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authorzimoun <zimon.toutoune@gmail.com>2022-11-17 03:50:10 +0100
committerRicardo Wurmus <rekado@elephly.net>2022-11-24 12:31:22 +0100
commit533a3d991437b452a10190a941b3226f70e685b5 (patch)
tree3b34e3efb5680e2a94d65aeb43eda167c28ccdd7 /gnu/packages/ed.scm
parentb6117c18376174cb0909d5395d176f4473481437 (diff)
downloadguix-533a3d991437b452a10190a941b3226f70e685b5.tar.gz
guix-533a3d991437b452a10190a941b3226f70e685b5.zip
gnu: r-geneoverlap: Update to 1.34.0.
* gnu/packages/bioconductor.scm (r-geneoverlap): Update to 1.34.0.
Diffstat (limited to 'gnu/packages/ed.scm')
0 files changed, 0 insertions, 0 deletions
t FHS directories are in $PATH in the container and that $PATH can be preserved. Co-authored-by: Ludovic Courtès <ludo@gnu.org> John Kehayias 2022-11-15shell: Detect --symlink spec problems early....* guix/scripts/pack.scm (symlink-spec-option-parser): Remove extraneous char-set. Raise an exception when the target is an absolute file name. (guix-pack): Move with-error-handler earlier. * guix/scripts/shell.scm (guix-shell): Likewise. * guix/scripts/environment.scm (guix-environment): Wrap the whole guix-environment* call with the with-error-handling handler. * tests/guix-environment-container.sh: Add tests. * tests/guix-pack.sh: Adjust symlink spec. Maxim Cournoyer 2022-11-15guix: shell: Add '--symlink' option....* guix/scripts/pack.scm (%options): Extract symlink parsing logic to... (symlink-spec-option-parser): ... here. (self-contained-tarball/builder): Add a comment mentioning why a relative file name is used for the link target. * guix/scripts/environment.scm (show-environment-options-help): Document new --symlink option. (%default-options): Add default value for symlinks. (%options): Register new symlink option. (launch-environment/container): Add #:symlinks argument and extend doc, and create symlinks using evaluate-populate-directive. (guix-environment*): Pass symlinks arguments to launch-environment/container. * doc/guix.texi (Invoking guix shell): Document it. * tests/guix-shell.sh: Add a --symlink (negative) test. * tests/guix-environment-container.sh: Add tests. Maxim Cournoyer 2022-11-06shell: Fix '--emulate-fhs' sometimes not including 'glibc-for-fhs'....Fixes <https://issues.guix.gnu.org/58861>. Previously the order of the options giving to 'guix shell' could mean that the 'glibc-for-fhs' package included with the '--emulate-fhs' option would not appear in the container. For example, using the development option with a package using the 'gnu-build-system', e.g. 'guix shell -CFD hello', would include the regular 'glibc' package. The option ordered mattered: 'guix shell -CD hello -F' would include the expected 'glibc-for-fhs'. We fix this by having 'glibc-for-fhs' added to the package list just before calling 'options-with-caching' so the option order given by the user does not matter. * guix/scripts/shell.scm (%options): Move the '--emulate-fhs' (expression . ...) component from here... (parse-args): ... to here. * tests/guix-environment-container.sh: Add a test to check that 'glibc-for-fhs' is in the container even when 'glibc' is included in the 'guix shell' package list. Signed-off-by: Ludovic Courtès <ludo@gnu.org> John Kehayias 2022-10-13shell: Handle '--emulate-fhs' in 'guix shell', not in 'guix environment'....Previously, using 'guix shell -CF coreutils' twice (such that the profile is cache) would result in: guix shell: error: '--profile' cannot be used with package options This patch fixes it by moving argument handling to (guix scripts shell), before 'options-with-caching' is called. * guix/scripts/environment.scm (show-environment-options-help) (%options): Remove '--emulate-fhs'. (guix-environment*): Pass OPTS as-is to 'options/resolve-packages'. * guix/scripts/shell.scm (show-help, %options): Add '--emulate-fhs'. Add the (expression . ...) component to RESULT right from the argument handler. * tests/guix-environment-container.sh: Change '--emulate-fhs' tests to use 'guix shell' instead of 'guix environment'. Ludovic Courtès 2022-10-13environment: Add '--emulate-fhs'....* guix/scripts/environment.scm (show-environment-options-help, %options): Add '--emulate-fhs'. (setup-fhs): New procedure. Setup for the Filesystem Hierarchy Standard (FHS) container. Defines and uses FHS-SYMLINKS and LINK-CONTENTS to create FHS expected directories and creates /etc/ld.so.conf. (launch-environment): Add 'emulate-fhs?' key and implement it to set $PATH and generate /etc/ld.so.cache before calling COMMAND. (launch-environment/container): Add 'emulate-fhs?' and 'setup-hook' keys and implement them. Define and use FHS-MAPPINGS, to set up additional bind mounts in the container to follow FHS expectations. (guix-environment*): Add glibc-for-fhs to the container packages when 'emulate-fhs?' key is in OPTS. * doc/guix.texi (Invoking guix shell): Document '--emulate-fhs'. (Invoking guix environment): Document '--emulate-fhs'. * tests/guix-environment-container.sh: Add tests for '--emulate-fhs'. Co-authored-by: Ludovic Courtès <ludo@gnu.org> John Kehayias