f0f839c124
gnu: r-deepsnv: Update to 1.38.0.
...
* gnu/packages/bioconductor.scm (r-deepsnv): Update to 1.38.0.
[inputs]: Remove zlib.
[native-inputs]: Add r-knitr.
2021-06-05 09:12:40 +02:00
dec096f827
gnu: r-decipher: Update to 2.20.0.
...
* gnu/packages/bioconductor.scm (r-decipher): Update to 2.20.0.
[propagated-inputs]: Add r-dbi, r-iranges, r-s4vectors, and r-xvector.
2021-06-05 09:12:40 +02:00
116df58449
gnu: r-cummerbund: Update to 2.34.0.
...
* gnu/packages/bioconductor.scm (r-cummerbund): Update to 2.34.0.
2021-06-05 09:12:40 +02:00
e6c5d8ce2c
gnu: r-coverageview: Update to 1.30.0.
...
* gnu/packages/bioconductor.scm (r-coverageview): Update to 1.30.0.
2021-06-05 09:12:40 +02:00
7bac473d06
gnu: r-biocgenerics: Update to 0.38.0.
...
* gnu/packages/bioconductor.scm (r-biocgenerics): Update to 0.38.0.
2021-06-05 09:12:40 +02:00
b05761a5a9
gnu: r-biocversion: Update to 3.13.1.
...
* gnu/packages/bioconductor.scm (r-biocversion): Update to 3.13.1.
2021-06-05 09:12:40 +02:00
405b386656
gnu: r-aneufinder: Update to 1.20.0.
...
* gnu/packages/bioconductor.scm (r-aneufinder): Update to 1.20.0.
2021-06-05 09:12:40 +02:00
75817956c1
gnu: r-hdf5array: Update to 1.20.0.
...
* gnu/packages/bioconductor.scm (r-hdf5array): Update to 1.20.0.
[arguments]: Remove.
[propagated-inputs]: Add r-rhdf5filters.
2021-06-05 09:12:40 +02:00
bfa23ec526
gnu: r-cytoml: Update to 2.4.0.
...
* gnu/packages/bioconductor.scm (r-cytoml): Update to 2.4.0.
[arguments]: Remove.
2021-06-05 09:12:40 +02:00
764e2dba20
gnu: r-flowworkspace: Update to 4.4.0.
...
* gnu/packages/bioconductor.scm (r-flowworkspace): Update to 4.4.0.
[arguments]: Remove.
[propagated-inputs]: Add r-delayedarray and r-s4vectors.
2021-06-05 09:12:40 +02:00
b9751b629c
gnu: r-ncdfflow: Update to 2.38.0.
...
* gnu/packages/bioconductor.scm (r-ncdfflow): Update to 2.38.0.
[arguments]: Remove.
2021-06-05 09:12:40 +02:00
5c37a048bb
gnu: r-cytolib: Update to 2.4.0.
...
* gnu/packages/bioconductor.scm (r-cytolib): Update to 2.4.0.
[arguments]: Remove.
[native-inputs]: Remove pkg-config.
2021-06-05 09:12:40 +02:00
782d27f77d
gnu: r-rhdf5: Update to 2.36.0.
...
* gnu/packages/bioconductor.scm (r-rhdf5): Update to 2.36.0.
[arguments]: Remove.
2021-06-05 09:12:40 +02:00
87d06a725f
gnu: r-mzr: Update to 2.26.0.
...
* gnu/packages/bioconductor.scm (r-mzr): Update to 2.26.0.
[arguments]: Remove obsolute substitution.
2021-06-05 09:12:40 +02:00
5d13aab6ca
gnu: r-msnid: Update to 1.26.0.
...
* gnu/packages/bioconductor.scm (r-msnid): Update to 1.26.0.
[arguments]: Set HOME variable.
2021-06-05 09:12:40 +02:00
d0a7dc0cb6
gnu: r-bioccheck: Update to 1.28.0.
...
* gnu/packages/bioconductor.scm (r-bioccheck): Update to 1.28.0.
[arguments]: Remove.
2021-06-05 09:12:39 +02:00
1b0338d76b
gnu: r-rhdf5lib: Update to 1.14.0.
...
* gnu/packages/bioconductor.scm (r-rhdf5lib): Update to 1.14.0.
[source]: Update deletions.
[arguments]: Update substitutions.
[inputs]: Move zlib from here...
[propagated-inputs]: ...to here.
2021-06-05 09:12:39 +02:00
53ec97713a
gnu: Add r-metapod.
...
* gnu/packages/bioconductor.scm (r-metapod): New variable.
2021-06-05 09:12:39 +02:00
8caab75883
gnu: Add r-ggtree.
