From d5452aa201a2f297e503658576ee99a7c070787c Mon Sep 17 00:00:00 2001 From: Clément Lassieur Date: Sat, 2 Jun 2018 12:54:16 +0200 Subject: gnu: emacs-elfeed: Update to 3.0.0. * gnu/packages/emacs.scm (emacs-elfeed): Update to 3.0.0. --- gnu/packages/emacs.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/emacs.scm b/gnu/packages/emacs.scm index 4aafb7355e..7694d2410b 100644 --- a/gnu/packages/emacs.scm +++ b/gnu/packages/emacs.scm @@ -4170,7 +4170,7 @@ (define-public emacs-projectile (define-public emacs-elfeed (package (name "emacs-elfeed") - (version "2.3.0") + (version "3.0.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/skeeto/elfeed/archive/" @@ -4178,7 +4178,7 @@ (define-public emacs-elfeed (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1fd1mx0q1qb9vgdzls5ppxfriyid48blg8smgjspiazp7kxakzxv")))) + "1wkdrxr6zzqb48czqqv34l87bx8aqjk1739ddqg933aqh241kfvn")))) (build-system emacs-build-system) (arguments `(#:tests? #t -- cgit v1.2.3 From d22546cf80696719cfb76aec2ffdf44863be3fbc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 1 Jun 2018 17:10:48 +0200 Subject: gnu: r-minimal: Update to 3.5.0. * gnu/packages/statistics.scm (r-with-tests): New variable derived from r-minimal; update to 3.5.0. [arguments]: Build recommended packages. (r-minimal): Inherit from r-with-tests. [arguments]: Disable recommended packages and tests. --- gnu/packages/statistics.scm | 29 ++++++++++++++++++++--------- 1 file changed, 20 insertions(+), 9 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 7d5c552a3e..7a6b674a1d 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -113,10 +113,10 @@ (define-public pspp ;; Update this package together with the set of recommended packages: r-boot, ;; r-class, r-cluster, r-codetools, r-foreign, r-kernsmooth, r-lattice, ;; r-mass, r-matrix, r-mgcv, r-nlme, r-nnet, r-rpart, r-spatial, r-survival. -(define-public r-minimal +(define r-with-tests (package - (name "r-minimal") - (version "3.4.4") + (name "r-with-tests") + (version "3.5.0") (source (origin (method url-fetch) (uri (string-append "mirror://cran/src/base/R-" @@ -124,7 +124,7 @@ (define-public r-minimal version ".tar.gz")) (sha256 (base32 - "0dq3jsnwsb5j3fhl0wi3p5ycv8avf8s5j1y4ap3d2mkjmcppvsdk")))) + "0w38865laqg28cdhikxdxhx4rfp0kgcn72gakwypsy91br9ja5zx")))) (build-system gnu-build-system) (arguments `(#:disallowed-references (,tzdata-for-tests) @@ -217,11 +217,9 @@ (define-public r-minimal (add-after 'build 'install-info (lambda _ (zero? (system* "make" "install-info"))))) #:configure-flags - `(;; Do not build the recommended packages. The build system creates - ;; random temporary directories and embeds their names in some - ;; package files. We build these packages with the r-build-system - ;; instead. - "--without-recommended-packages" + `(;; We build the recommended packages here, because they are needed in + ;; order to run the test suite. We disable them in the r-minimal + ;; package. "--with-cairo" "--with-blas=-lopenblas" "--with-libpng" @@ -292,6 +290,19 @@ (define-public r-minimal available, greatly increasing its breadth and scope.") (license license:gpl3+))) +(define-public r-minimal + (package (inherit r-with-tests) + (name "r-minimal") + (arguments + `(#:tests? #f + ,@(substitute-keyword-arguments (package-arguments r-with-tests) + ((#:configure-flags flags) + ;; Do not build the recommended packages. The build system creates + ;; random temporary directories and embeds their names in some + ;; package files. We build these packages with the r-build-system + ;; instead. + `(cons "--without-recommended-packages" ,flags))))))) + (define-public rmath-standalone (package (inherit r-minimal) (name "rmath-standalone") -- cgit v1.2.3 From 2f5b3d8e90105b40695e33398b985c278410e5cf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:40:06 +0200 Subject: gnu: r-hpar: Update to 1.22.2. * gnu/packages/bioconductor.scm (r-hpar): Update to 1.22.2. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 788e1e7def..5ae4fc1ac2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -64,14 +64,14 @@ (define-public r-bsgenome-dmelanogaster-ucsc-dm6 (define-public r-hpar (package (name "r-hpar") - (version "1.20.0") + (version "1.22.2") (source (origin (method url-fetch) (uri (bioconductor-uri "hpar" version)) (sha256 (base32 - "0s5v79mgxdx862v1jrdf5pdap81nz5vjx25ni8s3sl97ldckf6j8")))) + "1b72hvzasf6q739gmx6jblbzzyq22l7crrkbbfkihv3v7s94g388")))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/hpar/") (synopsis "Human Protein Atlas in R") -- cgit v1.2.3 From 72427c721dae18e8fc176c5bd29b3977ccab6dc3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:40:22 +0200 Subject: gnu: r-regioner: Update to 1.12.0. * gnu/packages/bioconductor.scm (r-regioner): Update to 1.12.0. [propagated-inputs]: Add r-s4vectors. --- gnu/packages/bioconductor.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5ae4fc1ac2..d1e39bc16c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -82,14 +82,14 @@ (define-public r-hpar (define-public r-regioner (package (name "r-regioner") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 - "1vprp3l929hwzmvgskbhawfgnrymwc9n2rxd16rgagnv1dxnjxfp")))) + "09bzlaqdgy7wmzly3zc9y2da50d07mlixlnpaxdxpiwdk8qmhxsb")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs @@ -98,7 +98,8 @@ (define-public r-regioner ("r-bsgenome" ,r-bsgenome) ("r-rtracklayer" ,r-rtracklayer) ("r-genomeinfodb" ,r-genomeinfodb) - ("r-iranges" ,r-iranges))) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors))) (home-page "https://bioconductor.org/packages/regioneR/") (synopsis "Association analysis of genomic regions") (description "This package offers a statistical framework based on -- cgit v1.2.3 From 45bbccf4e7393822a547cdabfcbd8d7b963e1e88 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:40:51 +0200 Subject: gnu: r-diffbind: Update to 2.8.0. * gnu/packages/bioconductor.scm (r-diffbind): Update to 2.8.0. [propagated-inputs]: Add r-genomicranges, r-ggplot2, and r-summarizedexperiment. --- gnu/packages/bioconductor.scm | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d1e39bc16c..5baf390fea 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -110,14 +110,14 @@ (define-public r-regioner (define-public r-diffbind (package (name "r-diffbind") - (version "2.6.6") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "1sm5h6nq77hjfis6kr1nqyizcxgfz87dgpqc4fxlfqkmsd9n3vkp")))) + "1w1hybzd732ccg3q8zhirwfilq8sx3frv1x98zfyj3svzw98fish")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (inputs @@ -129,6 +129,8 @@ (define-public r-diffbind ("r-dplyr" ,r-dplyr) ("r-edger" ,r-edger) ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) ("r-ggrepel" ,r-ggrepel) ("r-gplots" ,r-gplots) ("r-iranges" ,r-iranges) @@ -139,6 +141,7 @@ (define-public r-diffbind ("r-rcpp" ,r-rcpp) ("r-rsamtools" ,r-rsamtools) ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-systempiper" ,r-systempiper) ("r-zlibbioc" ,r-zlibbioc))) (home-page "http://bioconductor.org/packages/DiffBind") -- cgit v1.2.3 From 43734b47279b7e0d689297aff614b53b61495569 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:41:30 +0200 Subject: gnu: r-ripseeker: Update to 1.20.0. * gnu/packages/bioconductor.scm (r-ripseeker): Update to 1.20.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5baf390fea..16b5e71452 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -155,14 +155,14 @@ (define-public r-diffbind (define-public r-ripseeker (package (name "r-ripseeker") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RIPSeeker" version)) (sha256 (base32 - "0bqkzwrncww7il36273chkd3gfxmii7p566ycki9qij419pwr35y")))) + "0y9cvzqslfxj3z9mnp47mknff0pky2g5x8x1z1s5yjcx35q89xfi")))) (properties `((upstream-name . "RIPSeeker"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From f794e85daa8c401ab22b5bdacd897ccf9ea3b266 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:41:47 +0200 Subject: gnu: r-chippeakanno: Update to 3.14.0. * gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.14.0. [propagated-inputs]: Add r-biostrings, r-delayedarray, r-genomicranges, r-iranges, and r-s4vectors. --- gnu/packages/bioconductor.scm | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 16b5e71452..536349049c 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -226,23 +226,27 @@ (define-public r-multtest (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.12.7") + (version "3.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "1zab489d7a6bh6ylc68x6yn47gdkmr7p3677grx9l2qafrryjr04")))) + "1kcnc3cnmrhdk1x7q3y6zsz09pgd3xn9xy1hfbxz48cajlb18ad0")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-delayedarray" ,r-delayedarray) ("r-go-db" ,r-go-db) ("r-biomart" ,r-biomart) ("r-bsgenome" ,r-bsgenome) ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) ("r-genomeinfodb" ,r-genomeinfodb) + ("r-iranges" ,r-iranges) ("r-matrixstats" ,r-matrixstats) ("r-annotationdbi" ,r-annotationdbi) ("r-limma" ,r-limma) @@ -254,6 +258,7 @@ (define-public r-chippeakanno ("r-dbi" ,r-dbi) ("r-ensembldb" ,r-ensembldb) ("r-biobase" ,r-biobase) + ("r-s4vectors" ,r-s4vectors) ("r-seqinr" ,r-seqinr) ("r-idr" ,r-idr) ("r-genomicalignments" ,r-genomicalignments) -- cgit v1.2.3 From 674870888323c54983cf6d7a4c3b387a7cb598d4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:42:34 +0200 Subject: gnu: r-marray: Update to 1.58.0. * gnu/packages/bioconductor.scm (r-marray): Update to 1.58.0. [propagated-inputs]: Remove r-biobase. --- gnu/packages/bioconductor.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 536349049c..443480c4bd 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -281,16 +281,15 @@ (define-public r-chippeakanno (define-public r-marray (package (name "r-marray") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "marray" version)) (sha256 - (base32 "14c93i86yc7jn4ax8p4l0z6v9xisw1bv7gzb4a0gbxhxn7mddaic")))) + (base32 "0539flh3y1qy5b1bamkfwbskis765c5s33v1y9j51n33mxb9h08d")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-limma" ,r-limma))) + `(("r-limma" ,r-limma))) (home-page "http://bioconductor.org/packages/marray") (synopsis "Exploratory analysis for two-color spotted microarray data") (description "This package contains class definitions for two-color spotted -- cgit v1.2.3 From 205df4a4cba69354f6a171a6de98a09ac5fcc170 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:42:55 +0200 Subject: gnu: r-cghbase: Update to 1.40.0. * gnu/packages/bioconductor.scm (r-cghbase): Update to 1.40.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 443480c4bd..a7dc553ec5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -300,12 +300,12 @@ (define-public r-marray (define-public r-cghbase (package (name "r-cghbase") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHbase" version)) (sha256 - (base32 "0fynvcsjdbgp69i0nxrc8ni58rhb1kx9k5r3nb91n9i8s43gjqlm")))) + (base32 "1hf44vma3kgwr61kjbszvfxkava8bjqnam1mdncqvczbypb2xwaq")))) (properties `((upstream-name . "CGHbase"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 5c0df206cf2a553cfffb7fd61315673354de1680 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:43:06 +0200 Subject: gnu: r-cghcall: Update to 2.42.0. * gnu/packages/bioconductor.scm (r-cghcall): Update to 2.42.0. --- gnu/packages/bioconductor.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a7dc553ec5..0235f100e2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -320,12 +320,12 @@ (define-public r-cghbase (define-public r-cghcall (package (name "r-cghcall") - (version "2.40.0") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHcall" version)) (sha256 - (base32 "11pi6awz3858yb4s0z3qf3kcmsdgp6d4aj41g4lfix1sv5amllch")))) + (base32 "0y71vfxv9x0am3xvv520yr95cb7m7y92dhdx1vkqki80jrmf12dz")))) (properties `((upstream-name . "CGHcall"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 81b0181b6f3dff9c4a9142c467528aaab7e5f95b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:43:18 +0200 Subject: gnu: r-qdnaseq: Update to 1.16.0. * gnu/packages/bioconductor.scm (r-qdnaseq): Update to 1.16.0. [propagated-inputs]: Add r-biocparallel. --- gnu/packages/bioconductor.