From bfa0d1e77351ee0be85c06595e6eb398731adde2 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:24:27 +0200 Subject: gnu: r-sva: Update to 3.24.4. * gnu/packages/bioinformatics.scm (r-sva): Update to 3.24.4. --- gnu/packages/bioinformatics.scm | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 909044f2fd..c4414ba8b5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8619,18 +8619,21 @@ (define-public r-copywriter (define-public r-sva (package (name "r-sva") - (version "3.24.0") + (version "3.24.4") (source (origin (method url-fetch) (uri (bioconductor-uri "sva" version)) (sha256 (base32 - "04pxl61iyc845wmqca1qv8kbb8zcp0qp72zgvgki3zzmrph9a362")))) + "0wcway4ai9im81xnrzb1vij2iidq5pw24qhjfgacmhxvx3dzhbsc")))) (build-system r-build-system) (propagated-inputs `(("r-genefilter" ,r-genefilter) - ("r-mgcv" ,r-mgcv))) + ("r-mgcv" ,r-mgcv) + ("r-biocparallel" ,r-biocparallel) + ("r-matrixstats" ,r-matrixstats) + ("r-limma" ,r-limma))) (home-page "http://bioconductor.org/packages/sva") (synopsis "Surrogate variable analysis") (description -- cgit v1.2.3 From 9eb2714625a68d5108e8371c8fef23c5694b631e Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:25:00 +0200 Subject: gnu: r-copywriter: Update to 2.8.1. * gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.8.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c4414ba8b5..678ce454b4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8579,14 +8579,14 @@ (define-public r-copyhelper (define-public r-copywriter (package (name "r-copywriter") - (version "2.8.0") + (version "2.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "CopywriteR" version)) (sha256 (base32 - "183nmrqmdf9syqljslvwv7mhs9ar5xizzq98imgsc80q0m25ncjf")))) + "0xgqnq5v5213b3nzvlmjysjb7w1bc0iblqpmzbjqn7n0ib0qyhbm")))) (properties `((upstream-name . "CopywriteR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 8cfaa9ab4e7b87dffc29e6f34e3ca81a48ff92f4 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:25:26 +0200 Subject: gnu: r-genomicfeatures: Update to 1.28.4. * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.28.4. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 678ce454b4..c68f0c4014 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7133,13 +7133,13 @@ (define-public r-rtracklayer (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.28.0") + (version "1.28.4") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "1pjxlr34ygv8pvfwpyq268wpgqzphiwpij85fyhjqdwdp0a253ik")))) + "01ylvg275iy0cvsbxkbfxcf9pi9al597v5wnlqi2xdpmrcxyc3q0")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) -- cgit v1.2.3 From 15afa9bf8f8e4a76ad03bb61e9c9e4e66d36bb5d Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:26:00 +0200 Subject: gnu: r-rtracklayer: Update to 1.36.4. * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.36.4. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c68f0c4014..5723947ab2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7088,13 +7088,13 @@ (define-public r-genomicalignments (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.36.0") + (version "1.36.4") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "0dv7p3wzmx57inznf6fb06417zcm48g7fpazyahxny7bqgzwq0ig")))) + "050q1rv04w31168ljr975vxva31n9lqdx84rnmsk6zcr6p640ffp")))) (build-system r-build-system) (arguments `(#:phases -- cgit v1.2.3 From 26760c80cd453d56fcd78dfeddb80b105a68792b Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:26:33 +0200 Subject: gnu: r-genomicalignments: Update to 1.12.1. * gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.12.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5723947ab2..993cb1c371 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7055,13 +7055,13 @@ (define-public r-summarizedexperiment (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.12.