...
* gnu/packages/bioconductor.scm (r-ggtree): New variable.
2021-06-05 09:12:39 +02:00
ab4a91b252
gnu: Add r-treeio.
...
* gnu/packages/bioconductor.scm (r-treeio): New variable.
2021-06-05 09:12:39 +02:00
fd4fa40ac4
gnu: Add r-scaledmatrix.
...
* gnu/packages/bioconductor.scm (r-scaledmatrix): New variable.
2021-06-05 09:12:39 +02:00
efefb2be3a
gnu: Add r-trajectoryutils.
...
* gnu/packages/bioconductor.scm (r-trajectoryutils): New variable.
2021-06-05 09:12:39 +02:00
ce99b4da63
gnu: Add r-restfulr.
...
* gnu/packages/bioconductor.scm (r-restfulr): New variable.
2021-06-05 09:12:39 +02:00
ab66c9a2cd
gnu: Add r-arrow.
...
* gnu/packages/cran.scm (r-arrow): New variable.
2021-06-05 09:12:39 +02:00
b71f21339f
gnu: Add r-ggpointdensity.
...
* gnu/packages/cran.scm (r-ggpointdensity): New variable.
2021-06-05 09:12:39 +02:00
41ea9bed97
gnu: Add r-ggnewscale.
...
* gnu/packages/cran.scm (r-ggnewscale): New variable.
2021-06-05 09:12:39 +02:00
d5c08f11e1
gnu: Add r-aplot.
...
* gnu/packages/cran.scm (r-aplot): New variable.
2021-06-05 09:12:39 +02:00
c343c3bc1f
guix: Update to Bioconductor 3.13.
...
* guix/build-system/r.scm (bioconductor-uri): Update version.
* guix/import/cran.scm (%bioconductor-version): Update.
2021-06-05 09:12:39 +02:00
f98837a6ba
gnu: pigx-rnaseq: Update to 0.0.13.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.13.
[arguments]: Remove obsolete substitutions.
[inputs]: Remove fastqc and trim-galore; add hisat2 and fastp.
2021-06-05 09:12:39 +02:00
683eb7c5b1
gnu: Remove remnants of nettle 3.5.
...
The source of nettle-3.5 was already using the source of nettle-3.7.
* gnu/packages/nettle.scm
(nettle-3.5): Rename to 'nettle'.
(nettle-3.7): Remove variable.
(nettle): Remove alias.
2021-06-05 02:09:03 -04:00
5d547f74ed
gnu: nasm: Update to 2.15.05.
...
* gnu/packages/assembly.scm (nasm): Update to 2.15.05.
[phases]{dont-build-ps-pdf-outputs}: Adjust patching to changes in the source.
2021-06-05 00:14:57 -04:00
7382aa00b8
gnu: python-scanpy: Update to 1.7.2.
...
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.7.2.
2021-06-04 23:51:35 +02:00
e639da604f
gnu: python-anndata: Update to 0.7.6.
...
* gnu/packages/python-xyz.scm (python-anndata): Update to 0.7.6.
2021-06-04 23:51:24 +02:00
d1827d5c63
gnu: wireguard-tools: Set #:sh argument of 'wrap-program'.
...
* gnu/packages/vpn.scm
(wireguard-tools)[arguments]<#:phases>{wrap-wg-quick}:
Set #:sh argument of ‘wrap-program’.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:33 +02:00
96a2ae40fb
gnu: protonvpn-cli: Set #:sh argument of 'wrap-program'.
...
* gnu/packages/vpn.scm
(protonvpn-cli)[arguments]<#:phases>{wrap-wrapper}:
Set #:sh argument of ‘wrap-program’.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:33 +02:00
b74085ce36
gnu: openconnect-sso: Set #:sh argument of 'wrap-program'.
...
* gnu/packages/vpn.scm
(openconnect-sso)[arguments]<#:phases>{wrap-qt-process-path}
Set #:sh argument of ‘wrap-program’.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:33 +02:00
3bbb0ec888
gnu: vpnc-scripts: Set #:guile argument of 'wrap-script'.
...
* gnu/packages/vpn.scm
(vpnc-scripts)[arguments]<#:phases>{wrap-scripts}:
Set #:guile argument of ‘wrap-script’.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:33 +02:00
a4e38cc216
gnu: clipmenu: Set #:guile argument of 'wrap-script'.
...
* gnu/packages/xdisorg.scm
(clipmenu)[arguments]<#:phases>{wrap-script}:
Set #:guile argument of ‘wrap-script’.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:33 +02:00
0758ee8002
gnu: sieve-connect: Set #:guile argument of 'wrap-script'.
