +03:00
Caleb Ristvedt 8971f626f2
database: separate transaction-handling and retry-handling.
Previously call-with-transaction would both retry when SQLITE_BUSY errors were
thrown and do what its name suggested (start and rollback/commit a
transaction).  This changes it to do only what its name implies, which
simplifies its implementation.  Retrying is provided by the new
call-with-SQLITE_BUSY-retrying procedure.

* guix/store/database.scm (call-with-transaction): no longer restarts, new
  #:restartable? argument controls whether "begin" or "begin immediate" is
  used.
  (call-with-SQLITE_BUSY-retrying, call-with-retrying-transaction,
  call-with-retrying-savepoint): new procedures.
  (register-items): use call-with-retrying-transaction to preserve old
  behavior.

* .dir-locals.el (call-with-retrying-transaction,
  call-with-retrying-savepoint): add indentation information.
2020-06-10 21:54:35 -05:00
Caleb Ristvedt 37545de4a3
database: ensure update-or-insert is run within a transaction
update-or-insert can break if an insert occurs between when it decides whether
to update or insert and when it actually performs that operation.  Putting the
check and the update/insert operation in the same transaction ensures that the
update/insert will only succeed if no other write has occurred in the middle.

* guix/store/database.scm (call-with-savepoint): new procedure.
  (update-or-insert): use call-with-savepoint to ensure the read and the
  insert/update occur within the same transaction.
2020-06-10 21:54:35 -05:00
Caleb Ristvedt 5d6e225528
database: rewrite query procedures in terms of with-statement.
Most of our queries would fail to finalize their statements properly if sqlite
returned an error during their execution.  This resolves that, and also makes
them somewhat more concise as a side-effect.

This also makes some small changes to improve certain queries where behavior
was strange or overly verbose.

* guix/store/database.scm (call-with-statement): new procedure.
  (with-statement): new macro.
  (last-insert-row-id, path-id, update-or-insert, add-references): rewrite to
  use with-statement.
  (update-or-insert): factor last-insert-row-id out of the end of both
  branches.
  (add-references): remove pointless last-insert-row-id call.

* .dir-locals.el (with-statement): add indenting information.
2020-06-10 21:54:35 -05:00
Caleb Ristvedt 3cd92a855e
database: work around guile-sqlite3 bug preventing statement reset
guile-sqlite3 provides statement caching, making it unnecessary for sqlite to
keep re-preparing statements that are frequently used.  Unfortunately it
doesn't quite emulate the semantics of sqlite_finalize properly, because it
doesn't cause a commit if the statement being finalized is the last "active"
statement (see https://notabug.org/guile-sqlite3/guile-sqlite3/issues/12).  We
work around this by wrapping sqlite-finalize with our own version that ensures
sqlite-reset is called, which does The Right Thing™.

