gnu: r-qvalue: Update to 2.34.0. - guix - Wojtek's customized Guix

diff options

author	Ricardo Wurmus <rekado@elephly.net>	2023-11-03 17:18:39 +0100
committer	Ricardo Wurmus <rekado@elephly.net>	2023-11-03 22:49:18 +0100
commit	9b9726239a5ecb1ced0cf16d4bb865f266fb28f4 (patch)
tree	0829c5fd9638ea6a53c559c24b624be584a2aa5e /tests/modules.scm
parent	721c52eca797f8d5235a3fd126bc0d2ca028cc85 (diff)
download	guix-9b9726239a5ecb1ced0cf16d4bb865f266fb28f4.tar.gz guix-9b9726239a5ecb1ced0cf16d4bb865f266fb28f4.zip

gnu: r-qvalue: Update to 2.34.0.

* gnu/packages/bioconductor.scm (r-qvalue): Update to 2.34.0. Change-Id: Ibc6f25bf2dcee3d98845fffd456ea923f853fd2a

Diffstat (limited to 'tests/modules.scm')

0 files changed, 0 insertions, 0 deletions

(method url-fetch) + ;; See for a list of + ;; mirrors. + (uri (list (string-append + "ftp://mirror.switch.ch/mirror/OpenLDAP/" + "openldap-release/openldap-" version ".tgz") + (string-append + "https://www.openldap.org/software/download/OpenLDAP/" + "openldap-release/openldap-" version ".tgz") + (string-append + "ftp://ftp.dti.ad.jp/pub/net/OpenLDAP/" + "openldap-release/openldap-" version ".tgz"))) + (sha256 + (base32 + "0nmlyqhc52v24b4awh914sczmvxbazgq2cnlycvb9dgcwvhlgfn7")))))) + (define-public nss-pam-ldapd (package (name "nss-pam-ldapd") -- cgit v1.2.3 From 61609fb88e143f48d34f434e7aeda08f74d68353 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Feb 2021 21:30:39 +0100 Subject: gnu: r-diffbind: Update to 3.0.13. * gnu/packages/bioconductor.scm (r-diffbind): Update to 3.0.13. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f1af34844f..d383005a76 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1796,14 +1796,14 @@ signal in the input, that lead to spurious peaks during peak calling.") (define-public r-diffbind (package (name "r-diffbind") - (version "3.0.8") + (version "3.0.13") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "11svdfjp4faswrmzwkryzhd0ji2pl9vwsd35lvbfjgakbpxnyn8a")))) + "0kxn59v93hl5pq8d156lnbz0sslpnxyjcfrvq2gzgd91sd587qmn")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 669ea5ab097e4557e41ae10cab8bd195c590173c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Feb 2021 21:30:46 +0100 Subject: gnu: r-matrixgenerics: Update to 1.2.1. * gnu/packages/bioconductor.scm (r-matrixgenerics): Update to 1.2.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d383005a76..61dfc242fb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2062,13 +2062,13 @@ enrichedGO (addGeneIDs).") (define-public r-matrixgenerics (package (name "r-matrixgenerics") - (version "1.2.0") + (version "1.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MatrixGenerics" version)) (sha256 (base32 - "1a3sw79185d6rld3wlrynkzcbp754a7jkracrmvn0ra964ia8zvc")))) + "163f0z33cv6038gcjdxn1hadcg9b09qgvm6zc5zn97y4rc8grkrb")))) (properties `((upstream-name . "MatrixGenerics"))) (build-system r-build-system) -- cgit v1.2.3 From ebf9ad7984e7b53afdb156ac4aa57c653351412b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Feb 2021 21:30:49 +0100 Subject: gnu: r-enrichplot: Update to 1.10.2. * gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.10.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 61dfc242fb..a05906bd4c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4013,14 +4013,14 @@ data.") (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.10.1") + (version "1.10.2") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "0h0455plh8bxnpizgfxij9625ff32rs1a51yzpnrf5hl27xbfkdd")))) + "0lm5yapd567jxcnz9m4a623aymf3q00svjrxp3rf0r9j77dgyisv")))) (build-system r-build-system) (propagated-inputs `(("r-cowplot" ,r-cowplot) -- cgit v1.2.3 From 6d0709231f66d53418188eccdd56ce1de82224fd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Feb 2021 21:30:53 +0100 Subject: gnu: r-clusterprofiler: Update to 3.18.1. * gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 3.18.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a05906bd4c..91873c4fc3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -4049,14 +4049,14 @@ All the visualization methods are developed based on ggplot2 graphics.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "3.18.0") + (version "3.