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Author SHA1 Message Date
Ludovic Courtès
3d85c3ec65
gnu: pciutils: Fix compilation error on GNU/Hurd. 
* gnu/packages/patches/pciutils-hurd-fix.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/pciutils.scm (pciutils)[arguments]: Add
'apply-hurd-patch' phase when (hurd-target?) is true.
[inputs]: Add "hurd-patch" entry when (hurd-target?) is true.
 2020-12-09 14:13:33 +01:00
Ludovic Courtès
f066e65713
services: guix-publish: Depend on 'avahi-daemon' when needed. 
* gnu/services/base.scm (guix-publish-shepherd-service): Add
'user-processes' to 'requirement'.  When ADVERTISE? is true, also add
'avahi-daemon'.
 2020-12-09 14:13:32 +01:00
Ludovic Courtès
59a6780f70
services: avahi: Depend on 'user-processes'. 
* gnu/services/avahi.scm (avahi-shepherd-service): Add 'user-processes'
to 'requirement'.
 2020-12-09 14:13:32 +01:00
Ricardo Wurmus
ebf11de4e3
gnu: r-diffbind: Update to 3.0.8. 
* gnu/packages/bioconductor.scm (r-diffbind): Update to 3.0.8.
 2020-12-09 12:12:48 +01:00
Ricardo Wurmus
4617cc7fd5
gnu: r-rhtslib: Propagate zlib. 
* gnu/packages/bioinformatics.scm (r-rhtslib)[inputs]: Move zlib from here...
[propagated-inputs]: ...to here.
(r-variantannotation, r-rsamtools, r-bamsignals, r-rhdf5,
r-methylkit)[inputs]: Remove zlib.
* gnu/packages/bioconductor.scm (r-diffbind, r-quasr, r-cytolib, r-ncdfflow,
r-flowworkspace, r-seqbias)[inputs]: Remove zlib.
 2020-12-09 12:12:48 +01:00
Ricardo Wurmus
7601015fc9
gnu: r-delayedmatrixstats: Update to 1.12.1. 
* gnu/packages/bioconductor.scm (r-delayedmatrixstats): Update to 1.12.1.
[propagated-inputs]: Add r-matrixgenerics.
 2020-12-09 12:12:48 +01:00
zimoun
cde035e67f
gnu: r-gqtlstats: Update to 1.21.3. 
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.21.3.
 2020-12-09 12:12:48 +01:00
zimoun
6a4818716d
gnu: r-gqtlbase: Update to 1.21.1. 
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>

* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.21.1.
[arguments]: Add phase to patch broken NAMESPACE file.
 2020-12-09 12:12:48 +01:00
zimoun
64f9fb308f
gnu: r-bigmelon: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-bigmelon): Update to 1.16.0.
 2020-12-09 12:12:48 +01:00
zimoun
9f6e2bfe1f
gnu: r-watermelon: Update to 1.34.0. 
* gnu/packages/bioconductor.scm (r-watermelon): Update to 1.34.0.
 2020-12-09 12:12:47 +01:00
zimoun
8db36c1f68
gnu: r-yarn: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-yarn): Update to 1.16.0.
 2020-12-09 12:12:47 +01:00
zimoun
adf6edc750
gnu: r-quantro: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-quantro): Update to 1.24.0.
 2020-12-09 12:12:47 +01:00
zimoun
4eeaa159d2
gnu: r-lumi: Update to 2.42.0. 
* gnu/packages/bioconductor.scm (r-lumi): Update to 2.42.0.
 2020-12-09 12:12:47 +01:00
zimoun
0b7dd44706
gnu: r-methylumi: Update to 2.36.0. 
* gnu/packages/bioconductor.scm (r-methylumi): Update to 2.36.0.
 2020-12-09 12:12:47 +01:00
zimoun
e5a4198bc3
gnu: r-minfi: Update to 1.36.0. 
* gnu/packages/bioconductor.scm (r-minfi): Update to 1.36.0.
 2020-12-09 12:12:47 +01:00
zimoun
45dfb75166
gnu: Add r-catalyst. 
* gnu/packages/bioconductor.scm (r-catalyst): New variable.
 2020-12-09 12:12:47 +01:00
zimoun
43bf50ecae
gnu: r-ggcyto: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-ggcyto): Update to 1.18.0.
 2020-12-09 12:12:47 +01:00
zimoun
b856a48768
gnu: r-scdd: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-scdd): Update to 1.14.0.
 2020-12-09 12:12:47 +01:00
zimoun
3f04b8167b
gnu: r-chipcomp: Update to 1.20.0. 
* gnu/packages/bioconductor.scm (r-chipcomp): Update to 1.20.0.
 2020-12-09 12:12:47 +01:00
zimoun
1174317e03
gnu: r-pcatools: Update to 2.2.0. 
* gnu/packages/bioconductor.scm (r-pcatools): Update to 2.2.0.
 2020-12-09 12:12:47 +01:00
zimoun
970984237a
gnu: r-biocviews: Update to 1.58.1. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.58.1.

Co-authored-by: Ricardo Wurmus <reka@elephly.net>.
 2020-12-09 12:12:47 +01:00
zimoun
b03c955c6f
gnu: r-scran: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-scran): Update to 1.18.0.
[propagated-inputs]: Add r-bluster, r-scuttle.  Remove r-iranges.

