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-rw-r--r--gnu/packages/bioconductor.scm4
1 files changed, 2 insertions, 2 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 323c0eb5b6..82cc60c9ff 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -22129,13 +22129,13 @@ variable and significantly correlated genes.")
(define-public r-sparsearray
(package
(name "r-sparsearray")
- (version "1.2.3")
+ (version "1.2.4")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "SparseArray" version))
(sha256
- (base32 "19cy1nmmi65fxh012ymgp1kg112yl1m0khcs4y034p5iwlfv7fp6"))))
+ (base32 "0gz1j8g020bp88i5idrhj9qrixgar3wvxxna46ds60q6d8lsn4vi"))))
(properties `((upstream-name . "SparseArray")))
(build-system r-build-system)
(propagated-inputs (list r-biocgenerics
with current installer's run-command. * gnu/installer/newt.scm (newt-run-command): New variable. (newt-installer): Use it. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org> Josselin Poiret 2022-02-02installer: Use new installer-log-line everywhere....* gnu/installer.scm (installer-program) * gnu/installer/final.scm (install-locale) * gnu/installer/newt.scm (init) * gnu/installer/newt/final.scm (run-final-page) * gnu/installer/newt/page.scm (run-form-with-clients) * gnu/installer/newt/partition.scm (run-partitioning-page) * gnu/installer/parted.scm (eligible-devices, mkpart, luks-format-and-open, luks-close, mount-user-partitions, umount-user-partitions, free-parted): * gnu/installer/steps.scm (run-installer-steps): * gnu/installer/utils.scm (run-command, send-to-clients): Use it. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org> Josselin Poiret 2022-02-02installer: Use define instead of let at top-level....* gnu/installer.scm (installer-program): Improve readability by using define at top-level. Signed-off-by: Mathieu Othacehe <othacehe@gnu.org> Josselin Poiret 2022-02-02installer: Add crash dump upload support....Suggested-by: Josselin Poiret <dev@jpoiret.xyz> * gnu/installer/dump.scm: New file. * gnu/installer/newt/dump.scm: New file. * gnu/local.mk (INSTALLER_MODULES): Add them. * gnu/installer/record.scm (<installer>)[dump-page]: New field. * gnu/installer/steps.scm (%current-result): New variable. (run-installer-steps): Update it. * gnu/installer.scm (installer-program): Add tar and gip to the installer path. Add guile-webutils and gnutls to the Guile extensions. Generate and send the crash dump report. * gnu/installer/newt.scm (exit-error): Add a report argument. Display the report id. (dump-page): New procedure. (newt-installer): Update it. Mathieu Othacehe 2022-01-14installer: Check if ci.guix.gnu.org can be reached....* gnu/installer.scm (installer-program): Add gnutls extension. * gnu/installer/newt/network.scm (wait-service-online): Check if the CI server can be reached. Mathieu Othacehe 2021-09-23installer: Support XFS....* gnu/installer/newt/partition.scm (run-fs-type-page): Add ‘xfs’ to the list box. * gnu/installer/parted.scm (user-fs-type-name, user-fs-type->mount-type) (partition-filesystem-user-type): Add ‘xfs’ mapping. (create-xfs-file-system): New procedure. (format-user-partitions): Use it. * gnu/installer.scm (set-installer-path): Add xfsprogs. Tobias Geerinckx-Rice 2021-01-12installer: Fix crash in parameters menu....Fixes: <https://issues.guix.gnu.org/45378>. * gnu/installer/newt/keymap.scm (run-layout-page): Return false when "Continue" button is pressed. (run-keymap-page): Do not try to compute variants if layout is false. Also do not try to format the result if layout is false. * gnu/installer.scm (compute-keymap-step): Do not apply keymap if "run-keymap-page" returns false. Mathieu Othacehe 2020-12-11install: Discover local substitute servers....