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0235f100e2..ed35b4c61a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -343,16 +343,17 @@ (define-public r-cghcall (define-public r-qdnaseq (package (name "r-qdnaseq") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QDNAseq" version)) (sha256 - (base32 "0lgbv4s0xqgrs7q6ynb3c273sf7pyrp51jnc8ravq1z5g0a2zshy")))) + (base32 "1pj69mfyxwfd0d7h4kls9xq96sdc55y3rv20qpla50hw9libcwwd")))) (properties `((upstream-name . "QDNAseq"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) + ("r-biocparallel" ,r-biocparallel) ("r-cghbase" ,r-cghbase) ("r-cghcall" ,r-cghcall) ("r-dnacopy" ,r-dnacopy) -- cgit v1.2.3 From 02be818044278cb5376f9ec53c68f12899bf43ff Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:43:41 +0200 Subject: gnu: r-annotate: Update to 1.58.0. * gnu/packages/bioinformatics.scm (r-annotate): Update to 1.58.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e0bfaac06e..632a74cea0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6149,14 +6149,14 @@ (define-public r-vegan (define-public r-annotate (package (name "r-annotate") - (version "1.56.2") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotate" version)) (sha256 (base32 - "0ybg9k1s289h15nj1kp9821i1rsk1gkn8i8blplmk7gsgpbw1f42")))) + "1qmncyvy147a1ll3iri45p822kcs3s7583jfnq9jf6sz9ilk8cjf")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit v1.2.3 From 14e9235f0ceed6191a936c66dfe93b895ad6ef47 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:43:54 +0200 Subject: gnu: r-copynumber: Update to 1.20.0. * gnu/packages/bioinformatics.scm (r-copynumber): Update to 1.20.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 632a74cea0..bdfe2c04a4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6176,13 +6176,13 @@ (define-public r-annotate (define-public r-copynumber (package (name "r-copynumber") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "copynumber" version)) (sha256 (base32 - "01kcwzl485yjrkgyg8117b1il957ss0v6rq4bbxf4ksd5fzcjmyx")))) + "0y9nnwb0psphp3ix88wj2f8z5gr45r5znf55w892ysm27isdpmms")))) (build-system r-build-system) (propagated-inputs `(("r-s4vectors" ,r-s4vectors) -- cgit v1.2.3 From 4d70c8c486ffc238f9bbe96a01de8e6c69165ad8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:44:06 +0200 Subject: gnu: r-geneplotter: Update to 1.58.0. * gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.58.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bdfe2c04a4..44fdd1f16f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6199,14 +6199,14 @@ (define-public r-copynumber (define-public r-geneplotter (package (name "r-geneplotter") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneplotter" version)) (sha256 (base32 - "1z3g7frc1iviwrsv2dlm4nqvkc0685h4va0388yfxn102ln8wwma")))) + "055g28xgiazl4l0gkg8xiamks64f5yckjjyvw1abd6d6qjavwx0g")))) (build-system r-build-system) (propagated-inputs `(("r-annotate" ,r-annotate) -- cgit v1.2.3 From 41657b15f4de4a403fe1fe6cf86c05b69602ceb3 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:44:18 +0200 Subject: gnu: r-genefilter: Update to 1.62.0. * gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.62.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 44fdd1f16f..2df630dc37 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6224,14 +6224,14 @@ (define-public r-geneplotter (define-public r-genefilter (package (name "r-genefilter") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "173swlg6gj4kdllbqvyiw5dggbcxiwlwpqmllsv4dxzn7h25i3g7")))) + "14l0ff02spmjwxj0m1czhg5vlkgwcfi73cym8m2n9vn6i7bjdaqi")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) -- cgit v1.2.3 From 51c1f96ebc9e2198e4f4da92d0c91280f20e8bae Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:44:32 +0200 Subject: gnu: r-deseq2: Update to 1.20.0. * gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.20.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2df630dc37..31b93984f2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6251,14 +6251,14 @@ (define-public r-genefilter (define-public r-deseq2 (package (name "r-deseq2") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "1iyimg1s0x5pdmvl8x08s8h0v019y0nhjzs50chagbpk2x91fsmv")))) + "1wjnfpb41a9mmf9a22bz4zh7r1d4id50vpdc1mn5vfzrz7li9qik")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 16da69b5e68d5103c245d686c8f0a61768a5f3e5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:45:25 +0200 Subject: gnu: r-dexseq: Update to 1.26.0. * gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.26.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 31b93984f2..8f2764ab96 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6288,14 +6288,14 @@ (define-public r-deseq2 (define-public r-dexseq (package (name "r-dexseq") - (version "1.24.4") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "1a80yv742fx5c7qav7imsdybphf0d5bixsqyf8w5zng7fk8j16d5")))) + "1mqb3mdxcsi3largsl7k27bvqrgps9ixv806xvmf29pw0xn05sg1")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 5516db9e7004dc3f4e9647b370146dc9e8c51b3c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:45:36 +0200 Subject: gnu: r-annotationforge: Update to 1.22.0. * gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.22.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8f2764ab96..debba7529f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6331,14 +6331,14 @@ (define-public r-dexseq (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "01vbrf76vqfvxh6vpfxkjwccxggnha3byqzj333glqz2b6kwx5q1")))) + "12ffj7h95adiya5mzyjxazqn1qgr434ajpabfcyhrj5v83s4vk65")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) -- cgit v1.2.3 From 9177ac2295845c51afeba13af3945ce54960d0a6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:45:49 +0200 Subject: gnu: r-rbgl: Update to 1.56.0. * gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.56.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index debba7529f..fca84dda4c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6361,14 +6361,14 @@ (define-public r-annotationforge (define-public r-rbgl (package (name "r-rbgl") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RBGL" version)) (sha256 (base32 - "18jad23i3899ypv4bg3l47cvvs3qnj1pqis2p9x0135yv5y6wnv7")))) + "0hj972mmqpyi5fx1rq33kysavdyz4nspi6gcffzi3rv339m0anhf")))) (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs `(("r-graph" ,r-graph))) -- cgit v1.2.3 From f1094f50a798bc8966533c193ed290e5724e3f2c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:46:02 +0200 Subject: gnu: r-gseabase: Update to 1.42.0. * gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.42.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fca84dda4c..b549c32d21 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6382,14 +6382,14 @@ (define-public r-rbgl (define-public r-gseabase (package (name "r-gseabase") - (version "1.40.1") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GSEABase" version)) (sha256 (base32 - "10cmjxahg2plwacfan6g0k8cwyzya96ypc7m1r79gwqkyykxw5fz")))) + "11bv92svik399q677jv96b71i4bq68xxyxn1yijpdik2lq4hgl7a")))) (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From d8410d6610e948efab2fbfe35289e8215098d686 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:46:14 +0200 Subject: gnu: r-category: Update to 2.46.0. * gnu/packages/bioinformatics.scm (r-category): Update to 2.46.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b549c32d21..f2b5660298 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6409,14 +6409,14 @@ (define-public r-gseabase (define-public r-category (package (name "r-category") - (version "2.44.0") + (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Category" version)) (sha256 (base32 - "0mkav04vbla0xfa0dssxdd0rjs589sxi83xklf5iq5hj3dm8y0i8")))) + "03wfqa8d1dgwsm327zl2mpkq7dq3mzhq12598qz3ylfhrwplbgx0")))) (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 9da8e275caab5831fc74d38406857af7c4bd78eb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:46:28 +0200 Subject: gnu: r-gostats: Update to 2.46.0. * gnu/packages/bioinformatics.scm (r-gostats): Update to 2.46.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f2b5660298..ac05329799 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6440,14 +6440,14 @@ (define-public r-category (define-public r-gostats (package (name "r-gostats") - (version "2.44.0") + (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOstats" version)) (sha256 (base32 - "04gqfdlx9fxf97qf0l28x4aaqvl10n6v58qiz5fiaw05sbj1pf1i")))) + "1i5mydz5d95w2k28qr9j01hmbnl2id55jq94jvcpcyp1pvinkdq0")))) (properties `((upstream-name . "GOstats"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From eabe78facafcee9aa170f292f630e45df9955720 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:46:39 +0200 Subject: gnu: r-shortread: Update to 1.38.0. * gnu/packages/bioinformatics.scm (r-shortread): Update to 1.38.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ac05329799..2eac1d5208 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6471,14 +6471,14 @@ (define-public r-gostats (define-public r-shortread (package (name "r-shortread") - (version "1.36.1") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "1cyv47632m9ljkxfsvnvmd19sb607ys5kz8fwh6v39dnw16g0a6m")))) + "038z3z7qaw5bpgjzy91sjkybsny6jwjjsrnnq4gdqdw9ss1qy1fb")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs -- cgit v1.2.3 From 712fe39680bafa6f70688eb6e7b760d89ee2acbf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:46:51 +0200 Subject: gnu: r-systempiper: Update to 1.14.0. * gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.14.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2eac1d5208..afd89e5954 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6513,14 +6513,14 @@ (define-public r-shortread (define-public r-systempiper (package (name "r-systempiper") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "11mj8pjq5vj25768vmagpzv74fvi3p3kdk5zdlznqyiaggri04cv")))) + "1550pd63mmky0vgkmpni7zf14kqz1741wv63nfaw29kcmhh3m5lm")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 9370b8ee9f35e838fe63bdc8e5a26def3a072c35 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:47:04 +0200 Subject: gnu: r-grohmm: Update to 1.14.0. * gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.14.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index afd89e5954..8f5a8373a7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6559,14 +6559,14 @@ (define-public r-systempiper (define-public r-grohmm (package (name "r-grohmm") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "groHMM" version)) (sha256 (base32 - "0cjkj0ypyc4dfi9s8dh88kh6q4xlpnc0wal7njg4b4gqj0l2hva7")))) + "1kjb14apyly44qdlx2ld6gr69wlazd4mbhs58l35hir12aphgrzp")))) (properties `((upstream-name . "groHMM"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From e5907a44e1fbb208f7250cae636d35e2dcf5c8c9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:47:15 +0200 Subject: gnu: r-biocgenerics: Update to 0.26.0. * gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.26.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8f5a8373a7..28863c1c8b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6878,13 +6878,13 @@ (define-public r-acsnminer (define-public r-biocgenerics (package (name "r-biocgenerics") - (version "0.24.0") + (version "0.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocGenerics" version)) (sha256 (base32 - "03wxvhxyrhipbgcg83lqlfn7p9gbzzrnl48y0dq7303xgp232zai")))) + "19qxhy2cd3pykkhzbb5q3crgaxf65cpzf2mkfsz16gqhi8flj72p")))) (properties `((upstream-name . "BiocGenerics"))) (build-system r-build-system) -- cgit v1.2.3 From 97af51ef40ea172324ee50d0a2c6dc9a099f8f9a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:47:27 +0200 Subject: gnu: r-biocinstaller: Update to 1.30.0. * gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.30.