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2020-06-11gnu: r-rcpparmadillo: Update to 0.9.900.1.0....* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.9.900.1.0. Ricardo Wurmus
2020-06-11gnu: r-backports: Update to 1.1.7....* gnu/packages/statistics.scm (r-backports): Update to 1.1.7. Ricardo Wurmus
2020-06-11gnu: 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. Ricardo Wurmus
2020-06-11gnu: 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. Ricardo Wurmus
2020-06-11gnu: r-ggplot2: Update to 3.3.1....* gnu/packages/statistics.scm (r-ggplot2): Update to 3.3.1. [native-inputs]: Add r-knitr. Ricardo Wurmus
2020-06-11gnu: r-nlme: Update to 3.1-148....* gnu/packages/statistics.scm (r-nlme): Update to 3.1-148. Ricardo Wurmus
2020-06-11gnu: r-foreign: Update to 0.8-80....* gnu/packages/statistics.scm (r-foreign): Update to 0.8-80. Ricardo Wurmus
2020-06-11gnu: php: Update to 7.4.7....* gnu/packages/php.scm (php): Update to 7.4.7. Julien Lepiller
2020-06-11gnu: 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. Jakub Kądziołka
2020-06-11gnu: java-jakarta-oro: Use a mirror URL....* gnu/packages/java.scm (java-jakarta-oro)[source]: Download using an apache mirror:// URL. Efraim Flashner
2020-06-11gnu: java-commons-httpclient: Use a mirror URL....* gnu/packages/java.scm (java-commons-httpclient)[source]: Use an apache mirror:// URL. Efraim Flashner
2020-06-11gnu: ant-bootstrap: Use a mirror URL....* gnu/packages/java.scm (ant-bootstrap)[source]: Use an apache mirror:// URL. Efraim Flashner
2020-06-11gnu: maven-artifact: Use a mirror URL....* gnu/packages/maven.scm (maven-artifact)[source]: Use an apache mirror:// URL. Efraim Flashner
2020-06-11gnu: maven-wagon-provider-api: Use a mirror URL....* gnu/packages/maven.scm (maven-wagon-provider-api)[source]: Use an apache mirror:// URL. Efraim Flashner
2020-06-11gnu: maven-plugin-annotations: Use a mirror URL....* gnu/packages/maven.scm (maven-plugin-annotations)[source]: Use an apache mirror:// URL. Efraim Flashner
2020-06-11gnu: maven-shared-utils: Use a mirror URL....* gnu/packages/maven.scm (maven-shared-utils)[source]: Use an apache mirror:// URL. Efraim Flashner
2020-06-11gnu: serf: Use a mirror URL....* gnu/packages/web.scm (serf)[source]: Use an apache mirror:// URL. Efraim Flashner
2020-06-11gnu: subversion: Use a mirror URL....* gnu/packages/version-control.scm (subversion)[source]: Use an apache mirror:// URL. Efraim Flashner
2020-06-11gnu: 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. Efraim Flashner
2020-06-11gnu: 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. Efraim Flashner
2020-06-11gnu: 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. Efraim Flashner
2020-06-11gnu: 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. Efraim Flashner
2020-06-10database: 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. Caleb Ristvedt
2020-06-10database: 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. Caleb Ristvedt
2020-06-10database: 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. Caleb Ristvedt
2020-06-10database: 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). Caleb Ristvedt
2020-06-10gnu: fet: Update to 5.45.0....* gnu/packages/education.scm (fet): Update to 5.45.0. Nicolas Goaziou
2020-06-10gnu: scintilla: Update to 4.4.3....* gnu/packages/text-editors.scm (scintilla): Update to 4.4.3. Nicolas Goaziou
2020-06-10gnu: thinkfan: Update to 1.2....* gnu/packages/linux.scm (thinkfan): Update to 1.2. [home-page]: Switch to an up-to-date home page. Nicolas Goaziou
2020-06-10gnu: progress: Update to 0.15....* gnu/packages/admin.scm (progress): Update to 0.15. Tobias Geerinckx-Rice
2020-06-10gnu: man-pages: Update to 5.07....* gnu/packages/man.scm (man-pages): Update to 5.07. Tobias Geerinckx-Rice
2020-06-10gnu: ipopt: Fix source URI....* gnu/packages/maths.scm (ipopt)[source]: Fix URI. Nicolas Goaziou
2020-06-10gnu: grfcodec: Fix source URL....* gnu/packages/game-development.scm (grfcodec)[source]: Use HTTPS for URL. Re-indent package. Nicolas Goaziou
2020-06-10gnu: cuirass: Update to 0.0.1-2280ae18....* gnu/packages/ci.scm (cuirass): Update to 0.0.1-2280ae18. Mathieu Othacehe
2020-06-10gnu: ipopt: Use HTTPS home page URI....* gnu/packages/maths.scm (ipopt)[home-page]: Use HTTPS URI. Nicolas Goaziou
2020-06-10gnu: grfcodec: Use HTTPS home page URI....* gnu/packages/game-development.scm (grfcodec)[home-page]: Use HTTPS URI. Nicolas Goaziou
2020-06-10gnu: fsarchiver: Use HTTPS home page URI....* gnu/packages/file-systems.scm (fsarchiver)[home-page]: Use HTTPS URI. Nicolas Goaziou
2020-06-10gnu: asciidoc: Use HTTPS home page URI....* gnu/packages/documentation.scm (asciidoc)[home-page]: Use HTTPS URI. Nicolas Goaziou
2020-06-10gnu: grammalecte: Update to 1.10.0....* gnu/packages/dictionaries.scm (grammalecte): Update to 1.10.0. Nicolas Goaziou
2020-06-10gnu: qtpass: Wrap binary....* gnu/packages/password-utils.scm (qtpass)[arguments]: Import qt-utils modules. Add phase to wrap qtpass binary. Efraim Flashner
2020-06-10gnu: qtpass: Update to 1.3.2....* gnu/packages/password-utils.scm (qtpass): Update to 1.3.2. Efraim Flashner
2020-06-10gnu: mu: Update to 1.4.10....* gnu/packages/mail.scm (mu): Update to 1.4.10. Tobias Geerinckx-Rice
2020-06-10gnu: herbstluftwm: Update to 0.8.3....* gnu/packages/wm.scm (herbstluftwm): Update to 0.8.3. Tobias Geerinckx-Rice
2020-06-10gnu: ethtool: Update to 5.7....* gnu/packages/networking.scm (ethtool): Update to 5.7. Tobias Geerinckx-Rice
2020-06-10gnu: haproxy: Update to 2.1.6....* gnu/packages/networking.scm (haproxy): Update to 2.1.6. Tobias Geerinckx-Rice
2020-06-10gnu: dlib: Update to 19.20....* gnu/packages/machine-learning.scm (dlib): Update to 19.20. Tobias Geerinckx-Rice
2020-06-10gnu: pd: Update to 0.51-0....* gnu/packages/music.scm (pd): Update to 0.51-0. Tobias Geerinckx-Rice
2020-06-10gnu: pd: Use HTTPS home page....* gnu/packages/music.scm (pd)[home-page]: Use HTTPS. Tobias Geerinckx-Rice
2020-06-10gnu: pd: Don't hard-code Tk version....* gnu/packages/music.scm (pd)[arguments]: Construct the wish file name from the tk package version. Tobias Geerinckx-Rice
2020-06-10gnu: libnumbertext: Update to 1.0.6....* gnu/packages/libreoffice.scm (libnumbertext): Update to 1.0.6. Tobias Geerinckx-Rice
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