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2020-06-11gnu: r-fitdistrplus: Update to 1.1-1.Ricardo Wurmus
* gnu/packages/cran.scm (r-fitdistrplus): Update to 1.1-1. [propagated-inputs]: Remove r-npsurv. [native-inputs]: Add r-knitr.
2020-06-11gnu: r-sp: Update to 1.4-2.Ricardo Wurmus
* gnu/packages/cran.scm (r-sp): Update to 1.4-2.
2020-06-11gnu: r-ggally: Update to 2.0.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-ggally): Update to 2.0.0. [propagated-inputs]: Add r-lifecycle and r-scales.
2020-06-11gnu: r-getoptlong: Update to 1.0.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-getoptlong): Update to 1.0.0. [propagated-inputs]: Add r-crayon. [native-inputs]: Add r-knitr.
2020-06-11gnu: r-globaloptions: Update to 0.1.2.Ricardo Wurmus
* gnu/packages/cran.scm (r-globaloptions): Update to 0.1.2. [native-inputs]: Add r-knitr.
2020-06-11gnu: r-pkgload: Update to 1.1.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-pkgload): Update to 1.1.0. [propagated-inputs]: Add r-cli and r-crayon.
2020-06-11gnu: r-glue: Update to 1.4.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-glue): Update to 1.4.1.
2020-06-11gnu: r-ape: Update to 5.4.Ricardo Wurmus
* gnu/packages/cran.scm (r-ape): Update to 5.4.
2020-06-11gnu: r-haven: Update to 2.3.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-haven): Update to 2.3.1. [native-inputs]: Add r-knitr. [propagated-inputs]: Add r-vctrs.
2020-06-11gnu: r-d3r: Update to 0.9.0.Ricardo Wurmus
* gnu/packages/cran.scm (r-d3r): Update to 0.9.0. [propagated-inputs]: Add r-rlang.
2020-06-11gnu: r-servr: Update to 0.17.Ricardo Wurmus
* gnu/packages/cran.scm (r-servr): Update to 0.17.
2020-06-11gnu: r-httpuv: Update to 1.5.4.Ricardo Wurmus
* gnu/packages/cran.scm (r-httpuv): Update to 1.5.4.
2020-06-11gnu: r-modelr: Update to 0.1.8.Ricardo Wurmus
* gnu/packages/cran.scm (r-modelr): Update to 0.1.8. [propagated-inputs]: Remove r-dplyr; add r-vctrs.
2020-06-11gnu: r-ellipsis: Update to 0.3.1.Ricardo Wurmus
* gnu/packages/cran.scm (r-ellipsis): Update to 0.3.1.
2020-06-11gnu: r-ggpmisc: Update to 0.3.5.Ricardo Wurmus
* 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.
2020-06-11gnu: r-lubridate: Update to 1.7.9.Ricardo Wurmus
* gnu/packages/statistics.scm (r-lubridate): Update to 1.7.9.
2020-06-11gnu: r-sn: Update to 1.6-2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-sn): Update to 1.6-2.
2020-06-11gnu: r-mnormt: Update to 2.0.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-mnormt): Update to 2.0.0. [propagated-inputs]: Add r-tmvnsim.
2020-06-11gnu: Add r-tmvnsim.Ricardo Wurmus
* gnu/packages/statistics.scm (r-tmvnsim): New variable.
2020-06-11gnu: r-car: Update to 3.0-8.Ricardo Wurmus
* gnu/packages/statistics.scm (r-car): Update to 3.0-8.
2020-06-11gnu: r-cardata: Update to 3.0-4.Ricardo Wurmus
* gnu/packages/statistics.scm (r-cardata): Update to 3.0-4.
2020-06-11gnu: r-tidyr: Update to 1.1.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-tidyr): Update to 1.1.0.
2020-06-11gnu: r-mvtnorm: Update to 1.1-1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-mvtnorm): Update to 1.1-1.
2020-06-11gnu: r-glmnet: Update to 4.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-glmnet): Update to 4.0. [native-inputs]: Add r-knitr.
2020-06-11gnu: r-rmarkdown: Update to 2.2.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rmarkdown): Update to 2.2. [native-inputs]: Add r-knitr.
2020-06-11gnu: r-rcpparmadillo: Update to 0.9.900.1.0.Ricardo Wurmus
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.9.900.1.0.