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "1aagyrdk5309a7awg42lg0bpirp91i6i2ddvpmrs38pzriwahnjy")))) + "127690sys4i5q3l4vxnjg4xg8q19qlw2258vgs5d1156w9ypp04h")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) -- cgit v1.2.3 From f41150f13d1dc956c78792aa69c0d7eaad14de19 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:26:55 +0200 Subject: gnu: r-summarizedexperiment: Update to 1.6.3. * gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.6.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 993cb1c371..c660898e5d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7024,13 +7024,13 @@ (define-public r-delayedarray (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.6.0") + (version "1.6.3") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "1szjbzzz4pyip891nji71caalxh0rhqiv7rpv6q54swlrqpfkqkw")))) + "0j7xn7pk52d383fb1wplcggacl2586c4zi0alkgfc3wz7qq9w13s")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) -- cgit v1.2.3 From adf5d0a0bc5d675a9ffff857f7121d6c49d26d75 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:27:16 +0200 Subject: gnu: r-delayedarray: Update to 0.2.7. * gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.2.7. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c660898e5d..a8b2f3c705 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6994,13 +6994,13 @@ (define-public r-rsamtools (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.2.0") + (version "0.2.7") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "0pcsk0f2dg2ldzprs1cccqrk53jrysmm6ccgjj5wh6z3x17g7g2r")))) + "02dfqp4md9xaqjj712ijc3jswghmipr5hwkd5hr0x1xi6l2fb69g")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) -- cgit v1.2.3 From 5077bc3e2e08135048b806a239b07f19b8398161 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:27:35 +0200 Subject: gnu: r-biostrings: Update to 2.44.2. * gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.44.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a8b2f3c705..60597cd9c8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6924,13 +6924,13 @@ (define-public r-biocparallel (define-public r-biostrings (package (name "r-biostrings") - (version "2.44.0") + (version "2.44.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "0ixgx12cx2z4n2khxq83crz9gc21qckj2v78y2p31567kfsw7clg")))) + "12c5abgshwq86357jr0r9039y6vl4d6ngysy89rsnr23ldnsirjp")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) -- cgit v1.2.3 From 1ff74d074ee06c1858daa7455a2103e542f14364 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:27:57 +0200 Subject: gnu: r-biocparallel: Update to 1.10.1. * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.10.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 60597cd9c8..3c9a42d8fe 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6900,13 +6900,13 @@ (define-public r-biomart (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "01ph0kq70b5gkd7n6a4myjlvwzgc0hi4xfwz8h17h06n9p5sdwa9")))) + "08mdfxyk9nwz77v0xhlvs19p2wj0phgm5c5b25vm0xh3749njsp0")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) -- cgit v1.2.3 From 0c6494a1db94b4d0816e4b1f705b11fbba77f197 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:28:16 +0200 Subject: gnu: r-biomart: Update to 2.32.1. * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.32.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3c9a42d8fe..15c40c9415 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6870,13 +6870,13 @@ (define-public r-annotationdbi (define-public r-biomart (package (name "r-biomart") - (version "2.32.0") + (version "2.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "0knkxh23vl9pa0by03xr6dy9aiah714cmf54jl828k51l9wv5l2j")))) + "0fhpbjlsgbqxrpj6nzhhk9q3ph81n5x4p7mmd097xjjn6b05w1d8")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) -- cgit v1.2.3 From 62eb93a7d07d7a744260476cc5060dd338d772ff Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:28:32 +0200 Subject: gnu: r-annotationdbi: Update to 1.38.2. * gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.38.