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 28863c1c8b..647d8226a3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6898,13 +6898,13 @@ (define-public r-biocgenerics (define-public r-biocinstaller (package (name "r-biocinstaller") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocInstaller" version)) (sha256 (base32 - "19fga27bv6q9v5mpil74y76lahmnwvpg2h33rdx1r79nvljkd19d")))) + "1xg1gi1hf5vflp71ji21gnmr4kcjpx8a6c47cllpc7yqnjv5nfg0")))) (properties `((upstream-name . "BiocInstaller"))) (build-system r-build-system) -- cgit v1.2.3 From e5f52b692ae7f4542912f528939d5b82e5e543a9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:47:39 +0200 Subject: gnu: r-biocviews: Update to 1.48.0. * gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.48.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 647d8226a3..3e1881b21e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6917,13 +6917,13 @@ (define-public r-biocinstaller (define-public r-biocviews (package (name "r-biocviews") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "09zyqj1kqc089lmh9sliy0acanx9zimcasvp71dsrg2bqm08r1md")))) + "1yx2lir67ny0j150wyfqca0wsxp84byri8nscbs9qlndkh2jppq9")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) -- cgit v1.2.3 From dc6c168ac17e77c83224eaa408375ab957319386 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:47:54 +0200 Subject: gnu: r-biocstyle: Update to 2.8.2. * gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.8.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3e1881b21e..5f50dfb996 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6968,13 +6968,13 @@ (define-public r-bookdown (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.6.1") + (version "2.8.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "03pp04pkcq99kdv2spzr995h2cxsza7l6w3d4gp4112m06prcybm")))) + "17m901ylz00w1a3nq5f910v55zixm1nr6rb3qrsbhqd94qzr0l2p")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) -- cgit v1.2.3 From 3679a2fec44e11fb2e43c06e733e9e85c445f024 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:48:05 +0200 Subject: gnu: r-bioccheck: Update to 1.16.0. * gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.16.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5f50dfb996..3d5e719818 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6993,13 +6993,13 @@ (define-public r-biocstyle (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "1nzp8kgw13z9pgf885rplj6k37jcldfhbz0adqclxr2gq0yalmyx")))) + "1srp1g809f1nn0fyqknr7r6dq89bw1xpjvmygr7cw6ffknbc671s")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) -- cgit v1.2.3 From 607acf3194a9458a3eced9349387e4a3fa262a52 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:48:17 +0200 Subject: gnu: r-dnacopy: Update to 1.54.0. * gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.54.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3d5e719818..b7e034ec04 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7084,13 +7084,13 @@ (define-public r-optparse (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "127il5rlg1hzjlhwhs64x3nm18p00q1pd9ckb2b9ifl0rax95wai")))) + "03hfhmmc5y60r2gcgm367w2fr7qj115l74m9bp3h9qpn5yci0d8n")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) -- cgit v1.2.3 From 33cd15fa8424d2822dcf95ac306f7ca6f8f14188 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:48:29 +0200 Subject: gnu: r-s4vectors: Update to 0.18.2. * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.18.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b7e034ec04..41c7cdad32 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7106,13 +7106,13 @@ (define-public r-dnacopy (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.16.0") + (version "0.18.2") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "03s8vz33nl6mivjb7dbvj702dkypi340lji1sjban03fyyls0hw0")))) + "0qvj2j0zl4djjl7vrwc6xak6h8dxr53iwypfbcvfb3sh7jwhdiz5")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) -- cgit v1.2.3 From 8b44c28f5d55efbcf75f7353552431a6ea446bdf Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:48:42 +0200 Subject: gnu: r-iranges: Update to 2.14.10. * gnu/packages/bioinformatics.scm (r-iranges): Update to 2.14.10. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 41c7cdad32..c5b55c4824 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7158,13 +7158,13 @@ (define-public r-seqinr (define-public r-iranges (package (name "r-iranges") - (version "2.12.0") + (version "2.14.10") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "1vqczb9wlxsmpwpqig6j1dmiblcfpq6mgnq8qwzcrvddm4cp47m5")))) + "10ccw930vfmkskkrzbps14xglqlkxf588623dr7f1a9ckx7yr2p6")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) -- cgit v1.2.3 From 953c8b18f88628289e6753a01c32db62dec4483f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:48:54 +0200 Subject: gnu: r-genomeinfodb: Update to 1.16.0. * gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.16.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c5b55c4824..09d06f178e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7210,13 +7210,13 @@ (define-public r-genomeinfodbdata (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "1jhm0imkac4gvchbjxj408aakk39xdv2fyh818d3lk295bz6bnyp")))) + "0yhnqhaydmmq7ihmhj3rbal4afq5p993l2qqrd0n5wmbyg7glg2d")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) -- cgit v1.2.3 From 4639025284808908d6b60deb2cd54ba64654a944 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:49:06 +0200 Subject: gnu: r-edger: Update to 3.22.2. * gnu/packages/bioinformatics.scm (r-edger): Update to 3.22.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 09d06f178e..ad9aec8879 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7238,13 +7238,13 @@ (define-public r-genomeinfodb (define-public r-edger (package (name "r-edger") - (version "3.20.9") + (version "3.22.2") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "0y52snwbz37xzdd7gihdkqczbndlfzmmypv6hri3ymjyfmlx6qaw")))) + "07py2g6vg9jbflwhc1hnzr2silbinrjwxq3mkq30nzjgf0n0hrf3")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From d358a5a0c1e2726384b0b4c2911c4ed6741fae7b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:49:17 +0200 Subject: gnu: r-variantannotation: Update to 1.26.0. * gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.26.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ad9aec8879..88e252b1f9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7266,13 +7266,13 @@ (define-public r-edger (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.24.5") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "07ywn3c4w83l3sr76d0z3b1nv9icgdh3phsjlc6cfx7i6nfmvxw2")))) + "06bccdf57vja7m63chmgc4539lwng3q3b8zxn285fj8524l6mcn7")))) (properties `((upstream-name . "VariantAnnotation"))) (inputs -- cgit v1.2.3 From 0a465e5694068306d90e3d9634fbff9370720c99 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:49:31 +0200 Subject: gnu: r-limma: Update to 3.36.1. * gnu/packages/bioinformatics.scm (r-limma): Update to 3.36.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 88e252b1f9..2680d170dc 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7304,13 +7304,13 @@ (define-public r-variantannotation (define-public r-limma (package (name "r-limma") - (version "3.34.9") + (version "3.36.1") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "1y2fm61g5i0fn0j3l31xvwh9zww9bpkc4nwzb1d0yv1cag20jkdc")))) + "1982g5v35ilfgxm2vkq1p3j1bbir795pjvfzx4nzam2rlqqymbqm")))) (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 c2401d06c5ba1603de31e04ba955609514d42d27 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:49:44 +0200 Subject: gnu: r-xvector: Update to 0.20.0. * gnu/packages/bioinformatics.scm (r-xvector): Update to 0.20.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2680d170dc..4dfd8825a2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7323,13 +7323,13 @@ (define-public r-limma (define-public r-xvector (package (name "r-xvector") - (version "0.18.0") + (version "0.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XVector" version)) (sha256 (base32 - "1i4i3kdxr78lr1kcxq657p11ybi7kq10c8kyaqyh6gfc8i9rhvmk")))) + "1zjlhh9lsyhg0js1858csyw2389kbrzdqnqnha833wazkwxilp3f")))) (properties `((upstream-name . "XVector"))) (build-system r-build-system) -- cgit v1.2.3 From e51afc63b7924f632722c691e3ef0808e70d38f1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:49:57 +0200 Subject: gnu: r-genomicranges: Update to 1.32.3. * gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.32.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4dfd8825a2..66b645e08b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7359,13 +7359,13 @@ (define-public r-xvector (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.30.3") + (version "1.32.3") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "07cszc9ri94nzk4dffwnsj247ih6pchnrzrvnb0q4dkk33gwy8n1")))) + "03gmka6rlz18vd4229796l5l3l6446v5cb90sn2nb5knjbp84hni")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) -- cgit v1.2.3 From 6fd71f1b6a102da3258e6af7d0b5cc8bd297fc24 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:50:13 +0200 Subject: gnu: r-biobase: Update to 2.40.0. * gnu/packages/bioinformatics.scm (r-biobase): Update to 2.40.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 66b645e08b..862b6b98d7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7388,13 +7388,13 @@ (define-public r-genomicranges (define-public r-biobase (package (name "r-biobase") - (version "2.38.0") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 - "1cgm1ja1kp56zdlzyy9ggbkfn8r2vbsd4hncmz8g4hjd47fg18kg")))) + "1iwds2a5ir29k19dbpynlc7nn836cw2gamchhgpi2jf2xar9m9jz")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) -- cgit v1.2.3 From 77f66feee7821902965571be5ae6f43caa848147 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:50:34 +0200 Subject: gnu: r-annotationdbi: Update to 1.42.1. * gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.42.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 862b6b98d7..e5d0f02727 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7410,13 +7410,13 @@ (define-public r-biobase (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.40.0") + (version "1.42.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "1dh4qs1a757n640gs34lf6z2glc96nan86x0sqaw5csadl2rhnlc")))) + "0afkbzli08vq02r2pr9phrz3rxd6ilp1w7yw8y99nbjiz14f8b1c")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) -- cgit v1.2.3 From 1763cba80ebf99d19faa0c02ef409bbf4a07d365 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:50:56 +0200 Subject: gnu: r-biomart: Update to 2.36.1. * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.36.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e5d0f02727..0bccc6c443 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7437,13 +7437,13 @@ (define-public r-annotationdbi (define-public r-biomart (package (name "r-biomart") - (version "2.34.2") + (version "2.36.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "1zlgs2zg0lmnk572p55n7m34nkxka8w10x8f2ndssjkffl2csy79")))) + "0b70s350ffc74v3xz5c3jpazr9zxdb7gjmjfj7aghlsrizrspill")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) -- cgit v1.2.3 From e6eac58d4c01a999ab9503a1657503fb9643a35b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:51:12 +0200 Subject: gnu: r-biocparallel: Update to 1.14.1. * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.14.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0bccc6c443..9caa32f690 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7470,13 +7470,13 @@ (define-public r-biomart (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.12.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "13ng3n2wsgl3fh0v6jnz3vg51k5c1sh44pqdvblcrcd1qyjmmqhd")))) + "00qg1kg2l9qqpyjaw5q910cmf84vwfiw1fhsx3ig784gwinwgj6n")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) -- cgit v1.2.3 From 942655add1b2eeeac614133fe5019503f08bc885 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:51:35 +0200 Subject: gnu: r-biostrings: Update to 2.48.0. * gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.48.