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "07xkc515gp9j4axg0qh39ni65mcbjgxmzjh5wxd86w64lz7xh8b9")))) + "04v1xsxfxxy8rdjfswv4crpzkx9592r2sh3cjh1kb54sd4lyb6si")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) -- cgit v1.2.3 From 691178d67b91a0150ed1dd0e3540441cecc83e61 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Feb 2021 21:30:56 +0100 Subject: gnu: r-multidataset: Update to 1.18.1. * gnu/packages/bioconductor.scm (r-multidataset): Update to 1.18.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 91873c4fc3..d325254b56 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5877,14 +5877,14 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.") (define-public r-multidataset (package (name "r-multidataset") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiDataSet" version)) (sha256 (base32 - "025gfgn83ancp0khdmq2y4lwm97v5zqnjksi79rr0w175syznx5w")))) + "0v3ljpkggrpc7zp72z417jkzjq17abwsvsxh33fb8s3i2s4ycaa4")))) (properties `((upstream-name . "MultiDataSet"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 9470f901d93b7163fb4d146046b456c9343e4fa1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Feb 2021 21:30:59 +0100 Subject: gnu: r-cytolib: Update to 2.2.1. * gnu/packages/bioconductor.scm (r-cytolib): Update to 2.2.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d325254b56..551b9952b9 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6103,14 +6103,14 @@ cluster count and membership by stability evidence in unsupervised analysis.") (define-public r-cytolib (package (name "r-cytolib") - (version "2.2.0") + (version "2.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "cytolib" version)) (sha256 (base32 - "1wylzps7wbvm64k62w5bbi8l74gaqca96psfapxfg6mcac5yz4qw")))) + "0y8mxrg3jh9bahsf9rblgyja37m1x1ncxfnrli91xjyg0582kh7r")))) (properties `((upstream-name . "cytolib"))) (build-system r-build-system) (arguments -- cgit v1.2.3 From 6f37c3ea405556ffd9c7bc4a161c77780604fcc6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Feb 2021 21:31:02 +0100 Subject: gnu: r-gdsfmt: Update to 1.26.1. * gnu/packages/bioconductor.scm (r-gdsfmt): Update to 1.26.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 551b9952b9..be8ca27e9e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6965,14 +6965,14 @@ metrics, with methods for objects produced by the @code{methylumi} and (define-public r-gdsfmt (package (name "r-gdsfmt") - (version "1.26.0") + (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "gdsfmt" version)) (sha256 (base32 - "0x8ik179sf38ihx2y24cvsa9d8isdmx2z27sjhcwq0r3xpjxpz1a")) + "0f5vn8h5fzzazcv92sgrf85hc4xkkizk2wwml9mzjd8ya2fkwg8n")) (modules '((guix build utils))) ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build ;; them and link with system libraries instead. -- cgit v1.2.3 From da109ae738b7419ca546f018051755921cc686db Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Feb 2021 21:31:05 +0100 Subject: gnu: r-chemminer: Update to 3.42.1. * gnu/packages/bioconductor.scm (r-chemminer): Update to 3.42.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index be8ca27e9e..3ddd7f0a57 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7812,14 +7812,14 @@ visualizing RNA-sequencing datasets and differentially expressed genes.") (define-public r-chemminer (package (name "r-chemminer") - (version "3.42.0") + (version "3.42.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ChemmineR" version)) (sha256 (base32 - "14q9zhhxgkx5skj424i2rbjdbp5j8jfkxspkhnkwv5i45cvkgh19")))) + "1853w19042c53whdnrfg1v8f07wpswf2si8q4613yrcamzg2zjkx")))) (properties `((upstream-name . "ChemmineR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 18ebacaa1ca2b178ce071c5f774b082d5e0e3ee0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Feb 2021 21:31:08 +0100 Subject: gnu: r-preprocesscore: Update to 1.52.1. * gnu/packages/bioconductor.scm (r-preprocesscore): Update to 1.52.