* gnu/installer/substitutes.scm: New file. * gnu/installer/newt/substitutes.scm: New file. * gnu/local.mk (INSTALLER_MODULES): Add them. * po/guix/POTFILES.in: Add gnu/installer/newt/substitutes.scm. * gnu/installer/proxy.scm (with-silent-shepherd): Move to ... * gnu/installer/utils.scm: ... here. * gnu/installer/record.scm (<installer>)[substitutes-page]: New field. * gnu/installer/newt.scm (substitutes-page): New procedure, (newt-installer): register it. * gnu/installer.scm (installer-steps): Add "substitutes-page" step. * gnu/system/install.scm (%installation-services): Add avahi-service-type and enable substitute server discover in guix-service-type. [<name-service-switch>]: Set it to %mdns-host-lookup-nss. Mathieu Othacehe 2020-10-18installer: Call setlocale after init gettext....* gnu/installer.scm (installer-program)[init-gettext]: Change locale from C, installed at the program start. Miguel Ángel Arruga Vivas 2020-09-23installer: Fix docstring typo....* gnu/installer.scm (build-compiled-file): Fix a typo in the docstring. Tobias Geerinckx-Rice 2020-08-25Remove "guile-zlib" extension when unused....This is a follow-up of 755f365b02b42a5d1e8ef3000dadef069553a478. As (zlib) is autoloaded in (gnu build linux-modules), "guile-zlib" is needed as an extension only when it is effectively used. * gnu/installer.scm (installer-program): Remove "guile-zlib" from the extensions. * gnu/machine/ssh.scm (machine-check-initrd-modules): Ditto. * gnu/services.scm (activation-script): Ditto. * gnu/services/base.scm (default-serial-port): Ditto, (agetty-shepherd-service): ditto, (udev-service-type): ditto. * gnu/system/image.scm (gcrypt-sqlite3&co): Ditto. * gnu/system/shadow.scm (account-shepherd-service): Ditto. Mathieu Othacehe 2020-08-25linux-libre: Support module compression....This commit adds support for GZIP compression for linux-libre kernel modules. The initrd modules are kept uncompressed as the initrd is already compressed as a whole. The linux-libre kernel also supports XZ compression, but as Guix does not have any available bindings for now, and the compression time is far more significant, GZIP seems to be a better option. * gnu/build/linux-modules.scm (modinfo-section-contents): Use 'call-with-gzip-input-port' to read from a module file using '.gz' extension, (strip-extension): new procedure, (dot-ko): adapt to support compression, (ensure-dot-ko): ditto, (file-name->module-name): ditto, (find-module-file): ditto, (load-linux-module*): ditto, (module-name->file-name/guess): ditto, (module-name-lookup): ditto, (write-module-name-database): ditto, (write-module-alias-database): ditto, (write-module-device-database): ditto. * gnu/installer.scm (installer-program): Add "guile-zlib" to the extensions. * gnu/machine/ssh.scm (machine-check-initrd-modules): Ditto. * gnu/services.scm (activation-script): Ditto. * gnu/services/base.scm (default-serial-port): Ditto, (agetty-shepherd-service): ditto, (udev-service-type): ditto. * gnu/system/image.scm (gcrypt-sqlite3&co): Ditto. * gnu/system/linux-initrd.scm (flat-linux-module-directory): Add "guile-zlib" to the extensions and make sure that the initrd only contains uncompressed module files. * gnu/system/shadow.scm (account-shepherd-service): Add "guile-zlib" to the extensions. * guix/profiles.scm (linux-module-database): Ditto. Mathieu Othacehe 2020-08-06installer: Remove logical devices....If a device contains an active logical volume, BLKRRPART will report that the device is busy. This will cause this device to be filtered by "non-install-devices" procedure, which is not desired. Make sure to deactivate all logical volumes before device probing. Fixes <https://issues.guix.gnu.org/42683>. * gnu/installer.scm (installer-program): Add lvm2-static to the inputs. * gnu/installer/parted.scm (remove-logical-devices): New procedure, (init-parted): call it. Mathieu Othacehe 2020-07-26installer: Add NTFS support....This adds support for creating and editing NTFS partitions. It is however not possible yet to create root NTFS partitions, as overlaying on top of a fuse