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9caa32f690..d921229529 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7495,13 +7495,13 @@ (define-public r-biocparallel (define-public r-biostrings (package (name "r-biostrings") - (version "2.46.0") + (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "0vg50qdlxqcm2d6axjnzg8wh8pr4c5gz03l8bdl0llmwzp0zclzk")))) + "118b490jk87ydigm6ln25ms4kskzkw0akmh77clzznhzpqnxsi6j")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) -- cgit v1.2.3 From d2367a89ddea3640323570d3ec757d28709e1c71 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:51:57 +0200 Subject: gnu: r-rsamtools: Update to 1.32.0. * gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.32.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d921229529..ed38e4c41f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7521,13 +7521,13 @@ (define-public r-biostrings (define-public r-rsamtools (package (name "r-rsamtools") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "0pjny5fjvbnfdyhl3bwxin678sha2drvs00sivxh3l772cn6yams")))) + "1s65y5wn4d0x8zsljg2kmhcl6r9884h95kr041j7hp49bmxg3an6")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) -- cgit v1.2.3 From 82f593f3787d3bb0386376ab26fc7da1fa161344 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:52:17 +0200 Subject: gnu: r-delayedarray: Update to 0.6.0. * gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.6.0. [propagated-inputs]: Add r-biocparallel. --- gnu/packages/bioinformatics.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ed38e4c41f..4d5fef5efc 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7565,18 +7565,19 @@ (define-public r-rsamtools (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.4.1") + (version "0.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "0s7h2giyvz04cg6248kbbzpwhxdrpnsvl2s8k5c8ricisd9aaz4b")))) + "0n3w57cwy911q812wc8658y0v3xgpmg379sj98kfqdxa80z1mxdf")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) ("r-s4vectors" ,r-s4vectors) ("r-iranges" ,r-iranges) ("r-matrixstats" ,r-matrixstats))) -- cgit v1.2.3 From 9bf4110ea17dbe5214a8a2737abe826bb08479a7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:52:44 +0200 Subject: gnu: r-summarizedexperiment: Update to 1.10.1. * gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.10.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4d5fef5efc..169615181f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7596,13 +7596,13 @@ (define-public r-delayedarray (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.8.1") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "19vlwnby83fqjrilsxvnvgz0gvby7mrxvlmx18nb3p1w591ddfjh")))) + "0v3zxl9cqsv79ag5cnvzlhvgaz5cr8f4rn7flmwnwpqd508cznl1")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) -- cgit v1.2.3 From 90102bd06bdc8755d4a38e0759d074606cace927 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:53:04 +0200 Subject: gnu: r-genomicalignments: Update to 1.16.0. * gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.16.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 169615181f..791c948877 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7627,13 +7627,13 @@ (define-public r-summarizedexperiment (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.14.2") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "1659nj1xps7vliy5955i51x6hvrf16n1z0dfh10mmpaaswn2d2mv")))) + "00pi2cnkkbj2023fg2x2cmglkdalwzy1vr3glsikwz7ix9yylcaw")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) -- cgit v1.2.3 From a30df29768890caa1da8a682f455fb9435b73486 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:53:35 +0200 Subject: gnu: r-rtracklayer: Update to 1.40.2. * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.40.2. [native-inputs]: Add pkg-config. --- gnu/packages/bioinformatics.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 791c948877..e803bbca2c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7660,13 +7660,13 @@ (define-public r-genomicalignments (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.38.3") + (version "1.40.2") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "1khzfczm35k5lq9h0jlqrq01192spzjyh8s6is89spj006flwn4k")))) + "0l90jn4df3akxl0n1i9wvnbjqrzjc0d15r8vqr7b15q2117mrn5r")))) (build-system r-build-system) (arguments `(#:phases @@ -7678,6 +7678,8 @@ (define-public r-rtracklayer (substitute* "NAMESPACE" (("import\\(zlibbioc\\)") "")) #t))))) + (native-inputs + `(("pkg-config" ,pkg-config))) (inputs `(("zlib" ,zlib))) (propagated-inputs -- cgit v1.2.3 From b4ad4ec6b41598d09dde665a33a6ae9b2a51313a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:54:15 +0200 Subject: gnu: r-genomicfeatures: Update to 1.32.0. * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.32.0. [propagated-inputs]: Remove r-rmysql. --- gnu/packages/bioinformatics.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e803bbca2c..721a25f9fe 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7707,13 +7707,13 @@ (define-public r-rtracklayer (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.30.3") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "010vn8hlwbnw12pd1d8pv6m12yp3xwx557gba5rbjq9p4qypnn3z")))) + "1cqcl72q0k5wylw1brn4g4h7xzys1v06piry19cvp0gjcvm5sp7a")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -7729,7 +7729,6 @@ (define-public r-genomicfeatures ("r-iranges" ,r-iranges) ("r-rcurl" ,r-rcurl) ("r-rsqlite" ,r-rsqlite) - ("r-rmysql" ,r-rmysql) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-xvector" ,r-xvector))) -- cgit v1.2.3 From 2f66fecd890320926159464ae79840767c79cb6a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:54:40 +0200 Subject: gnu: r-graph: Update to 1.58.0. * gnu/packages/bioinformatics.scm (r-graph): Update to 1.58.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 721a25f9fe..56c56346bd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7772,13 +7772,13 @@ (define-public r-go-db (define-public r-graph (package (name "r-graph") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 - "15aajjp8h2z14p80c8hyd4rrmr9vqsm7bvwb989jxjl4k6g52an1")))) + "1zx445lk36g1s6i5dbhhf00nzzazyklfjxxjfax6q8hnhvgm9759")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics))) -- cgit v1.2.3 From f2eb2e453e8f64c84435dbdaac4229b95e338183 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:54:55 +0200 Subject: gnu: r-topgo: Update to 2.32.0. * gnu/packages/bioinformatics.scm (r-topgo): Update to 2.32.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 56c56346bd..a5b205c27b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7791,13 +7791,13 @@ (define-public r-graph (define-public r-topgo (package (name "r-topgo") - (version "2.30.1") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "topGO" version)) (sha256 (base32 - "1cgz4knxr328xfqlhl6ypxl6x86rfrlqz748kn94ainxjzz55i6x")))) + "05yxnkid8bgw9lkm90if9fg63djhgvbailfa3qsfqa5c0zjmixw1")))) (properties `((upstream-name . "topGO"))) (build-system r-build-system) -- cgit v1.2.3 From 89ef133ebd1d0f31de4167a48356481e19fe003a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:55:10 +0200 Subject: gnu: r-bsgenome: Update to 1.48.0. * gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.48.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a5b205c27b..7318e16b35 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7824,13 +7824,13 @@ (define-public r-topgo (define-public r-bsgenome (package (name "r-bsgenome") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome" version)) (sha256 (base32 - "1jbzq7lm2iajajn2bifxnkss0k9fdvgqr30mral17cbhp5f6w4lq")))) + "1rk2piqq5dppkd51ln3r872d7ng3rvq98071mnd0xdv2xwnyn5g8")))) (properties `((upstream-name . "BSgenome"))) (build-system r-build-system) -- cgit v1.2.3 From 25d1df5764c538b893251cb88e647c9757449517 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:55:26 +0200 Subject: gnu: r-impute: Update to 1.54.0. * gnu/packages/bioinformatics.scm (r-impute): Update to 1.54.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7318e16b35..e7d191f27c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7885,13 +7885,13 @@ (define-public r-bsgenome-hsapiens-1000genomes-hs37d5 (define-public r-impute (package (name "r-impute") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "0b8r4swvyx3cjcc2ky8yn0ncpzlbi1pgfsn3wpbjmhh7sqrffm2n")))) + "1d3cpfaqlq2gnb3hsc2yhxwkrnbd7m6ifif32yp0ya0jr5brl4hr")))) (inputs `(("gfortran" ,gfortran))) (build-system r-build-system) -- cgit v1.2.3 From 5229cedf576bdd144ec6fc5d167fd18ae8fd98d7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:55:39 +0200 Subject: gnu: r-seqpattern: Update to 1.12.0. * gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.12.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e7d191f27c..08a01dcb06 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7905,13 +7905,13 @@ (define-public r-impute (define-public r-seqpattern (package (name "r-seqpattern") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqPattern" version)) (sha256 (base32 - "1kcm5w83q7w0v0vs7nyp4gq5z86c6n6pqy9zmyyhxcrns7f597pm")))) + "0dw0yldfcf0ibvpqxlpx1ijnjf9lma47w9w22siszzhw09i0wp3w")))) (properties `((upstream-name . "seqPattern"))) (build-system r-build-system) -- cgit v1.2.3 From 17d35de73fce32dd1166d3786776bd3d0ba2044d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:56:00 +0200 Subject: gnu: r-genomation: Update to 1.12.0. * gnu/packages/bioinformatics.scm (r-genomation): Update to 1.12.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 08a01dcb06..ae1f3dd094 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7932,13 +7932,13 @@ (define-public r-seqpattern (define-public r-genomation (package (name "r-genomation") - (version "1.11.3") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genomation" version)) (sha256 (base32 - "1d2g1v6xhrf3gm86pv8ln22df5g6v6k6i4i39v4j82zn4apany6v")))) + "1vdmdyrq0n7pf8cvy2950v7hrcrcbd9zl4fg7dcmyly3iiwdyirp")))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) -- cgit v1.2.3 From 8217c2d0bc680aeb9f4d65282b8431284258cf33 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:56:18 +0200 Subject: gnu: r-seqlogo: Update to 1.46.0. * gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.46.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ae1f3dd094..09ca946c72 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8110,14 +8110,14 @@ (define-public r-org-mm-eg-db (define-public r-seqlogo (package (name "r-seqlogo") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqLogo" version)) (sha256 (base32 - "1ql4q4vx0j61a893dqc3c8zxmgs8sqhy3j1qhyfdvbd01vw9w1kq")))) + "16xvqcdknix9vjm8mrixi6nyfsr45jm844jh1x90m8044lwrsic1")))) (properties `((upstream-name . "seqLogo"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/seqLogo") -- cgit v1.2.3 From 7e6537e257245715a647dfecb87c9453438bc1df Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:56:34 +0200 Subject: gnu: r-motifrg: Update to 1.24.0. * gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.24.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 09ca946c72..8a5d9fddd6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8356,14 +8356,14 @@ (define-public r-bsgenome-dmelanogaster-ucsc-dm3 (define-public r-motifrg (package (name "r-motifrg") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifRG" version)) (sha256 (base32 - "193zl2rlzwxv9p9q5i7rilj3w05ndqfyp9bdpvagp5s5cin4hf44")))) + "0mxhyidkyd2zqahdbg69y20r550z78lvr1r3pbjymnwfg4hcfq1p")))) (properties `((upstream-name . "motifRG"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 2c480bb01231238765657916fddd7bea7bdf7b3d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:56:48 +0200 Subject: gnu: r-zlibbioc: Update to 1.26.0. * gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.26.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8a5d9fddd6..f4ea3d43a5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8408,13 +8408,13 @@ (define-public r-qtl (define-public r-zlibbioc (package (name "r-zlibbioc") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zlibbioc" version)) (sha256 (base32 - "1zr9hbh55hglfpy15cpxwmddxblhyb0an15953l3rbhmlh2vpy92")))) + "1rwr0mci8a712q0isavi4jmhm94gwivc4nr8j7r4kw05flp4g7gz")))) (properties `((upstream-name . "zlibbioc"))) (build-system r-build-system) -- cgit v1.2.3 From 1a08bb8a177ff1b1cca363e5a8bccacf5111bb01 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:58:55 +0200 Subject: gnu: r-rhtslib: Update to 1.12.1. * gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.12.1. [native-inputs]: Remove autoconf. --- gnu/packages/bioinformatics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f4ea3d43a5..7755b28243 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8450,14 +8450,14 @@ (define-public r-r4rna (define-public r-rhtslib (package (name "r-rhtslib") - (version "1.10.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhtslib" version)) (sha256 (base32 - "1dw3p44bfr0m7w39ckc2k37sjcp1zz0b9g12mr8am15jaj6v0q2j")))) + "16ywnb8cmr2xabd1i21b92rfziw7xfbv25yv16ipw617p41wa39z")))) (properties `((upstream-name . "Rhtslib"))) (build-system r-build-system) (propagated-inputs @@ -8465,7 +8465,7 @@ (define-public r-rhtslib (inputs `(("zlib" ,zlib))) (native-inputs - `(("autoconf" ,autoconf))) + `(("pkg-config" ,pkg-config))) (home-page "https://github.com/nhayden/Rhtslib") (synopsis "High-throughput sequencing library as an R package") (description -- cgit v1.2.3 From 72f11ff9c5ba881e00cca043337928ff12464f67 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:59:23 +0200 Subject: gnu: r-bamsignals: Update to 1.12.0. * gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.12.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7755b28243..abcbb35643 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8477,14 +8477,14 @@ (define-public r-rhtslib (define-public r-bamsignals (package (name "r-bamsignals") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bamsignals" version)) (sha256 (base32 - "15id6mkj95skb4kfafvfs2j7ylydal60c3pspcl7llhwpq6vcqvl")))) + "09l4v414ijkjpkvcv2580v13v18ky196f0lv27ldblpa8bddvmns")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) -- cgit v1.2.3 From b6c2c8f781cb48d3f233651d438e5584384d3bb5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:59:37 +0200 Subject: gnu: r-mutationalpatterns: Update to 1.6.1. * gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.6.1. --- gnu/packages/bioinformatics.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index abcbb35643..12a4260bec 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8599,18 +8599,19 @@ (define-public rcas-web (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") - (version "1.4.3") + (version "1.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 - "0ml4gsp5dfv23xqrknxh25q8q65hly1xb1215lcwyc8hj9z8f941")))) + "1yq7351j42mjxn8fd3c5bdxzb2l5s4lvqhjdvv4rwj4f600n6wj9")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) + ;; These two packages are suggested packages ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5) ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) ("r-genomicranges" ,r-genomicranges) -- cgit v1.2.3 From c76e8baf9e57a45c19ccc0134499b493b55ea8a9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 11:59:53 +0200 Subject: gnu: r-tximport: Update to 1.8.0. * gnu/packages/bioinformatics.scm (r-tximport): Update to 1.8.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 12a4260bec..9138671d2f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8775,13 +8775,13 @@ (define-public r-gkmsvm (define-public r-tximport (package (name "r-tximport") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "1gyqcm91hxg1kgjqcz2qw1n56yp9pymjzs50rwcpb2893dr8sp2h")))) + "1qjc7ah9dzccpvcjrp9k4qnaz13x6kvy1c1xpdj503km6k528lip")))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/tximport") (synopsis "Import and summarize transcript-level estimates for gene-level analysis") -- cgit v1.2.3 From d73c5728f345174e9493a25646cd3d1a716fb8b5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:00:10 +0200 Subject: gnu: r-rhdf5: Update to 2.24.0. * gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.24.0. [arguments]: Remove. [propagated-inputs]: Remove r-zlibbioc; add r-rhdf5lib. [inputs]: Remove perl. --- gnu/packages/bioinformatics.scm | 29 ++++------------------------- 1 file changed, 4 insertions(+), 25 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9138671d2f..ce4ff64af6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8797,39 +8797,18 @@ (define-public r-tximport (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "145858qg1xan6imxcbprzq3yn3mdf532aahdr6cibvdjg47hs4c1")))) + "15cmmchhk8bnp94gxg0zk9qyzdjx5kv16dzpbnb62mkq7ydmifx6")))) (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'unpack-smallhdf5 - (lambda* (#:key outputs #:allow-other-keys) - (system* "tar" "-xzvf" - "src/hdf5source/hdf5small.tgz" "-C" "src/" ) - (substitute* "src/hdf5/configure" - (("/bin/mv") "mv")) - ;; Remove timestamp and host system information to make - ;; the build reproducible. - (substitute* "src/hdf5/src/libhdf5.settings.in" - (("Configured on: @CONFIG_DATE@") - "Configured on: Guix") - (("Uname information:.*") - "Uname information: Linux\n") - ;; Remove unnecessary store reference. - (("C Compiler:.*") - "C Compiler: GCC\n")) - #t))))) (propagated-inputs - `(("r-zlibbioc" ,r-zlibbioc))) + `(("r-rhdf5lib" ,r-rhdf5lib))) (inputs - `(("perl" ,perl) - ("zlib" ,zlib))) + `(("zlib" ,zlib))) (home-page "https://bioconductor.org/packages/rhdf5") (synopsis "HDF5 interface to R") (description -- cgit v1.2.3 From 62509bbc816440dd59ae6070717c6469af551a24 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:00:50 +0200 Subject: gnu: r-annotationfilter: Update to 1.4.0. * gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.4.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ce4ff64af6..fb2ce3c29d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8824,13 +8824,13 @@ (define-public r-rhdf5 (define-public r-annotationfilter (package (name "r-annotationfilter") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFilter" version)) (sha256 (base32 - "04zf864c1fvdlaay2r5cn30fc1n5i3czh31fs62qlrvs61wjiscs")))) + "1w8ypfdz4g7vnwfrvnhjcpm8waciqyq2cn883ajdwg4vv7a5mj9a")))) (properties `((upstream-name . "AnnotationFilter"))) (build-system r-build-system) -- cgit v1.2.3 From 8f94487da738aadc1e632012f1e0a03bf4defbe9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:01:03 +0200 Subject: gnu: r-chipseq: Update to 1.30.0. * gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.30.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fb2ce3c29d..ab2ff98073 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9127,14 +9127,14 @@ (define-public multiqc (define-public r-chipseq (package (name "r-chipseq") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chipseq" version)) (sha256 (base32 - "1ymcq77krwjzrkzzcw7i9909cmkqa7c0675z9wzvrrk81hgdssfq")))) + "09f8dgl5ni75qkf7nvvppwr3irpplv4xb3ks59ld7l8i2mplcrx7")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) -- cgit v1.2.3 From aae4f716dafe5535978a30cc8ac9c048e33f53f6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:01:15 +0200 Subject: gnu: r-copywriter: Update to 2.12.0. * gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.12.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ab2ff98073..5d3f16b74b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9179,14 +9179,14 @@ (define-public r-copyhelper (define-public r-copywriter (package (name "r-copywriter") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CopywriteR" version)) (sha256 (base32 - "17fy2lc5yf3nh6v077kv87h53n263hqz2540lzrl0vjiqrl2plca")))) + "0b7xwq1va2zclb54f07c5ipmmq4iv2hrlph3j93jz5hmyayv50z3")))) (properties `((upstream-name . "CopywriteR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 19ad568e79a59b2226bffd8bc1d0a1185ffe3009 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:01:43 +0200 Subject: gnu: r-methylkit: Update to 1.6.0. * gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.6.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5d3f16b74b..ff6b45e8e0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9219,13 +9219,13 @@ (define-public r-copywriter (define-public r-methylkit (package (name "r-methylkit") - (version "1.4.1") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 - "1k0nfn9318sgwm4z963bhnbp4c3zv85v3f9886vc5hgaisr0yvai")))) + "01qmndm5z21p78w7xfp8ynan6jpfg54rnkpj8b86rc081qh0sgjj")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 9547dd86138b9ff40e5d2eb39503cf0f65136bb7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:01:57 +0200 Subject: gnu: r-sva: Update to 3.28.0. * gnu/packages/bioinformatics.scm (r-sva): Update to 3.28.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ff6b45e8e0..a010fc188d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9265,14 +9265,14 @@ (define-public r-methylkit (define-public r-sva (package (name "r-sva") - (version "3.26.0") + (version "3.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sva" version)) (sha256 (base32 - "0q5xb68wfcnchy8rkv5ma67pmz1i91lsnvmwmj8f1c3w4xan3pgw")))) + "0a3jqbz0jp1jxrnjkqfpmca840yqcdwxprdl608bzzx2zb4jl52s")))) (build-system r-build-system) (propagated-inputs `(("r-genefilter" ,r-genefilter) -- cgit v1.2.3 From a02b82088fe0cf949cea15de011c157d9e916022 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:02:10 +0200 Subject: gnu: r-protgenerics: Update to 1.12.0. * gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.12.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a010fc188d..955decdead 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9375,14 +9375,14 @@ (define-public r-maldiquant (define-public r-protgenerics (package (name "r-protgenerics") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ProtGenerics" version)) (sha256 (base32 - "16ijp50448wnabp43klx943rhdvh7x45hvy7cnpq1s4dckxhhyni")))) + "05jbadw2aiwy8vi2ia0jxg06cmwhly2cq4dy1ag7kdxf1c5i9ccn")))) (properties `((upstream-name . "ProtGenerics"))) (build-system r-build-system) (home-page "https://github.com/lgatto/ProtGenerics") -- cgit v1.2.3 From 39cc4917907c5f0376c30989970b857de49b8e77 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:04:03 +0200 Subject: gnu: r-mzr: Update to 2.14.0. * gnu/packages/bioinformatics.scm (r-mzr): Update to 2.14.0. [inputs]: Add zlib. [propagated-inputs]: Add r-rhdf5lib. --- gnu/packages/bioinformatics.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 955decdead..1ac5b7caa1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9395,14 +9395,14 @@ (define-public r-protgenerics (define-public r-mzr (package (name "r-mzr") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 - "1x3gp30sfxz2v3k3swih9kff9b2rvk7hzhnlkp6ywlnn2wgb0q8c")) + "190m2bq5bqxhljaj4f7vz9wj5h5laaxd8zp5jampnql6xc4zmarg")) (modules '((guix build utils))) (snippet '(begin @@ -9424,12 +9424,14 @@ (define-public r-mzr #t))))) (inputs `(("boost" ,boost) ; use this instead of the bundled boost sources - ("netcdf" ,netcdf))) + ("netcdf" ,netcdf) + ("zlib" ,zlib))) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-protgenerics" ,r-protgenerics) ("r-rcpp" ,r-rcpp) + ("r-rhdf5lib" ,r-rhdf5lib) ("r-zlibbioc" ,r-zlibbioc))) (home-page "https://github.com/sneumann/mzR/") (synopsis "Parser for mass spectrometry data files") -- cgit v1.2.3 From 82589f743003e57a4bf305b4a52185c5fdad6e43 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:04:28 +0200 Subject: gnu: r-affyio: Update to 1.50.0. * gnu/packages/bioinformatics.scm (r-affyio): Update to 1.50.