Co-authored-by: Ricardo Wurmus <reka@elephly.net>.
 2020-12-09 12:12:47 +01:00
zimoun
d4b5d18684
gnu: r-scater: Update to 1.18.3. 
* gnu/packages/bioconductor.scm (r-scater): Update to 1.18.3.
[propagated-inputs]: Add r-gridextra, r-scutlle.  Remove r-beachmat, r-rcpp.

Co-authored-by: Ricardo Wurmus <reka@elephly.net>.
 2020-12-09 12:12:46 +01:00
Ricardo Wurmus
0e60dda0ae
gnu: Add r-scuttle. 
* gnu/packages/bioconductor.scm (r-scuttle): New variable.
 2020-12-09 12:12:46 +01:00
zimoun
10c87ecf77
gnu: r-delayedmatrixstats: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-delayedmatrixstats): Update to 1.12.0.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
 2020-12-09 12:12:46 +01:00
zimoun
53affb349a
gnu: r-rhdf5: Update to 2.34.0. 
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.34.0.
[propagated-inputs]: Add r-rhdf5filters.
[arguments]: Avoid to have a plain directory on the list of libraries to
link.

Co-authored-by: Ricardo Wurmus <reka@elephly.net>.
 2020-12-09 12:12:46 +01:00
Ricardo Wurmus
86fcceeae1
gnu: Add r-rhdf5filters. 
* gnu/packages/bioinformatics.scm (r-rhdf5filters): New variable.
 2020-12-09 12:12:46 +01:00
zimoun
4ef898d449
gnu: r-singlecellexperiment: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-singlecellexperiment): Update to 1.12.0.
 2020-12-09 12:12:46 +01:00
zimoun
d0db04fcaf
gnu: r-yapsa: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-yapsa): Update to 1.16.0.
 2020-12-09 12:12:46 +01:00
zimoun
798ec28916
gnu: r-biocsingular: Update to 1.6.0. 
* gnu/packages/bioconductor.scm (r-biocsingular): Update to 1.6.0.
 2020-12-09 12:12:46 +01:00
zimoun
dd9341ffa3
gnu: r-genomicinteractions: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-genomicinteractions): Update to 1.24.0.
 2020-12-09 12:12:46 +01:00
zimoun
35dae95110
gnu: r-interactionset: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-interactionset): Update to 1.18.0.
 2020-12-09 12:12:46 +01:00
zimoun
60ad3c7b3b
gnu: r-genomationdata: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.22.0.
 2020-12-09 12:12:46 +01:00
Ricardo Wurmus
5e719988f2
gnu: Add r-sparsematrixstats. 
* gnu/packages/bioconductor.scm (r-sparsematrixstats): New variable.
 2020-12-09 12:12:46 +01:00
Roel Janssen
a23310ffc2
gnu: Add r-bluster. 
* gnu/packages/bioconductor.scm (r-bluster): New variable.
 2020-12-09 12:12:45 +01:00
Roel Janssen
aca4ebe40a
gnu: r-annaffy: Update to 1.62.0. 
* gnu/packages/bioconductor.scm (r-annaffy): Update to 1.62.0.
 2020-12-09 12:12:45 +01:00
zimoun
e707820442
gnu: r-sushi: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.28.0.
 2020-12-09 12:12:45 +01:00
zimoun
83129edfb7
gnu: r-gwascat: Update to 2.22.0. 
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.22.0.
[propagated-inputs]: Add r-biocfilecache, r-readr, r-snpstats, and
r-variantannotation; remove r-biocgenerics, r-ggplot2, r-rsamtools, and
r-rtracklayer.
 2020-12-09 12:12:45 +01:00
zimoun
717e53fdc0
gnu: r-gviz: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.34.0.
 2020-12-09 12:12:45 +01:00
zimoun
0a8d08e887
gnu: r-ldblock: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.20.0.
 2020-12-09 12:12:45 +01:00
zimoun
494010ad3e
gnu: r-erma: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-erma): Update to 1.6.0.
 2020-12-09 12:12:45 +01:00
zimoun
6e338901bf
gnu: r-snpstats: Update to 1.40.0. 
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.40.0.
 2020-12-09 12:12:45 +01:00
zimoun
74a11b21be
gnu: r-ggbio: Update to 1.38.0. 
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.38.0.
 2020-12-09 12:12:45 +01:00
zimoun
3c6eecdeed
gnu: r-biovizbase: Update to 1.38.0. 
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.38.0.
 2020-12-09 12:12:45 +01:00
zimoun
6e182c237a
gnu: r-organismdbi: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.32.0.
 2020-12-09 12:12:44 +01:00
zimoun
06fe3b7a53
gnu: r-ensembldb: Update to 2.14.0. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.14.0.
 2020-12-09 12:12:44 +01:00
zimoun
8962a13afe
gnu: r-dirichletmultinomial: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.32.0.
 2020-12-09 12:12:44 +01:00
Roel Janssen
4ef1e375b4
gnu: r-complexheatmap: Update to 2.6.2. 
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 2.6.2;
[propagated-inputs]: Add r-cairo, r-digest, r-iranges, r-matrixstats, and
r-s4vectors.
 2020-12-09 12:12:44 +01:00
zimoun
0fde2f9ad2
gnu: r-genomicfiles: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.26.0.
[propagated-inputs]: Add r-matrixgenerics.
 2020-12-09 12:12:44 +01:00
zimoun
78cadd0fef
gnu: r-gage: Update to 2.40.0. 
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.40.0.
 2020-12-09 12:12:44 +01:00