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 3ddd7f0a57..567f656850 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8574,14 +8574,14 @@ generated.") (define-public r-preprocesscore (package (name "r-preprocesscore") - (version "1.52.0") + (version "1.52.1") (source (origin (method url-fetch) (uri (bioconductor-uri "preprocessCore" version)) (sha256 (base32 - "1i5ky3bfbkrz4lgfs72fkckr8q3wq48p38mp05cjmnmh1chmdw38")))) + "1hz7rlpscaczvvcalky2f5bmr70aii455549m7f6wk10aklp3nll")))) (properties `((upstream-name . "preprocessCore"))) (build-system r-build-system) -- cgit v1.2.3 From f7947f89916e4d6b764c128f2f26623eb5b6734e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Feb 2021 21:31:11 +0100 Subject: gnu: r-hdf5array: Update to 1.18.1. * gnu/packages/bioconductor.scm (r-hdf5array): Update to 1.18.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 567f656850..a3b8603835 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8728,14 +8728,14 @@ provided.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "1hr149q03p09y1cjnx8av854j53041wfyq66xpsjw4mypzjf6f28")))) + "14v2adhwi0yac834g23kvfid740raclhmribzd28k10gsjk9cj7g")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (arguments -- cgit v1.2.3 From a1357422c3b2c65d774f74bb5897c3651aae642c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Feb 2021 21:31:14 +0100 Subject: gnu: r-rhdf5lib: Update to 1.12.1. * gnu/packages/bioconductor.scm (r-rhdf5lib): Update to 1.12.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a3b8603835..87e82e71a3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8769,14 +8769,14 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.12.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "0wia85a6dkgibsjcmpqas5068msck3h3bqpgw2x07bk189z4vay2")) + "14fnq4gijxp2l7985pksfk52i6klvy81r3892lnna73c6hh1dj28")) (modules '((guix build utils))) (snippet '(begin -- cgit v1.2.3 From 79d51ffecac5367899a7b448453660ff51392685 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Feb 2021 21:31:17 +0100 Subject: gnu: r-beachmat: Update to 2.6.4. * gnu/packages/bioconductor.scm (r-beachmat): Update to 2.6.4. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 87e82e71a3..19d75b316c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8853,14 +8853,14 @@ packages.") (define-public r-beachmat (package (name "r-beachmat") - (version "2.6.2") + (version "2.6.4") (source (origin (method url-fetch) (uri (bioconductor-uri "beachmat" version)) (sha256 (base32 - "1yxm5andf4hsxxsmwrn5vl79707yfqkhzzajq6fvhsmaad3f97n7")))) + "0vbqdkc52j2v1ghygmhy2cbgqm4l99vmv8930wkzkq1pm73pmjji")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) -- cgit v1.2.3 From cf3e7038209309316ac676a685000ba20106f611 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Feb 2021 21:31:21 +0100 Subject: gnu: r-scuttle: Update to 1.0.4. * gnu/packages/bioconductor.scm (r-scuttle): Update to 1.0.4. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 19d75b316c..9dbeb915fa 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8907,14 +8907,14 @@ libraries.") (define-public r-scuttle (package (name "r-scuttle") - (version "1.0.3") + (version "1.0.4") (source (origin (method url-fetch) (uri (bioconductor-uri "scuttle" version)) (sha256 (base32 - "0l2r6fhyd33dllf2mc5a1pd5sawfvcin54pgh9l1nafqzg3sdv2m")))) + "0vfhxyv81y525qgk0s3bxy1yypj16h1bl7sc1a1jdqx11fxxv2l8")))) (properties `((upstream-name . "scuttle"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From de4fc492700efaf9d8fd4614dfba7fb712446c0c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Feb 2021 21:31:24 +0100 Subject: gnu: r-scran: Update to 1.18.5. * gnu/packages/bioconductor.scm (r-scran): Update to 1.18.5. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9dbeb915fa..36a104f1f4 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8979,14 +8979,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.18.1") + (version "1.18.5") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "1zap12rm61z2hg6ykknbif478nr7g468v8mp50bj5hqgi69ywcww")))) + "0mk4bs7pkzbaiaaap75nzsrlwr883h45xnbpn94fy91i8d9w1xy1")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) -- cgit v1.2.3 From 8acfd9f3d4c1eb67684404732805b2723a55aba9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Feb 2021 21:31:27 +0100 Subject: gnu: r-sparsematrixstats: Update to 1.2.1. * gnu/packages/bioconductor.scm (r-sparsematrixstats): Update to 1.2.