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1ac5b7caa1..da4afc7747 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9447,14 +9447,14 @@ (define-public r-mzr (define-public r-affyio (package (name "r-affyio") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyio" version)) (sha256 (base32 - "1pzzp3d3dbmyf34gvivfiprkpscn36rgvhrq853a1d3avcwr5ak9")))) + "0sh5wnnchyfpq5n6rchbqmb27byn7kdzn5rgran6i39c81i5z22n")))) (build-system r-build-system) (propagated-inputs `(("r-zlibbioc" ,r-zlibbioc))) -- cgit v1.2.3 From 5837f1835be41fab16f033eef66adf7d80557d27 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:04:46 +0200 Subject: gnu: r-affy: Update to 1.58.0. * gnu/packages/bioinformatics.scm (r-affy): Update to 1.58.0. [inputs]: Add zlib. --- gnu/packages/bioinformatics.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index da4afc7747..b650e1245e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9471,14 +9471,14 @@ (define-public r-affyio (define-public r-affy (package (name "r-affy") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affy" version)) (sha256 (base32 - "0jmbkimma5ffsdkk3xp03g4lpz84gd95nkqakif2nqq6wmx0syrj")))) + "0sxq875sigm21sf3qncrfrwfdz9nqw1vldxn3d3hj6aq64jg1ki6")))) (build-system r-build-system) (propagated-inputs `(("r-affyio" ,r-affyio) @@ -9487,6 +9487,8 @@ (define-public r-affy ("r-biocinstaller" ,r-biocinstaller) ("r-preprocesscore" ,r-preprocesscore) ("r-zlibbioc" ,r-zlibbioc))) + (inputs + `(("zlib" ,zlib))) (home-page "https://bioconductor.org/packages/affy") (synopsis "Methods for affymetrix oligonucleotide arrays") (description -- cgit v1.2.3 From af8710624d2a58e2aea2142b43533800b817ba98 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:05:08 +0200 Subject: gnu: r-vsn: Update to 3.48.1. * gnu/packages/bioinformatics.scm (r-vsn): Update to 3.48.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b650e1245e..16ca1fea1f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9499,14 +9499,14 @@ (define-public r-affy (define-public r-vsn (package (name "r-vsn") - (version "3.46.0") + (version "3.48.1") (source (origin (method url-fetch) (uri (bioconductor-uri "vsn" version)) (sha256 (base32 - "18y62phzirj75gg6v5l41jwybmk23ia6w7qhch0kxc4bl2rysw6j")))) + "0k6mah3g3zqbfap31xmvig4fn452a18xwwa5y0mfj5mj8588p57h")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) -- cgit v1.2.3 From 7bd25829711fd3b46f1dde494390aa7a6223052a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:05:28 +0200 Subject: gnu: r-mzid: Update to 1.18.0. * gnu/packages/bioinformatics.scm (r-mzid): Update to 1.18.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 16ca1fea1f..e3daa4b7f3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9533,14 +9533,14 @@ (define-public r-vsn (define-public r-mzid (package (name "r-mzid") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzID" version)) (sha256 (base32 - "0yk70dka56zd8w62f03ggx3mandj91gfa767h9ajj0sd3mjmfqb9")))) + "060k0xlhg8q802c6zsb4b8ps0ccd9ybyaz0gnsvqkxb786i2vk40")))) (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 0f773b90db18e4e395e04276f902f279f236911d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:05:43 +0200 Subject: gnu: r-pcamethods: Update to 1.72.0. * gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.72.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e3daa4b7f3..25fa2fd514 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9563,14 +9563,14 @@ (define-public r-mzid (define-public r-pcamethods (package (name "r-pcamethods") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaMethods" version)) (sha256 (base32 - "0ii235g0x0492kh8cfrf28ni0b6vd6fh7kizkqmczzqggd6b1bk8")))) + "0v99yf8m7ryh6z0r3z0ggpqfnflcq5bn1q1i1cl9b7q4p6b4sa07")))) (properties `((upstream-name . "pcaMethods"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 250d78eac95c22c227aa38377627aa6e01f6b1bd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:06:13 +0200 Subject: gnu: r-msnbase: Update to 2.6.1. * gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.6.1. [propagated-inputs]: Add r-mass and r-scales. --- gnu/packages/bioinformatics.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 25fa2fd514..5a1443f83a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9593,14 +9593,14 @@ (define-public r-pcamethods (define-public r-msnbase (package (name "r-msnbase") - (version "2.4.2") + (version "2.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "1ig64bf881p118dwqfr0ry41m7yhnyv165smv8fdwfv7sb6sagif")))) + "0zrpx9r93q5ca2zdak5rs2m9sjm0wjdra1xfj3d3sx6p5gzfyg6n")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs @@ -9614,6 +9614,7 @@ (define-public r-msnbase ("r-iranges" ,r-iranges) ("r-lattice" ,r-lattice) ("r-maldiquant" ,r-maldiquant) + ("r-mass" ,r-mass) ("r-mzid" ,r-mzid) ("r-mzr" ,r-mzr) ("r-pcamethods" ,r-pcamethods) @@ -9622,6 +9623,7 @@ (define-public r-msnbase ("r-protgenerics" ,r-protgenerics) ("r-rcpp" ,r-rcpp) ("r-s4vectors" ,r-s4vectors) + ("r-scales" ,r-scales) ("r-vsn" ,r-vsn) ("r-xml" ,r-xml))) (home-page "https://github.com/lgatto/MSnbase") -- cgit v1.2.3 From bdc8b40af2553dcd27d8bb581a8865c7e9e08d87 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:06:43 +0200 Subject: gnu: r-msnid: Update to 1.14.0. * gnu/packages/bioinformatics.scm (r-msnid): Update to 1.14.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5a1443f83a..cee999ad81 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9636,14 +9636,14 @@ (define-public r-msnbase (define-public r-msnid (package (name "r-msnid") - (version "1.12.1") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 - "1zw508kk4f8brg69674wp18gqkpx2kpya5f6x9cl3qng7v4h5pxx")))) + "172q5chi44104iz4y0g42wrimfp7hlhrfa8vzybx6m0ccrkkhl17")))) (properties `((upstream-name . "MSnID"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 0ebd7a4c9f8df90637bca8566156aa6e6531ed35 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:07:01 +0200 Subject: gnu: r-aroma-light: Update to 3.10.0. * gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.10.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index cee999ad81..7c84c3bdc0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9768,14 +9768,14 @@ (define-public r-seurat (define-public r-aroma-light (package (name "r-aroma-light") - (version "3.8.0") + (version "3.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aroma.light" version)) (sha256 (base32 - "0crnk6851jwypqr5l5jcbbay0vi5vvdjyisaf6z2d69c39wmr6sc")))) + "1dxsiwsrwcq9mj573f9vpdzrhagdqzal328ma8076px4gg6khxkn")))) (properties `((upstream-name . "aroma.light"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 749b71267791368cb20af2682ae0bcc6503a0a7c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:07:22 +0200 Subject: gnu: r-deseq: Update to 1.32.0. * gnu/packages/bioinformatics.scm (r-deseq): Update to 1.32.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7c84c3bdc0..0ba21e366b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9795,14 +9795,14 @@ (define-public r-aroma-light (define-public r-deseq (package (name "r-deseq") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq" version)) (sha256 (base32 - "0mn5w3cy16iwwk8zxs7za6aa6cnrca75z0g45zd5zh1py5d7nfv9")))) + "0ykxw8ksif026xy25wx50j2sdsrp156aqkmhcgfjkpgcw699glnm")))) (properties `((upstream-name . "DESeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From a67dd4c5e936fc6cc635498f42e34df438ecc1af Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:07:38 +0200 Subject: gnu: r-edaseq: Update to 2.14.0. * gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.14.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0ba21e366b..addd9439f2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9826,14 +9826,14 @@ (define-public r-deseq (define-public r-edaseq (package (name "r-edaseq") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EDASeq" version)) (sha256 (base32 - "07zm89zcivyn2261aq9grqmly8ji482kr9h9dyfknfdfrpv7jpwv")))) + "1832pb3jkim4vrqzb8lajwx9r482bhww5n9nz3s6crvyamlp2dj0")))) (properties `((upstream-name . "EDASeq"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 420415b057511779f2357ca255bbee2547e397ed Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:07:49 +0200 Subject: gnu: r-interactivedisplaybase: Update to 1.18.0. * gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to 1.18.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index addd9439f2..69070af82b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9864,14 +9864,14 @@ (define-public r-edaseq (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "interactiveDisplayBase" version)) (sha256 (base32 - "01yb945jqqimwjgriza6yy4dnp303cdirxrhl4hjyprfdlmnz5p5")))) + "05w58z3i9vkma4jd6rhjaxls4yiq4kwrppgcdq9xrr1pxp99k575")))) (properties `((upstream-name . "interactiveDisplayBase"))) (build-system r-build-system) -- cgit v1.2.3 From 646439c7e383c03208ff9114ffa893fadd6d374d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:08:09 +0200 Subject: gnu: r-annotationhub: Update to 2.12.0. * gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.12.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 69070af82b..2d420af211 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9888,14 +9888,14 @@ (define-public r-interactivedisplaybase (define-public r-annotationhub (package (name "r-annotationhub") - (version "2.10.1") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "14v8g44a6zg9j2rwn9x9y8509k0wr2cw8yccliz24glplb40wva4")))) + "11gh7qkgazs90czdqgv74gh2hz26xrmdp6wsz9x5pygbxls8xdw3")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 15cc1a686752c681f2f15ef18d69e7b251cb41b6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:08:27 +0200 Subject: gnu: r-fastseg: Update to 1.26.0. * gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.26.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2d420af211..f704703346 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9923,14 +9923,14 @@ (define-public r-annotationhub (define-public r-fastseg (package (name "r-fastseg") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fastseg" version)) (sha256 (base32 - "0dd7nr3klwz9ailwshnbynhd62lwb8zbbpj6jf3igpb94yi6x2jp")))) + "1yw6hai6hb8qy7akdm4frfp6h4zy93zb68kdj094sanm7kgqmgik")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) -- cgit v1.2.3 From 419e438d52f2b669ec48d19b3a7f20e6c83f463a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:08:50 +0200 Subject: gnu: r-keggrest: Update to 1.20.0. * gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.20.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f704703346..dd6a6da1d6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9953,14 +9953,14 @@ (define-public r-fastseg (define-public r-keggrest (package (name "r-keggrest") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGREST" version)) (sha256 (base32 - "02gwmm79djj55a90dzc80hlgwc6bafl7xd7fnx2q59pk945k3z9c")))) + "1349vidgl9m10l1rbrp3pkwwgi2xcbsw9h9z2xqbvg97lmqc4r8j")))) (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 1ba126e0e4873f6012114067b9aeb468929cf380 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:09:08 +0200 Subject: gnu: r-gage: Update to 2.30.0. * gnu/packages/bioinformatics.scm (r-gage): Update to 2.30.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index dd6a6da1d6..9aee14a090 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9977,14 +9977,14 @@ (define-public r-keggrest (define-public r-gage (package (name "r-gage") - (version "2.28.2") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "0h0mlhns9j7cpfksvdlvx9jb7szm3r1dwqb3s4s8p8hmkb9byyii")))) + "0j3cqxy97lpf146wkmdfaq9680gicmzxvhp6w5pxq3j7ipiy7262")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit v1.2.3 From d1463f1b0c0d35f02ed24e03d6e7ede77a6dbe40 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:09:23 +0200 Subject: gnu: r-genomicfiles: Update to 1.16.0. * gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.16.