2020-06-11gnu: r-backports: Update to 1.1.7.Ricardo Wurmus
* gnu/packages/statistics.scm (r-backports): Update to 1.1.7.
2020-06-11gnu: r-dbplyr: Update to 1.4.4.Ricardo Wurmus
* gnu/packages/statistics.scm (r-dbplyr): Update to 1.4.4. [propagated-inputs]: Add r-blob and r-magrittr.
2020-06-11gnu: r-dplyr: Update to 1.0.0.Ricardo Wurmus
* 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.
2020-06-11gnu: r-ggplot2: Update to 3.3.1.Ricardo Wurmus
* gnu/packages/statistics.scm (r-ggplot2): Update to 3.3.1. [native-inputs]: Add r-knitr.
2020-06-11gnu: r-nlme: Update to 3.1-148.Ricardo Wurmus
* gnu/packages/statistics.scm (r-nlme): Update to 3.1-148.
2020-06-11gnu: r-foreign: Update to 0.8-80.Ricardo Wurmus
* gnu/packages/statistics.scm (r-foreign): Update to 0.8-80.
2020-06-11gnu: php: Update to 7.4.7.Julien Lepiller
* gnu/packages/php.scm (php): Update to 7.4.7.
2020-06-11gnu: sameboy: Update to 0.13.2.Jakub Kądziołka
* gnu/packages/emulators.scm (sameboy): Update to 0.13.2. [arguments]: Specify NATIVE_CC to avoid requiring the `cc' program.
2020-06-11gnu: java-jakarta-oro: Use a mirror URL.Efraim Flashner
* gnu/packages/java.scm (java-jakarta-oro)[source]: Download using an apache mirror:// URL.
2020-06-11gnu: java-commons-httpclient: Use a mirror URL.Efraim Flashner
* gnu/packages/java.scm (java-commons-httpclient)[source]: Use an apache mirror:// URL.
2020-06-11gnu: ant-bootstrap: Use a mirror URL.Efraim Flashner
* gnu/packages/java.scm (ant-bootstrap)[source]: Use an apache mirror:// URL.
2020-06-11gnu: maven-artifact: Use a mirror URL.Efraim Flashner
* gnu/packages/maven.scm (maven-artifact)[source]: Use an apache mirror:// URL.
2020-06-11gnu: maven-wagon-provider-api: Use a mirror URL.Efraim Flashner
* gnu/packages/maven.scm (maven-wagon-provider-api)[source]: Use an apache mirror:// URL.
2020-06-11gnu: maven-plugin-annotations: Use a mirror URL.Efraim Flashner
* gnu/packages/maven.scm (maven-plugin-annotations)[source]: Use an apache mirror:// URL.
2020-06-11gnu: maven-shared-utils: Use a mirror URL.Efraim Flashner
* gnu/packages/maven.scm (maven-shared-utils)[source]: Use an apache mirror:// URL.
2020-06-11gnu: serf: Use a mirror URL.Efraim Flashner
* gnu/packages/web.scm (serf)[source]: Use an apache mirror:// URL.
2020-06-11gnu: subversion: Use a mirror URL.Efraim Flashner
* gnu/packages/version-control.scm (subversion)[source]: Use an apache mirror:// URL.
2020-06-11gnu: lyx: Use qt-build-system.Efraim Flashner
* gnu/packages/tex.scm (lyx)[build-system]: Switch to qt-build-system. [arguments]: Remove imported modules. Remove custom 'wrap-qt phase.
2020-06-11gnu: lyx: Don't install to custom directory.Efraim Flashner
* 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.
2020-06-11gnu: lyx: Update to 2.3.5.1.Efraim Flashner
* 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.
2020-06-11gnu: lyx: Wrap binary.Efraim Flashner
Fixes <https://bugs.gnu.org/37147>. * gnu/packages/tex.scm (lyx)[arguments]: Import qt-utils. Add phase to wrap the lyx2.3 binary.
2020-06-10database: separate transaction-handling and retry-handling.Caleb Ristvedt
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.
2020-06-10database: ensure update-or-insert is run within a transactionCaleb Ristvedt
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.
2020-06-10database: rewrite query procedures in terms of with-statement.Caleb Ristvedt
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.
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