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 36a104f1f4..72643bb1da 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9022,14 +9022,14 @@ variable and significantly correlated genes.") (define-public r-sparsematrixstats (package (name "r-sparsematrixstats") - (version "1.2.0") + (version "1.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "sparseMatrixStats" version)) (sha256 (base32 - "0d1idbda1pzhdam9m0i5rn0c6pl7gwv0v3mcrv4wi5760v9qd5qh")))) + "01gnmy9zqd0ygm40vqkmqmiwfqmdawj4m81dysmmcdm7z80rn9ii")))) (properties `((upstream-name . "sparseMatrixStats"))) (build-system r-build-system) -- cgit v1.2.3 From 311bb4bc3d535606f7daa81ee737454827884e77 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Feb 2021 21:31:30 +0100 Subject: gnu: r-delayedmatrixstats: Update to 1.12.3. * gnu/packages/bioconductor.scm (r-delayedmatrixstats): Update to 1.12.3. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 72643bb1da..8fe56c4a5b 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -9050,14 +9050,14 @@ data in the column sparse format.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.12.1") + (version "1.12.3") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "1cyvj6ffl10vaiip146dldc1w8if854kpz9nhi50ndhpkmdb8sa0")))) + "1hb8jv5dy3svf7xan6rym7amwdqm5mvl9qx5xhmj1vkb81bizn7h")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) -- cgit v1.2.3 From 074d142ab66584520507c2cbf72bc368c995eafa Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Feb 2021 21:31:33 +0100 Subject: gnu: r-genefilter: Update to 1.72.1. * gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.72.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index cbf08c5dd2..be1568bb81 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7311,14 +7311,14 @@ includes software to (define-public r-genefilter (package (name "r-genefilter") - (version "1.72.0") + (version "1.72.1") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "0929g6c4v2qhgipgrh1a5gv6444sm2dp52x9c3qbk03i8wzc6633")))) + "1c6h3qnjvphs977qhv5vafvsb108r0q7xhaayly6qv6adqfn94rn")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran) -- cgit v1.2.3 From d3ac91dd9ddbe0b4ba1b85171f5fd18cc1b83d13 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Feb 2021 21:31:36 +0100 Subject: gnu: r-gseabase: Update to 1.52.1. * gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.52.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index be1568bb81..c733e33c8e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7477,14 +7477,14 @@ the graph algorithms contained in the Boost library.") (define-public r-gseabase (package (name "r-gseabase") - (version "1.52.0") + (version "1.52.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GSEABase" version)) (sha256 (base32 - "0lcxbxfg62zdf2nql49asn3555cqrrxpjm2xsxf7vlxv84dl6r44")))) + "0dawh1kjmf6921jm77j2s2phrq5237pjc4sdh8fkln89gf48zx6i")))) (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From babb2dce34774c7935980bd770ba2e15ddce7947 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Feb 2021 21:31:39 +0100 Subject: gnu: r-systempiper: Update to 1.24.3. * gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.24.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c733e33c8e..4d5d2d7df3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7611,14 +7611,14 @@ ungapped alignment formats.") (define-public r-systempiper (package (name "r-systempiper") - (version "1.24.2") + (version "1.24.3") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "0blvvci57q12sl18yvw07233rfnj47mfadzm0pdpig1ll5z6ld2j")))) + "0ffazyl2q9plbhwlxi04s3fvnli6qj95n7bkjc21535bbi08xfki")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 88fd569ddf3446d73c1d612b99a9d5465350c1db Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Feb 2021 21:31:42 +0100 Subject: gnu: r-s4vectors: Update to 0.28.1. * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.28.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4d5d2d7df3..799507a3fe 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8028,13 +8028,13 @@ checks on R packages that are to be submitted to the Bioconductor repository.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.28.0") + (version "0.