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9aee14a090..8d6df8ee88 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10006,14 +10006,14 @@ (define-public r-gage (define-public r-genomicfiles (package (name "r-genomicfiles") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFiles" version)) (sha256 (base32 - "0r0wmrs5jycf1kckhnc2sgjmp336srlcjdkpbb1ymm7kazdd0s9n")))) + "0bhsq5czigrjyl9gkb2kpkpl367b3ac5g8s280adkcxggn9g7sxq")))) (properties `((upstream-name . "GenomicFiles"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From d3fb2ad834ceb85c479471dcff1d931624286ab0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:09:42 +0200 Subject: gnu: r-complexheatmap: Update to 1.18.0. * gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 1.18.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8d6df8ee88..341b14476a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10039,14 +10039,14 @@ (define-public r-genomicfiles (define-public r-complexheatmap (package (name "r-complexheatmap") - (version "1.17.1") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ComplexHeatmap" version)) (sha256 (base32 - "1x6kp55iqqsd8bhdl3qch95nfiy2y46ldbbsx1sj1v8f0b0ywwcy")))) + "0z57mrginzd40niy51dvnyqgbrij05ji0dbwqs3x2as80sq28i3q")))) (properties `((upstream-name . "ComplexHeatmap"))) (build-system r-build-system) -- cgit v1.2.3 From 19adb8985433bb2e707b7cb3f43dda6f75e321bd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:10:00 +0200 Subject: gnu: r-dirichletmultinomial: Update to 1.22.0. * gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.22.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 341b14476a..ce54e1eb68 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10069,14 +10069,14 @@ (define-public r-complexheatmap (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DirichletMultinomial" version)) (sha256 (base32 - "1c4s6x0qm20556grcd1xys9kkpnlzpasaai474malwcg6qvgi4x1")))) + "0vcyp81b90in4ls5nbadc66cw2g9aydr94aqifq5j4b7diq74yfs")))) (properties `((upstream-name . "DirichletMultinomial"))) (build-system r-build-system) -- cgit v1.2.3 From bbcd19fb4d856a068ebce05c56c4d4506c04484d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:10:18 +0200 Subject: gnu: r-ensembldb: Update to 2.4.1. * gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.4.1. [propagated-inputs]: Remove r-annotationhub. --- gnu/packages/bioinformatics.scm | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ce54e1eb68..b5873cc492 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10098,19 +10098,18 @@ (define-public r-dirichletmultinomial (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.2.2") + (version "2.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "1yngndkf3588z91z0a2fvkg423p26ajm6xv1p27x0l9mzhhaqq3k")))) + "1l2b4cxiycv05mz4z4f3dhx57r9ksha02psc114h30ldm5rxz8w6")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-annotationfilter" ,r-annotationfilter) - ("r-annotationhub" ,r-annotationhub) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) -- cgit v1.2.3 From 94ae875c0a3999abe06cf273a2f934629fefeebe Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:10:47 +0200 Subject: gnu: r-organismdbi: Update to 1.22.0. * gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.22.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b5873cc492..10c669d3df 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10141,14 +10141,14 @@ (define-public r-ensembldb (define-public r-organismdbi (package (name "r-organismdbi") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OrganismDbi" version)) (sha256 (base32 - "0yxvhwn0m53wfwp0zi81x96argdf7cf1lpymc2as51apvfcnjdl8")))) + "0hb9ni41bjfy5s5ryw2qmqs2sx3i7j47w1g0l8g1pvn7ppnxb6cv")))) (properties `((upstream-name . "OrganismDbi"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 34cc18d4dece2ca225bd0ab9175204e02327e214 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:11:02 +0200 Subject: gnu: r-biovizbase: Update to 1.28.0. * gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.28.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 10c669d3df..17e656d814 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10173,14 +10173,14 @@ (define-public r-organismdbi (define-public r-biovizbase (package (name "r-biovizbase") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biovizBase" version)) (sha256 (base32 - "14l4vhj0a4ssr9m9zdzz3qpd4qw1mhgq5bmxq7jhrq3j9kmd6i2f")))) + "0lkiqdr3ics6hgv47lwkykcy761823bbkhffbn4ykyfzyqwl4p67")))) (properties `((upstream-name . "biovizBase"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From e214a6e6ff67f8e2186cd36bb849d805de58499d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:11:18 +0200 Subject: gnu: r-ggbio: Update to 1.28.0. * gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.28.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 17e656d814..10736eb386 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10214,14 +10214,14 @@ (define-public r-biovizbase (define-public r-ggbio (package (name "r-ggbio") - (version "1.26.1") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggbio" version)) (sha256 (base32 - "1xlmlngn27iwnr21s9di4059kav1a7c1sajx08wja8yn8f7j06hp")))) + "0wszh3w8yia5zw758h837i1q35k99sn444y2hahcxqbdmmlbf7in")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit v1.2.3 From dcd1f0236cf3450bbbf957d94cd29e78e5d64731 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:11:33 +0200 Subject: gnu: r-gqtlbase: Update to 1.12.0. * gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.12.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 10736eb386..262eed3f5f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10290,14 +10290,14 @@ (define-public r-gprofiler (define-public r-gqtlbase (package (name "r-gqtlbase") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gQTLBase" version)) (sha256 (base32 - "1756vfcj2dkkgcmfkkg7qdaig36dv9gfvpypn9rbrky56wm1p035")))) + "1m3ajpqjhw1nwwsn372r44xfxq0a9a0pzsnrprzdjp6mh52p9b5m")))) (properties `((upstream-name . "gQTLBase"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From d26f95d0799d47f08914e4659404f82015b9a750 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:11:55 +0200 Subject: gnu: r-snpstats: Update to 1.30.0. * gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.30.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 262eed3f5f..fc284e06df 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10325,14 +10325,14 @@ (define-public r-gqtlbase (define-public r-snpstats (package (name "r-snpstats") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "snpStats" version)) (sha256 (base32 - "1x9qwynh2hwl24vq02naf4mchpch7xi2pkdrlgw896k28kx0lvir")))) + "0iydgfnm053iw860qa1bbh4f6nwzlsf3vhgq92gvl2v4xsz1jbbs")))) (properties `((upstream-name . "snpStats"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) -- cgit v1.2.3 From 9b0b108ed911f625bffd4243c8184e6f1402d30b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:12:10 +0200 Subject: gnu: r-erma: Update to 0.12.0. * gnu/packages/bioinformatics.scm (r-erma): Update to 0.12.0. [propagated-inputs]: Remove r-foreach; add r-biocparallel, r-genomeinfodb, and r-iranges. --- gnu/packages/bioinformatics.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fc284e06df..57a70cf332 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10384,24 +10384,26 @@ (define-public r-homo-sapiens (define-public r-erma (package (name "r-erma") - (version "0.10.1") + (version "0.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "erma" version)) (sha256 (base32 - "1fi8nc6fbd7i4p9i9hli31xplmdpsxqcdrb8v3nf8fx9klllbdav")))) + "1ka68n18yizlyvb8bpwwcl4hqbsasg8hw8jb3vgy3cd4szji87hh")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) - ("r-foreach" ,r-foreach) + ("r-biocparallel" ,r-biocparallel) + ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicfiles" ,r-genomicfiles) ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) ("r-homo-sapiens" ,r-homo-sapiens) + ("r-iranges" ,r-iranges) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-shiny" ,r-shiny) -- cgit v1.2.3 From 45c29a6e5cdbe675c33193d19b0a4dcddc31f183 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:12:54 +0200 Subject: gnu: r-ldblock: Update to 1.10.0. * gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.10.0. [propagated-inputs]: Add r-biocgenerics. --- gnu/packages/bioinformatics.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 57a70cf332..d51b9e9984 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10422,17 +10422,18 @@ (define-public r-erma (define-public r-ldblock (package (name "r-ldblock") - (version "1.8.1") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ldblock" version)) (sha256 (base32 - "1q8dz8wcq1r7kr635s9q21g36sxkdybk8khhpa4p57qv8r0gppl0")))) + "0c24zvnwsp39d3q0bps13sc441jj9ms2zi34xsb8c392lqmbypvd")))) (build-system r-build-system) (propagated-inputs - `(("r-erma" ,r-erma) + `(("r-biocgenerics" ,r-biocgenerics) + ("r-erma" ,r-erma) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicfiles" ,r-genomicfiles) ("r-go-db" ,r-go-db) -- cgit v1.2.3 From 6929b97583418fca05875339eac3ac3683780766 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:13:23 +0200 Subject: gnu: r-gqtlstats: Update to 1.12.0. * gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.12.0. [propagated-inputs]: Add r-homo-sapiens; remove r-ldblock. --- gnu/packages/bioinformatics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d51b9e9984..d8151d57ac 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10454,14 +10454,14 @@ (define-public r-ldblock (define-public r-gqtlstats (package (name "r-gqtlstats") - (version "1.10.1") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gQTLstats" version)) (sha256 (base32 - "0gvq1sf2zjbkk431x40z6wql3c1rpclnnwa2f1hvykb8mmw70kmq")))) + "19g8qhfgngdc14cw9k4i44cxhs3qva87x56gjzmn25k1yj8qgsp1")))) (properties `((upstream-name . "gQTLstats"))) (build-system r-build-system) (propagated-inputs @@ -10484,8 +10484,8 @@ (define-public r-gqtlstats ("r-ggplot2" ,r-ggplot2) ("r-gqtlbase" ,r-gqtlbase) ("r-hardyweinberg" ,r-hardyweinberg) + ("r-homo-sapiens" ,r-homo-sapiens) ("r-iranges" ,r-iranges) - ("r-ldblock" ,r-ldblock) ("r-limma" ,r-limma) ("r-mgcv" ,r-mgcv) ("r-plotly" ,r-plotly) -- cgit v1.2.3 From fecbbac286c94933a707513b1be35891e9a82984 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:13:51 +0200 Subject: gnu: r-gviz: Update to 1.24.0. * gnu/packages/bioinformatics.scm (r-gviz): Update to 1.24.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d8151d57ac..d13f1426f8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10508,14 +10508,14 @@ (define-public r-gqtlstats (define-public r-gviz (package (name "r-gviz") - (version "1.22.3") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "1grjzrjpzkw572pbvpsvdnfkfgwybl0cnjd7nnk2xdr26wnbsi9a")))) + "1fhli7ahkl5r43j0hc89ib41mfadj6qyrg36i03ncz8zs6iqwpx4")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 2d3c172b728362d3d815bbac33908923c0e8ee23 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:14:06 +0200 Subject: gnu: r-gwascat: Update to 2.12.0. * gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.12.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d13f1426f8..1662fef311 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10554,14 +10554,14 @@ (define-public r-gviz (define-public r-gwascat (package (name "r-gwascat") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gwascat" version)) (sha256 (base32 - "0n5x5i5v6a8wpn5mxmlpkl34b4kyypmymiwww6g61zch7xqrgywi")))) + "08ba9il4vbjjwlbwmqg4ai6ya1p09js9agn95sw0dhc9gqln42hx")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit v1.2.3 From 8db6256f4b16150c5b9684f6cdcf8723fbe82af6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:14:23 +0200 Subject: gnu: r-sushi: Update to 1.18.0. * gnu/packages/bioinformatics.scm (r-sushi): Update to 1.18.