partition does not seem supported. * gnu/installer.scm (installer-program): Add "ntfs-3g" to the inputs. * gnu/installer/parted.scm (user-fs-type-name, user-fs-type->mount-type, partition-filesystem-user-type, create-ntfs-file-system, format-user-partitions): Add NTFS support. * gnu/installer/newt/partition.scm (run-fs-type-page): Add NTFS support. Mathieu Othacehe 2020-06-26installer: Use latest Guile....Since the installer is loading Guix modules built with Guile 3.0.4, the installer script must be run by the same Guile version to avoid a bytecode incompatibility. This is a follow-up of a2991de0f44a5f4db71ddad67e914fe3344a4505. * gnu/installer.scm (installer-program): Use guile3.0-latest for the installation script. Mathieu Othacehe 2020-04-19Merge branch 'master' into core-updatesMarius Bakke 2020-04-18installer: Fix backtrace display....The 'syslog' macro cannot be resolved in the pre-unwind-handler context. Failed to resolve 'syslog' in this context resulted in the swallowing of all installation errors. Fixes 5c04b00cf463a543b8ffc9eb55991f6b4cc145dd. * gnu/installer.scm (installer-program): Use (gnu installer utils) module. Mathieu Othacehe 2020-04-16installer: Remove guile-newt definition....This is no longer necessary since 0.0.2 release of Guile-Newt. * gnu/installer.scm (guile-newt): Remove variable. Mathieu Othacehe 2020-04-15Merge branch 'master' into core-updatesMarius Bakke 2020-04-14installer: Open manual in the selected language on tty2....Fixes <https://bugs.gnu.org/40624>. Reported by Florian Pelz <pelzflorian@pelzflorian.de>. Regression introduced in b5c2d93d7a223155898dd0ed6932f6acf78ac454. * gnu/installer.scm (apply-locale): Remove 'lambda' around 'stop-service' and 'start-service' calls. Ludovic Courtès 2020-04-11Merge branch 'master' into core-updatesMarius Bakke 2020-04-09installer: Allow Alt+Shift toggle from non-Latin keyboard layouts....Fixes <https://bugs.gnu.org/40493>. * gnu/installer/newt/keymap.scm (%non-latin-layouts): New variable. (%non-latin-variants): New variable. (%latin-layout+variants): New variable. (toggleable-latin-layout): New procedure to compute combined layouts. (run-keymap-page): Use it. (keyboard-layout->configuration): Apply it in config.scm. (run-layout-page): Mention Alt+Shift. * gnu/installer/keymap.scm (kmscon-update-keymap): Pass on XKB options. * gnu/installer/record.scm (<installer>): Adjust code comments. * gnu/installer.scm (apply-keymap): Pass on XKB options. (installer-steps): Adjust code comments. * gnu/packages/patches/kmscon-runtime-keymap-switch.patch: Apply XKB options. Florian Pelz 2020-04-08Merge branch 'master' into core-updates... Conflicts: etc/news.scm gnu/local.mk gnu/packages/check.scm gnu/packages/cross-base.scm gnu/packages/gimp.scm gnu/packages/java.scm gnu/packages/mail.scm gnu/packages/sdl.scm gnu/packages/texinfo.scm gnu/packages/tls.scm gnu/packages/version-control.scm Marius Bakke 2020-04-08installer: Turn help menu into parameters menu....* gnu/local.mk (INSTALLER_MODULES): Rename help.scm into parameters.scm. * po/guix/POTFILES.in: Ditto. * gnu/installer/record.scm (<installer>): Rename help-menu into parameter-menu and help-page into parameters-page. * gnu/installer/newt/parameters.scm: Renamed from help.scm. Update information messages. * gnu/installer/newt.scm: Update accordingly. * gnu/installer/newt/keymap.scm: Ditto. Mathieu Othacehe 2020-04-06installer: Hide shepherd messages....* gnu/installer.scm (apply-locale): Set "shepherd-message-port" instead of redirecting stderr to make sure that nothing is printed on console. Mathieu Othacehe 2020-04-06installer: Add a help page....