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "0rfn46g2mfda01s75vpcfn5jc7xkp0jrl5v79gyd40jm37p4j1zv")))) + "0fhf4lsfxrim7glazh6ng46ykzaly5ggwpg170vcz4cc24prv0rh")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) -- cgit v1.2.3 From 809f725977ac226974ca5d30087aeae5948deec3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Feb 2021 21:31:46 +0100 Subject: gnu: r-iranges: Update to 2.24.1. * gnu/packages/bioinformatics.scm (r-iranges): Update to 2.24.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 799507a3fe..7a242c0871 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8055,13 +8055,13 @@ S4Vectors package itself.") (define-public r-iranges (package (name "r-iranges") - (version "2.24.0") + (version "2.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "1lfc8xz45v63y3q40im00i944hi0p9idwhx50w3nzkwdpk79315b")))) + "01mx46a82vd3gz705pj0kk4wpxg683s8jqxchzjia3gz00b4qw52")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) -- cgit v1.2.3 From 8e25b1acf94d3bb45bc8e5705acd0803ef62dc36 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Feb 2021 21:31:49 +0100 Subject: gnu: r-edger: Update to 3.32.1. * gnu/packages/bioinformatics.scm (r-edger): Update to 3.32.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7a242c0871..96a2bb7595 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8137,13 +8137,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-edger (package (name "r-edger") - (version "3.32.0") + (version "3.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "0dkjd6li270icy1x5qbzpakk9bx712mdm5k32lrr3yrggq92jhjg")))) + "1gaic8qf6a6sy0bmydh1xzf52w0wnq31aanpvw3a30pfsi218bcp")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 9b66b8017d4eb663df674bcca610d4a0c601b7cb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Feb 2021 21:31:52 +0100 Subject: gnu: r-biomart: Update to 2.46.3. * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.46.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 96a2bb7595..56ec3968a4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8340,13 +8340,13 @@ annotation data packages using SQLite data storage.") (define-public r-biomart (package (name "r-biomart") - (version "2.46.0") + (version "2.46.3") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "1zpdm8nw1d0m31pdmzw1dccbd6iczfhiklhm4d325zkzf3jrkvxf")))) + "0gwmd0ykpv0gyh34c56g5m12lil20fvig49f3ih1jxrxf3q4wmq7")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) -- cgit v1.2.3 From 3f7e96acc72d69a1e1570baa6e35ed13fd004665 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Feb 2021 21:31:55 +0100 Subject: gnu: r-delayedarray: Update to 0.16.1. * gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.16.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 56ec3968a4..c87285734d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8475,13 +8475,13 @@ tab-delimited (tabix) files.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.16.0") + (version "0.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "1564wnradxw15nsnv6w2wd3xngcs3xa1mlibbq3hygi5fcx4fk3g")))) + "1d75zrhha1v7dhbvjp6a4iap441l5k268w0jjxklpqywbqns7l3d")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) -- cgit v1.2.3 From 2596200514761a306395af1791ad231cb168c4f1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Feb 2021 21:31:58 +0100 Subject: gnu: r-methylkit: Update to 1.16.1. * gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.16.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c87285734d..b363903402 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9771,13 +9771,13 @@ number detection tools.") (define-public r-methylkit (package (name "r-methylkit") - (version "1.16.0") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 - "11pmn191n0ga28x1w20cm2cmw8kddl29q6h2xfjjba5bspp2g613")))) + "1c9b11gfh3cc37iwym9rgsba3mh2xkp78a1gvnjqhzlkiz667mn3")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 5103da059a654d9aa9b0424aba1eeb593ec16892 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Feb 2021 21:32:01 +0100 Subject: gnu: r-msnbase: Update to 2.16.1. * gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.16.