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 15c40c9415..6ea12caa1b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6843,13 +6843,13 @@ (define-public r-biobase (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.38.0") + (version "1.38.2") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "1xffm98s817mfc827cnr0by6167nlrl1glxzjawzz0rkghs41g27")))) + "1lsamnbf07zzsy5asy5hn97n2a4layv58w2bzd90ikcdx0gmzarj")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) -- cgit v1.2.3 From 1898a7832fbd6d103b5e2fba07f502588b7fe0c8 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:30:27 +0200 Subject: gnu: r-biobase: Update to 2.36.2. * gnu/packages/bioinformatics.scm (r-biobase): Update to 2.36.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6ea12caa1b..f09399e571 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6821,13 +6821,13 @@ (define-public r-genomicranges (define-public r-biobase (package (name "r-biobase") - (version "2.36.0") + (version "2.36.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 - "0x7pf5xsdcj12dbf5qqki2c6bd5madqg2fbiq5xgisarpc9v6c1m")))) + "0sr48nqx5bqid4g6lr9zr9286xh842w717yvmssvddb5xxynib6f")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) -- cgit v1.2.3 From 1b4738e23c88acdb89875c9247101e00514445e0 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:30:49 +0200 Subject: gnu: r-limma: Update to 3.32.5. * gnu/packages/bioinformatics.scm (r-limma): Update to 3.32.5. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f09399e571..947e8000e3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6737,13 +6737,13 @@ (define-public r-variantannotation (define-public r-limma (package (name "r-limma") - (version "3.32.0") + (version "3.32.5") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "0q7rqm86nwq0rg4fjggfr7xqybjrxj425vni3cva70b4c8d1h425")))) + "0p2ayha9g9w5r8s7pgdf16mkmdbqwh6f35jh07g3b8gyra48gwiw")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") -- cgit v1.2.3 From 48f5d283b2c38e8ea3958fc141df5a630e2f267c Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:31:08 +0200 Subject: gnu: r-variantannotation: Update to 1.22.3. * gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.22.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 947e8000e3..bace3de0e5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6699,13 +6699,13 @@ (define-public r-edger (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.22.0") + (version "1.22.3") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "05hpm4as36kvpiqhgnkfjwfx0a05p304c21ggba29iac4nanm8b3")))) + "0sr3vdn85x5zdxh80cfwlpfdpi2hmjy3fwi00ac3jya4v145vawr")))) (properties `((upstream-name . "VariantAnnotation"))) (inputs -- cgit v1.2.3 From 6252dd0f15925969d317fcf7b26940e7ec350bd8 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:31:28 +0200 Subject: gnu: r-genomeinfodb: Update to 1.12.2. * gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.12.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bace3de0e5..d866510960 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6644,13 +6644,13 @@ (define-public r-genomeinfodbdata (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.12.0") + (version "1.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "1bwwhscjl376a5p43mx8ijrqajxmgypbqhv049pgagl22hkkf0y3")))) + "1hjxgmcnrngp1307ipqaq9hgxz4j0ldn7d46knhzs30k2r4qnrfp")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) -- cgit v1.2.3 From 3ec25eb2a8d10bab2e5a7c2efdaea49d435b0840 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:31:46 +0200 Subject: gnu: r-iranges: Update to 2.10.2. * gnu/packages/bioinformatics.scm (r-iranges): Update to 2.10.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d866510960..6e323d3890 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6592,13 +6592,13 @@ (define-public r-seqinr (define-public r-iranges (package (name "r-iranges") - (version "2.10.0") + (version "2.10.2") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "0zp4mxm9h1p4krj7m7cinkvwa2ibqkq59jwpan97yvhb4z8q0d6n")))) + "1brmzs3rsf97gymridrh9c9r3vws8b3rpghaanxnniw36lmcajfy")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) -- cgit v1.2.3 From 9c4348d8c4532c63879ac3ea076ac255124328fb Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:32:11 +0200 Subject: gnu: r-dnacopy: Update to 1.50.1. * gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.50.