...
* gnu/packages/mail.scm
(sieve-connect)[arguments]<#:phases>{wrap-program}:
Set #:guile argument of ‘wrap-script’.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:33 +02:00
b2459387b9
gnu: nanopolish: Set #:guile argument of 'wrap-script'.
...
* gnu/packages/bioinformatics.scm
(nanopolish)[arguments]<#:phases>{wrap-programs}:
Set #:guile argument of ‘wrap-script’.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:33 +02:00
2d092a2afa
gnu: gess: Set #:guile argument of 'wrap-script'.
...
* gnu/packages/bioinformatics.scm
(gess)[arguments]<#:phases>{install}
Set #:guile argument of ‘wrap-script’.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:32 +02:00
c4989f7569
gnu: prinseq: Set #:guile argument of 'wrap-script'.
...
* gnu/packages/bioinformatics.scm
(prinseq)[arguments]<#:phases>{install}:
Set #:guile argument of ‘wrap-script’.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:32 +02:00
fadbac0ecc
gnu: proteinortho: Set #:guile argument of 'wrap-script'.
...
* gnu/packages/bioinformatics.scm
(proteinortho)[arguments]<#:phases>{wrap-programs}:
Set #:guile argument of ‘wrap-script’.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:32 +02:00
b202fdf131
gnu: bats: Set #:guile argument of 'wrap-script'.
...
* gnu/packages/bash.scm
(bats)[arguments]<#:builder>: Set #:guile argument
of ‘wrap-script’.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:32 +02:00
0a843e3643
gnu: carla: Set #:guile argument of 'wrap-script'.
...
* gnu/packages/audio.scm
(carla)[arguments]<#:phases>{wrap-executables}:
Set #:guile argument of ‘wrap-script’.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:32 +02:00
a62d17dc05
rakudo-build-system: Look up the interpreter in 'inputs'.
...
* guix/build/rakudo-build-system.scm (wrap): Pass
the shell interpreter from 'inputs' to 'wrap-program' using
'search-input-file'.
Partially-Fixes: <https://issues.guix.gnu.org/47869 >
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:32 +02:00
2ac898d7f8
qt-build-system: Look up the interpreter in 'inputs'.
...
* guix/build/qt-build-system.scm (wrap-all-programs): Pass
the shell interpreter from 'inputs' to 'wrap-program' using
'search-input-file'.
Partially-Fixes: <https://issues.guix.gnu.org/47869 >
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:32 +02:00
5b24cbee31
python-build-system: Look up the interpreter in 'inputs'.
...
* guix/build/python-build-system.scm (wrap): Pass the shell
interpreter from 'inputs' to 'wrap-program' using 'search-input-file'.
Partially-Fixes: <https://issues.guix.gnu.org/47869 >
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:31 +02:00
1dbc3b2b0c
glib-or-gtk-build-system: Look up the interpreter in 'inputs'.
...
* guix/build/glib-or-gtk-build-system.scm (wrap-all-programs): Pass
the shell interpreter from 'inputs' to 'wrap-program' using
'search-input-file'.
Partially-Fixes: <https://issues.guix.gnu.org/47869 >
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:31 +02:00
5378edeab4
utils: Define ‘search-input-file’ procedure.
...
The procedure ‘which’ from (guix build utils)
is used for two different purposes:
1. for finding the absolute file name of a binary
that needs to run during the build process
2. for finding the absolute file name of a binary,
for the target system (as in --target=TARGET),
e.g. for substituting sh->/gnu/store/.../bin/sh,
python->/gnu/store/.../bin/python.
When compiling natively (target=#f in Guix parlance),
this is perfectly fine.
However, when cross-compiling, there is a problem.
"which" looks in $PATH for binaries. That's good for purpose (1),
but incorrect for (2), as the $PATH contains binaries from native-inputs
instead of inputs.
This commit defines a ‘search-input-file’ procedure. It functions
like 'which', but instead of searching in $PATH, it searches in
the 'inputs' of the build phase, which must be passed to
‘search-input-file’ as an argument. Also, the file name must
include "bin/" or "sbin/" as appropriate.
* guix/build/utils.scm (search-input-file): New procedure.
* tests/build-utils.scm
("search-input-file: exception if not found")
("search-input-file: can find if existent"): Test it.
* doc/guix.texi (File Search): Document it.
Partially-Fixes: <https://issues.guix.gnu.org/47869 >
Co-Authored-By: Ludovic Courtès <ludo@gnu.org>
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2021-06-04 22:34:26 +02:00
Ricardo Wurmus
Maxim Cournoyer
Roel Janssen
Maxime Devos