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* gnu: r-haven: Update to 2.3.1.Ricardo Wurmus2020-06-11
| | | | | | * gnu/packages/cran.scm (r-haven): Update to 2.3.1. [native-inputs]: Add r-knitr. [propagated-inputs]: Add r-vctrs.
* gnu: r-d3r: Update to 0.9.0.Ricardo Wurmus2020-06-11
| | | | | * gnu/packages/cran.scm (r-d3r): Update to 0.9.0. [propagated-inputs]: Add r-rlang.
* gnu: r-servr: Update to 0.17.Ricardo Wurmus2020-06-11
| | | | * gnu/packages/cran.scm (r-servr): Update to 0.17.
* gnu: r-httpuv: Update to 1.5.4.Ricardo Wurmus2020-06-11
| | | | * gnu/packages/cran.scm (r-httpuv): Update to 1.5.4.
* gnu: r-modelr: Update to 0.1.8.Ricardo Wurmus2020-06-11
| | | | | * gnu/packages/cran.scm (r-modelr): Update to 0.1.8. [propagated-inputs]: Remove r-dplyr; add r-vctrs.
* gnu: r-ellipsis: Update to 0.3.1.Ricardo Wurmus2020-06-11
| | | | * gnu/packages/cran.scm (r-ellipsis): Update to 0.3.1.
* gnu: r-ggpmisc: Update to 0.3.5.Ricardo Wurmus2020-06-11
| | | | | | * gnu/packages/cran.scm (r-ggpmisc): Update to 0.3.5. [propagated-inputs]: Add r-magrittr, r-rlang, r-scales, and r-stringr. [native-inputs]: Add r-knitr.
* gnu: r-lubridate: Update to 1.7.9.Ricardo Wurmus2020-06-11
| | | | * gnu/packages/statistics.scm (r-lubridate): Update to 1.7.9.
* gnu: r-sn: Update to 1.6-2.Ricardo Wurmus2020-06-11
| | | | * gnu/packages/statistics.scm (r-sn): Update to 1.6-2.
* gnu: r-mnormt: Update to 2.0.0.Ricardo Wurmus2020-06-11
| | | | | * gnu/packages/statistics.scm (r-mnormt): Update to 2.0.0. [propagated-inputs]: Add r-tmvnsim.
* gnu: Add r-tmvnsim.Ricardo Wurmus2020-06-11
| | | | * gnu/packages/statistics.scm (r-tmvnsim): New variable.
* gnu: r-car: Update to 3.0-8.Ricardo Wurmus2020-06-11
| | | | * gnu/packages/statistics.scm (r-car): Update to 3.0-8.
* gnu: r-cardata: Update to 3.0-4.Ricardo Wurmus2020-06-11
| | | | * gnu/packages/statistics.scm (r-cardata): Update to 3.0-4.
* gnu: r-tidyr: Update to 1.1.0.Ricardo Wurmus2020-06-11
| | | | * gnu/packages/statistics.scm (r-tidyr): Update to 1.1.0.
* gnu: r-mvtnorm: Update to 1.1-1.Ricardo Wurmus2020-06-11
| | | | * gnu/packages/statistics.scm (r-mvtnorm): Update to 1.1-1.
* gnu: r-glmnet: Update to 4.0.Ricardo Wurmus2020-06-11
| | | | | * gnu/packages/statistics.scm (r-glmnet): Update to 4.0. [native-inputs]: Add r-knitr.
* gnu: r-rmarkdown: Update to 2.2.Ricardo Wurmus2020-06-11
| | | | | * gnu/packages/statistics.scm (r-rmarkdown): Update to 2.2. [native-inputs]: Add r-knitr.
* gnu: r-rcpparmadillo: Update to 0.9.900.1.0.Ricardo Wurmus2020-06-11
| | | | * gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.9.900.1.0.
* gnu: r-backports: Update to 1.1.7.Ricardo Wurmus2020-06-11
| | | | * gnu/packages/statistics.scm (r-backports): Update to 1.1.7.
* gnu: r-dbplyr: Update to 1.4.4.Ricardo Wurmus2020-06-11
| | | | | * gnu/packages/statistics.scm (r-dbplyr): Update to 1.4.4. [propagated-inputs]: Add r-blob and r-magrittr.
* gnu: r-dplyr: Update to 1.0.0.Ricardo Wurmus2020-06-11
| | | | | | * 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.
* gnu: r-ggplot2: Update to 3.3.1.Ricardo Wurmus2020-06-11
| | | | | * gnu/packages/statistics.scm (r-ggplot2): Update to 3.3.1. [native-inputs]: Add r-knitr.
* gnu: r-nlme: Update to 3.1-148.Ricardo Wurmus2020-06-11
| | | | * gnu/packages/statistics.scm (r-nlme): Update to 3.1-148.
* gnu: r-foreign: Update to 0.8-80.Ricardo Wurmus2020-06-11
| | | | * gnu/packages/statistics.scm (r-foreign): Update to 0.8-80.