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b363903402..78aab44319 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10111,14 +10111,14 @@ structure (pcaRes) to provide a common interface to the PCA results.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.16.0") + (version "2.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "0cvcdmq1glifga5qwv9j3lgj31dcrcc6ql4kkk83jy4y43v2zxlx")))) + "0hxzs9zzljywqxr7q388hshpy1pdryhl0zkwffqbxpf5pcf92d3h")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 0e3e26ca600a35454480264ad51d73e9fffe6c2b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Feb 2021 21:32:04 +0100 Subject: gnu: r-gage: Update to 2.40.1. * gnu/packages/bioinformatics.scm (r-gage): Update to 2.40.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 78aab44319..1a0e72ac4a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10430,14 +10430,14 @@ microarrays or GRanges for sequencing data.") (define-public r-gage (package (name "r-gage") - (version "2.40.0") + (version "2.40.1") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "0xm50wgjjjymv71mbv1clnhx4m12nrd1pc6vfplpdqr5q49v3yd5")))) + "1iawa03dy4bl333my69d4sk7d74cjzfg5dpcxga6q5dglan4sp8r")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit v1.2.3 From 175bea0ca42dba3e02109820efae0cac2804e73b Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Thu, 11 Feb 2021 16:11:16 -0500 Subject: doc: Try to improve the branching workflow. * doc/contributing.texi (Submitting Patches): Introduce the use of "-frozen" branch names. --- doc/contributing.texi | 10 ++++++---- doc/guix.texi | 2 +- 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/doc/contributing.texi b/doc/contributing.texi index f167df067c..24f5cafe06 100644 --- a/doc/contributing.texi +++ b/doc/contributing.texi @@ -1086,10 +1086,12 @@ everything has been successfully built. This allows us to fix issues before they hit users, and to reduce the window during which pre-built binaries are not available. -Generally, branches other than @code{master} are considered -@emph{frozen} if there has been a recent evaluation, or there is a -corresponding @code{-next} branch. Please ask on the mailing list or -IRC if unsure where to place a patch. +When we decide to start building the @code{staging} or +@code{core-updates} branches, they will be renamed with the suffix +@code{-frozen}, at which time only bug fixes may be pushed to them. At +the same time, a corresponding branch suffixed with @code{-next} will be +created to accept patches for the next cycle. Please ask on the mailing +list or IRC if unsure where to place a patch. @c TODO: It would be good with badges on the website that tracks these @c branches. Or maybe even a status page. diff --git a/doc/guix.texi b/doc/guix.texi index 7d18703283..8944f5129d 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -28,7 +28,7 @@ Copyright @copyright{} 2014, 2015, 2016 Alex Kost@* Copyright @copyright{} 2015, 2016 Mathieu Lirzin@* Copyright @copyright{} 2014 Pierre-Antoine Rault@* Copyright @copyright{} 2015 Taylan Ulrich Bayırlı/Kammer@* -Copyright @copyright{} 2015, 2016, 2017, 2019, 2020 Leo Famulari@* +Copyright @copyright{} 2015, 2016, 2017, 2019, 2020, 2021 Leo Famulari@* Copyright @copyright{} 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus@* Copyright @copyright{} 2016 Ben Woodcroft@* Copyright @copyright{} 2016, 2017, 2018 Chris Marusich@* -- cgit v1.2.3 From 160e4a95e7ef0880939afca7d0af4c9b5596bc6b Mon Sep 17 00:00:00 2001 From: Mădălin Ionel Patrașcu Date: Thu, 11 Feb 2021 22:03:29 +0100 Subject: gnu: bowtie1: Update to 1.3.0. * gnu/packages/bioinformatics.scm (bowtie1): Update to 1.3.0. [arguments]: Set CC in make flags. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioinformatics.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1a0e72ac4a..6f835b3875 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1654,14 +1654,14 @@ gapped, local, and paired-end alignment modes.") (define-public bowtie1 (package (name "bowtie1") - (version "1.2.3") + (version "1.3.0") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/bowtie-bio/bowtie/" - version "/bowtie-src-x86_64.zip"


context:
space:
mode: