From 975cfe26e185d3edff24fb1cd99733a845885d00 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 1 Mar 2020 19:14:07 +0100 Subject: gnu: r-gkmsvm: Update to 0.80.0. * gnu/packages/bioconductor.scm (r-gkmsvm): Update to 0.80.0. [propagated-inputs]: Remove r-biocgenerics, r-biostrings, r-genomeinfodb, r-iranges, r-rtracklayer, and r-s4vectors. --- gnu/packages/bioconductor.scm | 13 +++---------- 1 file changed, 3 insertions(+), 10 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e14f7bc93e..9697e9846a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3221,27 +3221,20 @@ (define-public r-ioniser (define-public r-gkmsvm (package (name "r-gkmsvm") - (version "0.79.0") + (version "0.80.0") (source (origin (method url-fetch) (uri (cran-uri "gkmSVM" version)) (sha256 (base32 - "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3")))) + "0ljcga246ad0ql8x3drvrdsyp0f20mgp3p6lnl79xb76qgfdnm0p")))) (properties `((upstream-name . "gkmSVM"))) (build-system r-build-system) (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-kernlab" ,r-kernlab) + `(("r-kernlab" ,r-kernlab) ("r-rcpp" ,r-rcpp) ("r-rocr" ,r-rocr) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) ("r-seqinr" ,r-seqinr))) (home-page "https://cran.r-project.org/web/packages/gkmSVM") (synopsis "Gapped-kmer support vector machine") -- cgit v1.2.3 From 8351faae8a4252cf1848bb845e8fcbd284ede156 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 1 Mar 2020 23:38:06 +0100 Subject: gnu: r-chippeakanno: Update to 3.20.1. * gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.20.1. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 9697e9846a..63e2d8bbe0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1648,14 +1648,14 @@ (define-public r-codedepends (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.20.0") + (version "3.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "0hp3s3shnrb55cxvx9wrdl67wqw9f55gdgx7262s4mahpxjswfsa")))) + "0kmfha4vprbi0z6n7v9w28xfrqcx5qad7yfr0b316j5aj8v9f4hc")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From aece78fe2fa2add8e0589e0529cc8ff5a213e30b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 1 Mar 2020 23:38:12 +0100 Subject: gnu: r-biocneighbors: Update to 1.4.2. * gnu/packages/bioconductor.scm (r-biocneighbors): Update to 1.4.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 63e2d8bbe0..5add7db8a1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2216,14 +2216,14 @@ (define-public r-ruvseq (define-public r-biocneighbors (package (name "r-biocneighbors") - (version "1.4.1") + (version "1.4.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocNeighbors" version)) (sha256 (base32 - "05vi1cij37s8wgj92k3l6a3f3dwldj8jvijdp4695zczka6kypdf")))) + "1bx7i5pifj8w89fnhfgcfgcar2ik2ad8wqs2rix7yks90vz185i6")))) (properties `((upstream-name . "BiocNeighbors"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 0a30342defe32d27049064491dc795570fd0f9fb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 1 Mar 2020 23:38:19 +0100 Subject: gnu: r-mlinterfaces: Update to 1.66.4. * gnu/packages/bioconductor.scm (r-mlinterfaces): Update to 1.66.4. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5add7db8a1..590ab80592 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3605,14 +3605,14 @@ (define-public r-clusterprofiler (define-public r-mlinterfaces (package (name "r-mlinterfaces") - (version "1.66.2") + (version "1.66.4") (source (origin (method url-fetch) (uri (bioconductor-uri "MLInterfaces" version)) (sha256 (base32 - "1wc280iw9vllg6f58vsdj895yaqs8w42kl7jk8sgii009gwlaj8d")))) + "19hlicdndy2p45y7w91gnwi3wgq5s465a646z3qqk8gmn5sn614q")))) (properties `((upstream-name . "MLInterfaces"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From e766ba9a52ba3551339e97700ee6b96fc8193a2d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 1 Mar 2020 23:38:26 +0100 Subject: gnu: r-cicero: Update to 1.4.2. * gnu/packages/bioconductor.scm (r-cicero): Update to 1.4.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 590ab80592..47a94fce93 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6021,14 +6021,14 @@ (define-public r-rcistarget (define-public r-cicero (package (name "r-cicero") - (version "1.4.1") + (version "1.4.2") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 - "07g6r335zqqy3r5v4x4glxdrcsq9bjhs9jmgvppiggv1h630a22w")))) + "154djqd32w87814ycfmfz27ikp17bnampvmvw5hzi5p2x9l3h82r")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) -- cgit v1.2.3 From 5f5e0830f6f74b8806dfd3d3f85dde50f44b3c15 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 1 Mar 2020 23:38:33 +0100 Subject: gnu: r-multiassayexperiment: Update to 1.12.3. * gnu/packages/bioconductor.scm (r-multiassayexperiment): Update to 1.12.3. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 47a94fce93..06027285a1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -7290,14 +7290,14 @@ (define-public r-experimenthub (define-public r-multiassayexperiment (package (name "r-multiassayexperiment") - (version "1.12.2") + (version "1.12.3") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiAssayExperiment" version)) (sha256 (base32 - "0722f3jl1xq8k8w7vrv986jd16bgysqp3n07pgmdn0hh1zh2mcqc")))) + "1vf6l88j3n6109j6sd08wfqxqpj2k20dvr8ll9zl1szsn18b4gny")))) (properties `((upstream-name . "MultiAssayExperiment"))) (build-system r-build-system) -- cgit v1.2.3 From b69c770305edee747ade8c8d6940115d80d33e79 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 2 Mar 2020 21:30:33 +0100 Subject: gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Update to 3.10.0. * gnu/packages/bioconductor.scm (r-txdb-mmusculus-ucsc-mm10-knowngene): Update to 3.10.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioconductor.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 06027285a1..63687036fc 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -618,14 +618,14 @@ (define-public r-txdb-mmusculus-ucsc-mm9-knowngene (define-public r-txdb-mmusculus-ucsc-mm10-knowngene (package (name "r-txdb-mmusculus-ucsc-mm10-knowngene") - (version "3.4.7") + (version "3.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene" version 'annotation)) (sha256 (base32 - "04impkl8zh1gpwwrpbf19jqznsjrq2306yyhm6cmx6hr1401bd6b")))) + "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9")))) (properties `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene"))) (build-system r-build-system) -- cgit v1.2.3