* guix/store/database.scm (sqlite-finalize): new procedure that shadows the
  sqlite-finalize from (sqlite3).
2020-06-10 21:54:32 -05:00
Nicolas Goaziou a4620c019b
gnu: fet: Update to 5.45.0.
* gnu/packages/education.scm (fet): Update to 5.45.0.
2020-06-10 22:17:11 +02:00
Nicolas Goaziou 4ee117d56b
gnu: scintilla: Update to 4.4.3.
* gnu/packages/text-editors.scm (scintilla): Update to 4.4.3.
2020-06-10 21:57:40 +02:00
Nicolas Goaziou a8c8b89048
gnu: thinkfan: Update to 1.2.
* gnu/packages/linux.scm (thinkfan): Update to 1.2.
[home-page]: Switch to an up-to-date home page.
2020-06-10 21:53:48 +02:00
Tobias Geerinckx-Rice c90730aefe
gnu: progress: Update to 0.15.
* gnu/packages/admin.scm (progress): Update to 0.15.
2020-06-10 20:36:37 +02:00
Tobias Geerinckx-Rice a474999c26
gnu: man-pages: Update to 5.07.
* gnu/packages/man.scm (man-pages): Update to 5.07.
2020-06-10 20:33:33 +02:00
Nicolas Goaziou 58cb52a31d
gnu: ipopt: Fix source URI.
* gnu/packages/maths.scm (ipopt)[source]: Fix URI.
2020-06-10 17:34:41 +02:00
Nicolas Goaziou 127c7fba1a
gnu: grfcodec: Fix source URL.
* gnu/packages/game-development.scm (grfcodec)[source]: Use HTTPS for URL.
Re-indent package.
2020-06-10 17:33:58 +02:00
Mathieu Othacehe c0f297e85f
gnu: cuirass: Update to 0.0.1-2280ae18.
* gnu/packages/ci.scm (cuirass): Update to 0.0.1-2280ae18.
2020-06-10 17:32:12 +02:00
Nicolas Goaziou d5fd9c7223
gnu: ipopt: Use HTTPS home page URI.
* gnu/packages/maths.scm (ipopt)[home-page]: Use HTTPS URI.
2020-06-10 17:27:41 +02:00
Nicolas Goaziou 0661638f5e
gnu: grfcodec: Use HTTPS home page URI.
* gnu/packages/game-development.scm (grfcodec)[home-page]: Use HTTPS URI.
2020-06-10 17:26:07 +02:00
Nicolas Goaziou bf8e10051b
gnu: fsarchiver: Use HTTPS home page URI.
* gnu/packages/file-systems.scm (fsarchiver)[home-page]: Use HTTPS URI.
2020-06-10 17:25:17 +02:00
Nicolas Goaziou 42d1159335
gnu: asciidoc: Use HTTPS home page URI.
* gnu/packages/documentation.scm (asciidoc)[home-page]: Use HTTPS URI.
2020-06-10 17:19:02 +02:00
Nicolas Goaziou b26ad6dbe2
gnu: grammalecte: Update to 1.10.0.
* gnu/packages/dictionaries.scm (grammalecte): Update to 1.10.0.
2020-06-10 17:04:25 +02:00
Efraim Flashner 73d9caba79
gnu: qtpass: Wrap binary.
* gnu/packages/password-utils.scm (qtpass)[arguments]: Import qt-utils
modules. Add phase to wrap qtpass binary.
2020-06-10 16:21:18 +03:00
Efraim Flashner e1e9baf22f
gnu: qtpass: Update to 1.3.2.
* gnu/packages/password-utils.scm (qtpass): Update to 1.3.2.
2020-06-10 16:19:57 +03:00
Tobias Geerinckx-Rice 88e1d36ba6
gnu: mu: Update to 1.4.10.
* gnu/packages/mail.scm (mu): Update to 1.4.10.
2020-06-10 05:15:52 +02:00
Tobias Geerinckx-Rice d87c9fc506
gnu: herbstluftwm: Update to 0.8.3.
* gnu/packages/wm.scm (herbstluftwm): Update to 0.8.3.
2020-06-10 05:09:29 +02:00
Tobias Geerinckx-Rice 75d493aea1
gnu: ethtool: Update to 5.7.
* gnu/packages/networking.scm (ethtool): Update to 5.7.
2020-06-10 05:09:29 +02:00
Tobias Geerinckx-Rice 01979fafb3
gnu: haproxy: Update to 2.1.6.
* gnu/packages/networking.scm (haproxy): Update to 2.1.6.
2020-06-10 05:09:29 +02:00
Tobias Geerinckx-Rice d2a7cb46a6
gnu: dlib: Update to 19.20.
* gnu/packages/machine-learning.scm (dlib): Update to 19.20.
2020-06-10 04:37:24 +02:00
Tobias Geerinckx-Rice f6b8b1817e
gnu: pd: Update to 0.51-0.
* gnu/packages/music.scm (pd): Update to 0.51-0.
2020-06-10 04:37:24 +02:00
Tobias Geerinckx-Rice 8c5b29c796
gnu: pd: Use HTTPS home page.
* gnu/packages/music.scm (pd)[home-page]: Use HTTPS.
2020-06-10 04:37:24 +02:00
Tobias Geerinckx-Rice 98f08a99c6
gnu: pd: Don't hard-code Tk version.
* gnu/packages/music.scm (pd)[arguments]: Construct the wish file name from the tk package version.
2020-06-10 04:37:24 +02:00
Tobias Geerinckx-Rice 7801e9f2d4
gnu: libnumbertext: Update to 1.0.6.
* gnu/packages/libreoffice.scm (libnumbertext): Update to 1.0.6.
2020-06-10 04:37:24 +02:00