* gnu: php: Update to 7.4.7.Julien Lepiller2020-06-11
| | | | * gnu/packages/php.scm (php): Update to 7.4.7.
* gnu: sameboy: Update to 0.13.2.Jakub Kądziołka2020-06-11
| | | | | * gnu/packages/emulators.scm (sameboy): Update to 0.13.2. [arguments]: Specify NATIVE_CC to avoid requiring the `cc' program.
* gnu: java-jakarta-oro: Use a mirror URL.Efraim Flashner2020-06-11
| | | | | * gnu/packages/java.scm (java-jakarta-oro)[source]: Download using an apache mirror:// URL.
* gnu: java-commons-httpclient: Use a mirror URL.Efraim Flashner2020-06-11
| | | | | * gnu/packages/java.scm (java-commons-httpclient)[source]: Use an apache mirror:// URL.
* gnu: ant-bootstrap: Use a mirror URL.Efraim Flashner2020-06-11
| | | | | * gnu/packages/java.scm (ant-bootstrap)[source]: Use an apache mirror:// URL.
* gnu: maven-artifact: Use a mirror URL.Efraim Flashner2020-06-11
| | | | | * gnu/packages/maven.scm (maven-artifact)[source]: Use an apache mirror:// URL.
* gnu: maven-wagon-provider-api: Use a mirror URL.Efraim Flashner2020-06-11
| | | | | * gnu/packages/maven.scm (maven-wagon-provider-api)[source]: Use an apache mirror:// URL.
* gnu: maven-plugin-annotations: Use a mirror URL.Efraim Flashner2020-06-11
| | | | | * gnu/packages/maven.scm (maven-plugin-annotations)[source]: Use an apache mirror:// URL.
* gnu: maven-shared-utils: Use a mirror URL.Efraim Flashner2020-06-11
| | | | | * gnu/packages/maven.scm (maven-shared-utils)[source]: Use an apache mirror:// URL.
* gnu: serf: Use a mirror URL.Efraim Flashner2020-06-11
| | | | * gnu/packages/web.scm (serf)[source]: Use an apache mirror:// URL.
* gnu: subversion: Use a mirror URL.Efraim Flashner2020-06-11
| | | | | * gnu/packages/version-control.scm (subversion)[source]: Use an apache mirror:// URL.
* gnu: lyx: Use qt-build-system.Efraim Flashner2020-06-11
| | | | | * gnu/packages/tex.scm (lyx)[build-system]: Switch to qt-build-system. [arguments]: Remove imported modules. Remove custom 'wrap-qt phase.
* gnu: lyx: Don't install to custom directory.Efraim Flashner2020-06-11
| | | | | | * 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.
* gnu: lyx: Update to 2.3.5.1.Efraim Flashner2020-06-11
| | | | | | | * 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.
* gnu: lyx: Wrap binary.Efraim Flashner2020-06-11
| | | | | | | Fixes <https://bugs.gnu.org/37147>. * gnu/packages/tex.scm (lyx)[arguments]: Import qt-utils. Add phase to wrap the lyx2.3 binary.
* database: separate transaction-handling and retry-handling.Caleb Ristvedt2020-06-10
| | | | | | | | | | | | | | | | | | | 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.
* database: ensure update-or-insert is run within a transactionCaleb Ristvedt2020-06-10
| | | | | | | | | | | 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.
* database: rewrite query procedures in terms of with-statement.Caleb Ristvedt2020-06-10
| | | | | | | | | | | | | | | | | | | 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.
* database: work around guile-sqlite3 bug preventing statement resetCaleb Ristvedt2020-06-10
| | | | | | | | | | | | | 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).
* gnu: fet: Update to 5.45.0.Nicolas Goaziou2020-06-10
| | | | * gnu/packages/education.scm (fet): Update to 5.45.0.
* gnu: scintilla: Update to 4.4.3.Nicolas Goaziou2020-06-10
| | | | * gnu/packages/text-editors.scm (scintilla): Update to 4.4.3.
* gnu: thinkfan: Update to 1.2.Nicolas Goaziou2020-06-10
| | | | | * gnu/packages/linux.scm (thinkfan): Update to 1.2. [home-page]: Switch to an up-to-date home page.
* gnu: progress: Update to 0.15.Tobias Geerinckx-Rice2020-06-10
| | | | * gnu/packages/admin.scm (progress): Update to 0.15.
* gnu: man-pages: Update to 5.07.Tobias Geerinckx-Rice2020-06-10
| | | | * gnu/packages/man.scm (man-pages): Update to 5.07.
* gnu: ipopt: Fix source URI.Nicolas Goaziou2020-06-10
| | | | * gnu/packages/maths.scm (ipopt)[source]: Fix URI.
* gnu: grfcodec: Fix source URL.Nicolas Goaziou2020-06-10
| | | | | * gnu/packages/game-development.scm (grfcodec)[source]: Use HTTPS for URL. Re-indent package.
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