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6e323d3890..4c21a21383 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6518,13 +6518,13 @@ (define-public r-optparse (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.50.0") + (version "1.50.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "0112ry62z18m7rdyrn3gvbxq2f6m44cawhcfb1f02z9xzlsj0k28")))) + "0f0x83db7rm5xf9fg5pjhvs4i165qqaf01lbwb8kj13fsqpwx15p")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) -- cgit v1.2.3 From 0ff478344bcbc81993395c3cb2dc81771753a1ed Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:32:31 +0200 Subject: gnu: r-biocstyle: Update to 2.4.1. * gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.4.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4c21a21383..8a9bd9c660 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6401,13 +6401,13 @@ (define-public r-bookdown (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.4.0") + (version "2.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "1n2c8rj920wmk3q2khmjfnhn5i4b3lmhx1whnghk0zk3jf88hvbi")))) + "0bmgmsfll923v573g0kyzlmjd7gly5jwgd8vkrcwvbam1gz75f2c")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) -- cgit v1.2.3 From bd4a0bab5f8eb89e39884f890ea8462366b5b93a Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:32:46 +0200 Subject: gnu: r-category: Update to 2.42.1. * gnu/packages/bioinformatics.scm (r-category): Update to 2.42.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8a9bd9c660..c856c5065d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5867,14 +5867,14 @@ (define-public r-gseabase (define-public r-category (package (name "r-category") - (version "2.42.0") + (version "2.42.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Category" version)) (sha256 (base32 - "0swcmihyjg0fhaaydl9hm24aj9zffw3bibza9y6sqs6jaqd97f09")))) + "1w186nhc85bglcgmbcrsdbb8l6rph21pl5kdwjqwkp0jnr9z0ifn")))) (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From fd215c2978cc0abe5aca85b647446c2e8a947284 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:33:07 +0200 Subject: gnu: r-annotationforge: Update to 1.18.1. * gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.18.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c856c5065d..4a8edad777 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5789,14 +5789,14 @@ (define-public r-deseq2 (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "01kd86vvgpa4a5zivcy4g6z8rhcykasdskrz8yqsqz211sd1xsr3")))) + "1366qvykd9cpcvwgc5g9mm9adw9rxw6p4814dd6l5fyb0pwpmysx")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) -- cgit v1.2.3 From f1915a5dd09bb18d06b57b118efd8a537e9754ce Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Wed, 2 Aug 2017 00:33:23 +0200 Subject: gnu: r-deseq2: Update to 1.16.1. * gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.16.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4a8edad777..b47d13ea55 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5752,14 +5752,14 @@ (define-public r-genefilter (define-public r-deseq2 (package (name "r-deseq2") - (version "1.16.0") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "0m0apn3xi4kdkinsj4xkw5cwysicyjr6xxlxhpa4scyv589am1s5")))) + "01pvyljxkwazxl510v7h0971nx65iqd2bdkbdhw3xzind0n9pdvq")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 92971d68ac942cd4a38092b4ccb20a8192a56aaf Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Thu, 3 Aug 2017 20:37:25 +1000 Subject: gnu: htseq: Update to 0.9.1. * gnu/packages/bioinformatics.scm (htseq): Update to 0.9.1. [arguments]: Use python-3 by removing field. [native-inputs]: Add 'python-cython'. [propagated-inputs]: Use python3 numpy package. [inputs]: Use python3 pysam package. Add 'python-matplotlib'. (python2-htseq): New variable. (clipper)[inputs]: Use it. --- gnu/packages/bioinformatics.scm | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b47d13ea55..4de245abe6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1636,7 +1636,7 @@ (define-public clipper (build-system python-build-system) (arguments `(#:python ,python-2)) ; only Python 2 is supported (inputs - `(("htseq" ,htseq) + `(("htseq" ,python2-htseq) ("python-pybedtools" ,python2-pybedtools) ("python-cython" ,python2-cython) ("python-scikit-learn" ,python2-scikit-learn) @@ -2981,7 +2981,7 @@ (define-public hmmer (define-public htseq (package (name "htseq") - (version "0.6.1") + (version "0.9.1") (source (origin (method url-fetch) (uri (string-append @@ -2989,14 +2989,16 @@ (define-public htseq version ".tar.gz")) (sha256 (base32 - "1i85ppf2j2lj12m0x690qq5nn17xxk23pbbx2c83r8ayb5wngzwv")))) + "11flgb1381xdhk43bzbfm3vhnszkpqg6jk76rpa5xd1zbrvvlnxg")))) (build-system python-build-system) - (arguments `(#:python ,python-2)) ; only Python 2 is supported + (native-inputs + `(("python-cython" ,python-cython))) ;; Numpy needs to be propagated when htseq is used as a Python library. (propagated-inputs - `(("python-numpy" ,python2-numpy))) + `(("python-numpy" ,python-numpy))) (inputs - `(("python-pysam" ,python2-pysam))) + `(("python-pysam" ,python-pysam) + ("python-matplotlib" ,python-matplotlib))) (home-page "http://www-huber.embl.de/users/anders/HTSeq/") (synopsis "Analysing high-throughput sequencing data with Python") (description @@ -3004,6 +3006,9 @@ (define-public htseq from high-throughput sequencing assays.") (license license:gpl3+))) +(define-public python2-htseq + (package-with-python2 htseq)) + (define-public java-htsjdk (package (name "java-htsjdk") -- cgit v1.2.3 From 75e6639f364d77378edbc10022bca09040336a56 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Thu, 3 Aug 2017 21:08:13 +1000 Subject: gnu: htseq: Use PyPI URI. This is a follow-up to 92971d68ac942cd4a38092b4ccb20a8192a56aaf. * gnu/packages/bioinformatics.scm (htseq)[source]: Use 'pypi-uri'. --- gnu/packages/bioinformatics.scm | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4de245abe6..e3c3bbc52f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2984,9 +2984,7 @@ (define-public htseq (version "0.9.1") (source (origin (method url-fetch) - (uri (string-append - "https://pypi.python.org/packages/source/H/HTSeq/HTSeq-" - version ".tar.gz")) + (uri (pypi-uri "HTSeq" version)) (sha256 (base32 "11flgb1381xdhk43bzbfm3vhnszkpqg6jk76rpa5xd1zbrvvlnxg")))) -- cgit v1.2.3 From 3f6ec083ecfd698f85841d04efe5f15794b2f75e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:29:47 +0200 Subject: gnu: r-bookdown: Update to 0.4. * gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.4. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e3c3bbc52f..8e1da7c4a9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6382,13 +6382,13 @@ (define-public r-biocviews (define-public r-bookdown (package (name "r-bookdown") - (version "0.3") + (version "0.4") (source (origin (method url-fetch) (uri (cran-uri "bookdown" version)) (sha256 (base32 - "0r9bchzg7im6psc3jphvshzbidc5bv5xaih1qg7b5518jy4iyvb9")))) + "1fp1k7hivrb7s2dwgrsqy9s7xg6pk9hczhrc149y1dwh901j6qvv")))) (build-system r-build-system) (propagated-inputs `(("r-htmltools" ,r-htmltools) -- cgit v1.2.3 From 7150f1c30c6f3da0114b56332d9860473c48760e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:30:08 +0200 Subject: gnu: r-optparse: Update to 1.4.4. * gnu/packages/bioinformatics.scm (r-optparse): Update to 1.4.4. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8e1da7c4a9..19826a333e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6498,14 +6498,14 @@ (define-public r-getopt (define-public r-optparse (package (name "r-optparse") - (version "1.3.2") + (version "1.4.4") (source (origin (method url-fetch) (uri (cran-uri "optparse" version)) (sha256 (base32 - "1g8as89r91xxi5j5azsd6vrfrhg84mnfx2683j7pacdp8s33radw")))) + "1ff4wmsszrb3spwfp7ynfs8w11qpy1sdzfxm1wk8dqqvdwris7qb")))) (build-system r-build-system) (propagated-inputs `(("r-getopt" ,r-getopt))) -- cgit v1.2.3 From 023aa8ff5839a295b4b42287ba50713775866131 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:30:31 +0200 Subject: gnu: r-seqinr: Update to 3.4-5. * gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.4-5. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 19826a333e..ccb31d0960 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6570,14 +6570,14 @@ (define-public r-s4vectors (define-public r-seqinr (package (name "r-seqinr") - (version "3.3-6") + (version "3.4-5") (source (origin (method url-fetch) (uri (cran-uri "seqinr" version)) (sha256 (base32 - "13d0qxm2244wgdl2dy2s8vnrnf5fx4n47if9gkb49dqx6c0sx8s2")))) + "17zv0n5cji17izwmwg0jcbxbjl3w5rls91w15svcnlpxjms38ahn")))) (build-system r-build-system) (propagated-inputs `(("r-ade4" ,r-ade4) -- cgit v1.2.3 From c8a9b2bcbff2d78609f8d34ad4d9ca41f17f4602 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:30:59 +0200 Subject: gnu: r-qtl: Update to 1.41-6. * gnu/packages/bioinformatics.scm (r-qtl): Update to 1.41-6. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ccb31d0960..907309d591 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7815,7 +7815,7 @@ (define-public r-motifrg (define-public r-qtl (package (name "r-qtl") - (version "1.40-8") + (version "1.41-6") (source (origin (method url-fetch) @@ -7823,7 +7823,7 @@ (define-public r-qtl version ".tar.gz")) (sha256 (base32 - "05bj1x2ry0i7yqiydlswb3d2h4pxg70z8w1072az1mrv1m54k8sp")))) + "067az4v432zxp6lxck8d7vlh9w4r13r0mvw5zsglyaqwsh3d9sad")))) (build-system r-build-system) (home-page "http://rqtl.org/") (synopsis "R package for analyzing QTL experiments in genetics") -- cgit v1.2.3 From 4e0c847d5965d86d334d04458387cedbd5b4e9d4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:31:27 +0200 Subject: gnu: r-wgcna: Update to 1.60. * gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.60. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 907309d591..76dfc88cbb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8065,14 +8065,14 @@ (define-public r-mutationalpatterns (define-public r-wgcna (package (name "r-wgcna") - (version "1.51") + (version "1.60") (source (origin (method url-fetch) (uri (cran-uri "WGCNA" version)) (sha256 (base32 - "0hzvnhw76vwg8bl8x368f0c5szpwb8323bmrb3bir93i5bmfjsxx")))) + "16mxhwzhh5q48wmz1iba2r21cp0n0v8g11am4pi52iv6g0663ixl")))) (properties `((upstream-name . "WGCNA"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 5e0de298926e3a4d6e444f91427e240cd1c3c4cc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 3 Aug 2017 17:31:50 +0200 Subject: gnu: r-seqminer: Update to 6.0. * gnu/packages/bioinformatics.scm (r-seqminer): Update to 6.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 76dfc88cbb..768f0897a4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8652,14 +8652,14 @@ (define-public r-sva (define-public r-seqminer (package (name "r-seqminer") - (version "5.9") + (version "6.0") (source (origin (method url-fetch) (uri (cran-uri "seqminer" version)) (sha256 (base32 - "0sfkxrc9gy5a8fadzyzfzh7l5grasm8cj6cd2nnpv85ws6mqr6qd")))) + "057j1l6dip35l1aivilapl2zv9db677b3di2pb3sfgq2sxg0ps3l")))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) -- cgit v1.2.3 From 7cb6155088ee10300d0247077b3bf48089912e86 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 3 Aug 2017 21:39:12 +0300 Subject: gnu: bioinformatics.scm: Use (gnu packages cran) module. This is a follow up to a8cba9dd112528d67a946eee057c838221eb5249. * gnu/packages/bioinformatics.scm: Add (gnu packages cran) to #:use-modules. --- gnu/packages/bioinformatics.scm | 1 + 1 file changed, 1 insertion(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 768f0897a4..3ec8b5ec71 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -48,6 +48,7 @@ (define-module (gnu packages bioinformatics) #:use-module (gnu packages boost) #:use-module (gnu packages compression) #:use-module (gnu packages cpio) + #:use-module (gnu packages cran) #:use-module (gnu packages curl) #:use-module (gnu packages documentation) #:use-module (gnu packages databases) -- cgit v1.2.3