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1662fef311..06959d3595 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10594,13 +10594,13 @@ (define-public r-gwascat (define-public r-sushi (package (name "r-sushi") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Sushi" version)) (sha256 (base32 - "0axaqm480z8d0b2ldgxwm0swava1p4irc62bpl17p2k8k78g687g")))) + "1m15hmg4k0qhshyn65xfj5hx7xbaf0kxqw70lxisak6pj1w00l41")))) (properties `((upstream-name . "Sushi"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 4dedecbe7078b8bc688ca4f610097ed8f078ff5d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:14:52 +0200 Subject: gnu: r-fithic: Update to 1.6.0. * gnu/packages/bioinformatics.scm (r-fithic): Update to 1.6.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 06959d3595..d761e1f569 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10616,13 +10616,13 @@ (define-public r-sushi (define-public r-fithic (package (name "r-fithic") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FitHiC" version)) (sha256 (base32 - "12ylhrppi051m7nqsgq95kzd9g9wmp34i0zzfi55cjqawlpx7c6n")))) + "06w4q836bi1mvkbl1saghv4r5p4hxpjg8cp7kgad13ls450kqmyd")))) (properties `((upstream-name . "FitHiC"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From c6c619c1790bf8e4b1348ba9601b7736dc58ed51 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:15:07 +0200 Subject: gnu: r-hitc: Update to 1.24.0. * gnu/packages/bioinformatics.scm (r-hitc): Update to 1.24.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d761e1f569..f74f2d69d4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10640,13 +10640,13 @@ (define-public r-fithic (define-public r-hitc (package (name "r-hitc") - (version "1.22.1") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HiTC" version)) (sha256 (base32 - "0da1jw9my2n2gihs31zyn14wwr23d8v2vij39ll7rm6fma3ydfbl")))) + "0qkk5139f51lwwy1yh7nbkflh5d69prirmhniwam34nlg9rzjm2z")))) (properties `((upstream-name . "HiTC"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From 5cd725d002a83d13cf58a2778866b61a1b980878 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:15:23 +0200 Subject: gnu: r-qvalue: Update to 2.12.0. * gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.12.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f74f2d69d4..d4b9e31cf2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10669,14 +10669,14 @@ (define-public r-hitc (define-public r-qvalue (package (name "r-qvalue") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "qvalue" version)) (sha256 (base32 - "1rd9rnf16kh8wc076kahd9hsb9rfwsbzmz3kjmp0pj6rbiq0051i")))) + "1ndwkj0hh7v4lwylq1v0fkxqs7mfmbcj8kxbdpj1wkvf131z2ns8")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) -- cgit v1.2.3 From 0840352835737e07a1f133acd69fff132db8ae4e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:15:39 +0200 Subject: gnu: r-hdf5array: Update to 1.8.0. * gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.8.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d4b9e31cf2..f51c247b40 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10698,14 +10698,14 @@ (define-public r-qvalue (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "0kcdza41saqv6vlpvqd841awbiwkg84lh0plx6c7fmfgbqv7a0jh")))) + "1l0276qxkhgdxsfck3jmi8jvnsr20g10gjki53g0mqa45wnhm3ck")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From e9c417361e2612a71344fccaaa58862c8aa02592 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:16:03 +0200 Subject: gnu: r-rhdf5lib: Update to 1.2.1. * gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.2.1. [arguments]: Adjust substitutions. --- gnu/packages/bioinformatics.scm | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f51c247b40..f4eb281cb7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10724,14 +10724,14 @@ (define-public r-hdf5array (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.0.0") + (version "1.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "0kkc4rprjbqn2wvbx4d49kk9l91vihccxbl4843qr1wqk6v33r1w")))) + "1y59acac6v8hrhv84gghn9ifsni9xxxacaj177rrl4frmkrz4x3c")))) (properties `((upstream-name . "Rhdf5lib"))) (build-system r-build-system) (arguments @@ -10742,10 +10742,10 @@ (define-public r-rhdf5lib (for-each delete-file '("configure" "configure.ac")) ;; Do not make other packages link with the proprietary libsz. (substitute* "R/zzz.R" - (("'%s/libhdf5_cpp.a %s/libhdf5.a %s/libsz.a'") - "'%s/libhdf5_cpp.a %s/libhdf5.a %s/libhdf5.a'") - (("'%s/libhdf5.a %s/libsz.a'") - "'%s/libhdf5.a %s/libhdf5.a'")) + (("'%s/libhdf5_cpp.a %s/libhdf5.a %s/libsz.a -lz'") + "'%s/libhdf5_cpp.a %s/libhdf5.a %s/libhdf5.a -lz'") + (("'%s/libhdf5.a %s/libsz.a -lz'") + "'%s/libhdf5.a %s/libhdf5.a -lz'")) (with-directory-excursion "src" (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source")) (rename-file (string-append "hdf5-" ,(package-version hdf5)) @@ -10772,8 +10772,7 @@ (define-public r-rhdf5lib (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n") ;; szip is non-free software (("cp \\$\\{SZIP_LIB\\}.*") "") - (("PKG_LIBS = \\$\\{HDF5_LIB\\} \\$\\{SZIP_LIB\\}") - "PKG_LIBS = ${HDF5_LIB}\n"))) + (("\\$\\{USER_LIB_DIR\\}libsz.a") ""))) #t))))) (inputs `(("zlib" ,zlib))) -- cgit v1.2.3 From fd613234b746ce45d60f300191f303982f1ac54d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:16:42 +0200 Subject: gnu: r-beachmat: Update to 1.2.1. * gnu/packages/bioinformatics.scm (r-beachmat): Update to 1.2.1. [inputs]: Add zlib. --- gnu/packages/bioinformatics.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f4eb281cb7..df2d9aa56c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10789,17 +10789,18 @@ (define-public r-rhdf5lib (define-public r-beachmat (package (name "r-beachmat") - (version "1.0.2") + (version "1.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "beachmat" version)) (sha256 (base32 - "0b6dzja5fbx4dawb7ixj67mlhw4fy62pfp20mfp918fy96zmdwqz")))) + "1w90v0jx1zgrfxzx99gdkk0dz2vi25hr51jml1bvq33i64rj7996")))) (build-system r-build-system) (inputs - `(("hdf5" ,hdf5))) + `(("hdf5" ,hdf5) + ("zlib" ,zlib))) (propagated-inputs `(("r-delayedarray" ,r-delayedarray) ("r-hdf5array" ,r-hdf5array) -- cgit v1.2.3 From d99e0938fa30954216bbe2dd3de9a4bd17cdf893 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 12:16:59 +0200 Subject: gnu: r-singlecellexperiment: Update to 1.2.0. * gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.2.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index df2d9aa56c..82177e754c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10817,14 +10817,14 @@ (define-public r-beachmat (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") - (version "1.0.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleCellExperiment" version)) (sha256 (base32 - "1r276i97w64a5vdlg6952gkj7bls909p42zl8fn8yz87cdwyaars")))) + "0mz3chia250v8v6q8r5cqv5fc4bpcw1hhrfr3p7l5i4xi85scpka")))) (properties `((upstream-name . "SingleCellExperiment"))) (build-system r-build-system) -- cgit v1.2.3 From 8ec56b2956697bedf9d85aa1cb03205639ada323 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 13:34:59 +0200 Subject: gnu: r-delayedmatrixstats: Update to 1.2.0. * gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.2.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 82177e754c..fb4a8c85c8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10930,14 +10930,14 @@ (define-public r-scran (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.0.3") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "1cxjbjdq9hg9cm95rci0al7a4pk2h73ym276ahw9q4977zbg6381")))) + "1dasghfy8x27zzmd0igag4mc1gxxxbchsl4hpc1050dj3wnw9w3y")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) -- cgit v1.2.3 From d7e3299987b2b08f06b545b3032f52f0a3421bc1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 13:35:20 +0200 Subject: gnu: r-scran: Update to 1.8.2. * gnu/packages/bioinformatics.scm (r-scran): Update to 1.8.2. [propagated-inputs]: Remove r-zoo; add r-delayedmatrixstats and r-delayedarray. --- gnu/packages/bioinformatics.scm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fb4a8c85c8..e9477501b3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10888,19 +10888,21 @@ (define-public r-scater (define-public r-scran (package (name "r-scran") - (version "1.6.9") + (version "1.8.2") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "0cs64cnf0xjcgmawr210y99j3gxs6aqgh8081n9827kkqnx2y5dm")))) + "0nbn5x75gf9d0p18w7vpkbv30cpdqvp5bz8xvila0h7jla7xdyih")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) ("r-biocgenerics" ,r-biocgenerics) ("r-biocparallel" ,r-biocparallel) + ("r-delayedarray" ,r-delayedarray) + ("r-delayedmatrixstats" ,r-delayedmatrixstats) ("r-dt" ,r-dt) ("r-dynamictreecut" ,r-dynamictreecut) ("r-edger" ,r-edger) @@ -10917,8 +10919,7 @@ (define-public r-scran ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-statmod" ,r-statmod) ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-viridis" ,r-viridis) - ("r-zoo" ,r-zoo))) + ("r-viridis" ,r-viridis))) (home-page "https://bioconductor.org/packages/scran") (synopsis "Methods for single-cell RNA-Seq data analysis") (description "This package implements a variety of low-level analyses of -- cgit v1.2.3 From 7799a01ef1b36c2a0f20ee07981bb5cd7fd64313 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 13:35:58 +0200 Subject: gnu: r-rgraphviz: Update to 2.24.0. * gnu/packages/graph.scm (r-rgraphviz): Update to 2.24.0. --- gnu/packages/graph.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index a9ee949855..b393919e66 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -155,14 +155,14 @@ (define-public r-diffusionmap (define-public r-rgraphviz (package (name "r-rgraphviz") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rgraphviz" version)) (sha256 (base32 - "1y9nyjffa9644jch0p2i3w302fmnyc2kb0c3z1f3d5zp1p4qmyqv")))) + "1037hzfxxcn46w6y88wm3kk2nixj0s8bk0hkmnshpxih3kmnvqby")))) (properties `((upstream-name . "Rgraphviz"))) (build-system r-build-system) ;; FIXME: Rgraphviz bundles the sources of an older variant of -- cgit v1.2.3 From 83402242eaacbea480a0aa746b024bf44ad23b7d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 13:36:09 +0200 Subject: gnu: r-mvtnorm: Update to 1.0-8. * gnu/packages/statistics.scm (r-mvtnorm): Update to 1.0-8. --- gnu/packages/statistics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm index 7a6b674a1d..9b27736f7a 100644 --- a/gnu/packages/statistics.scm +++ b/gnu/packages/statistics.scm @@ -3533,13 +3533,13 @@ (define-public r-r-rsp (define-public r-mvtnorm (package (name "r-mvtnorm") - (version "1.0-7") + (version "1.0-8") (source (origin (method url-fetch) (uri (cran-uri "mvtnorm" version)) (sha256 (base32 - "0f7hzflygdnbwvzadr3knhybhanwg7agqddclj6mhbvwqpgb0qyh")))) + "0la42lylb7cjrcrc285bn69bz9kyg556xw317iz139dp1yswl410")))) (build-system r-build-system) (inputs `(("gfortran" ,gfortran))) -- cgit v1.2.3 From 92963798a6b81989c52bc199ef224605d9b90063 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sat, 2 Jun 2018 13:42:05 +0200 Subject: gnu: r-scater: Update to 1.8.0. * gnu/packages/bioinformatics.scm (r-scater): Update to 1.8.0. [propagated-inputs]: Add r-delayedarray ad r-delayedmatrixstats; remove r-matrixstats and r-biomart. --- gnu/packages/bioinformatics.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'gnu/packages') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e9477501b3..2445991746 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10844,27 +10844,27 @@ (define-public r-singlecellexperiment (define-public r-scater (package (name "r-scater") - (version "1.6.3") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "0q3s96gf8saa1dq2fvmpl0jyj7bx3wrdfck3hanb8pxkcir2p7dn")))) + "0bhpikgz3b9f510dawsay4zry9rlp8vjx5n6zvwbcpwrd94p3903")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) - ("r-biomart" ,r-biomart) ("r-data-table" ,r-data-table) + ("r-delayedarray" ,r-delayedarray) + ("r-delayedmatrixstats" ,r-delayedmatrixstats) ("r-dplyr" ,r-dplyr) ("r-edger" ,r-edger) ("r-ggbeeswarm" ,r-ggbeeswarm) ("r-ggplot2" ,r-ggplot2) ("r-limma" ,r-limma) ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) ("r-plyr" ,r-plyr) ("r-rcpp" ,r-rcpp) ("r-reshape2" ,r-reshape2) -- cgit v1.2.3