* gnu/installer/newt/help.scm: New file. * gnu/local.mk (INSTALLER_MODULES): Add it. * po/guix/POTFILES.in: Add it. * gnu/installer/record.scm (<installer>): Add 'help-menu' and 'help-page' fields, (installer-help-menu, installer-help-page): new exported procedures. * gnu/installer/newt.scm (init): Set the help line, (help-menu, help-page): new procedures used ... (newt-installer): ... here. * gnu/installer/newt/keymap.scm (run-layout-page): Add a context argument to differenciate the help context from the main one, (run-keymap-page): add a context argument and pass it to run-layout-page. * gnu/installer.scm (compute-keymap-step): Add a context argument and pass it to 'installer-keymap-page', (installer-steps): set the help menu and pass the appropriate context to compute-keymap-step calls, (guile-newt): update to revision 2. Mathieu Othacehe 2020-04-06installer: Remove trailing tabs....* gnu/installer.scm (installer-steps): Remove trailing tabs. Mathieu Othacehe 2020-03-27Merge branch 'master' into core-updates... Conflicts: gnu/packages/icu4c.scm gnu/packages/man.scm gnu/packages/python-xyz.scm guix/scripts/environment.scm guix/scripts/pack.scm guix/scripts/package.scm guix/scripts/pull.scm guix/store.scm Marius Bakke 2020-03-22installer: Do not include the host (guix config)....Previously, "locales.drv" would depend on the host's (guix config). Thus, the derivation would depend on details of the user's installation. * gnu/installer.scm (not-config?): New procedure. (build-compiled-file): Pass it to 'source-module-closure' and use 'make-config.scm'. Ludovic Courtès 2020-03-10Merge branch 'master' into core-updatesMarius Bakke 2020-03-05installer: Use a Guile-Newt snapshot that supports 'form-watch-fd'....* gnu/installer.scm (guile-newt): New variable. Ludovic Courtès 2020-03-04Merge branch 'master' into core-updatesMarius Bakke 2020-02-22installer: Log important bits to syslog....* gnu/installer.scm (installer-program): Log crashes with 'syslog'. * gnu/installer/parted.scm (luks-format-and-open, luks-close) (mount-user-partitions, umount-user-partitions): Add 'syslog' calls. * gnu/installer/steps.scm (run-installer-steps): Log the running step with 'syslog'. * gnu/installer/utils.scm (run-shell-command): Add calls to 'syslog'. Ludovic Courtès 2020-02-14Merge branch 'master' into core-updatesMarius Bakke 2020-02-12installer: Fix installer restart dialog....* gnu/installer/newt/final.scm (run-install-failed-page): Propose between installer resume or restart. Do actually resume the installation by raising an &installer-step-abort condition if "Resume" button is pressed. Otherwise, keep going as the installer will be restarted by login. * gnu/installer.scm (installer-program): Remove the associated TODO comment. Mathieu Othacehe 2020-02-11system: Stop using canonical-package....Usage of canonical-package outside of thunked fields breaks cross-compilation, see: https://lists.gnu.org/archive/html/guix-devel/2019-12/msg00410.html. * gnu/installer.scm (installer-program): Remove canonical-package. * gnu/services/base.scm (<nscd-cache>): Ditto, (%base-services): ditto. * gnu/services/xorg.scm: Remove useless canonical-package import. * gnu/system.scm (%base-packages): Remove canonical-package. * gnu/system/install.scm (%installation-services): Ditto, (installation-os): ditto. * gnu/system/locale.scm (single-locale-directory): Ditto. Mathieu Othacehe 2020-01-05installer: Add JFS support....* gnu/installer/newt/partition.scm (run-fs-type-page): Add ‘jfs’ to the list box. * gnu/installer/parted.scm (user-fs-type-name, user-fs-type->mount-type) (partition-filesystem-user-type): Add ‘jfs’ mapping (create-jfs-file-system): New procedure. (format-user-partitions): Use it. * gnu/installer.scm (set-installer-path): Add jfsutils. Tobias Geerinckx-Rice 2019-08-26installer: Partition as the last step....Multiple users have been understandably displeased to find out that their network card was unsupported, and Internet access mandatory, after having already formatted their partitions. * gnu/installer.scm (installer-steps): Run the ‘partition’ step just before the ‘final’ one. Tobias Geerinckx-Rice