diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 52 |
1 files changed, 26 insertions, 26 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index cbf08c5dd2..6f835b3875 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1654,14 +1654,14 @@ gapped, local, and paired-end alignment modes.") (define-public bowtie1 (package (name "bowtie1") - (version "1.2.3") + (version "1.3.0") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/bowtie-bio/bowtie/" - version "/bowtie-src-x86_64.zip")) + version "/bowtie-" version "-src.zip")) (sha256 (base32 - "0vmiqdhc9dzyfy9sh6vgi7k9xy2hiw8g87vbamnc6cgpm179zsa4")) + "11dbihdnrizc6qhx9xsw77w3q5ssx642alaqzvhxx32ak9glvq04")) (modules '((guix build utils))) (snippet '(substitute* "Makefile" @@ -1672,7 +1672,7 @@ gapped, local, and paired-end alignment modes.") (arguments '(#:tests? #f ; no "check" target #:make-flags - (list "all" + (list "CC=gcc" "all" (string-append "prefix=" (assoc-ref %outputs "out"))) #:phases (modify-phases %standard-phases @@ -7311,14 +7311,14 @@ includes software to (define-public r-genefilter (package (name "r-genefilter") - (version "1.72.0") + (version "1.72.1") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "0929g6c4v2qhgipgrh1a5gv6444sm2dp52x9c3qbk03i8wzc6633")))) + "1c6h3qnjvphs977qhv5vafvsb108r0q7xhaayly6qv6adqfn94rn")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran) @@ -7477,14 +7477,14 @@ the graph algorithms contained in the Boost library.") (define-public r-gseabase (package (name "r-gseabase") - (version "1.52.0") + (version "1.52.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GSEABase" version)) (sha256 (base32 - "0lcxbxfg62zdf2nql49asn3555cqrrxpjm2xsxf7vlxv84dl6r44")))) + "0dawh1kjmf6921jm77j2s2phrq5237pjc4sdh8fkln89gf48zx6i")))) (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs @@ -7611,14 +7611,14 @@ ungapped alignment formats.") (define-public r-systempiper (package (name "r-systempiper") - (version "1.24.2") + (version "1.24.3") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "0blvvci57q12sl18yvw07233rfnj47mfadzm0pdpig1ll5z6ld2j")))) + "0ffazyl2q9plbhwlxi04s3fvnli6qj95n7bkjc21535bbi08xfki")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs @@ -8028,13 +8028,13 @@ checks on R packages that are to be submitted to the Bioconductor repository.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.28.0") + (version "0.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "0rfn46g2mfda01s75vpcfn5jc7xkp0jrl5v79gyd40jm37p4j1zv")))) + "0fhf4lsfxrim7glazh6ng46ykzaly5ggwpg170vcz4cc24prv0rh")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) @@ -8055,13 +8055,13 @@ S4Vectors package itself.") (define-public r-iranges (package (name "r-iranges") - (version "2.24.0") + (version "2.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "1lfc8xz45v63y3q40im00i944hi0p9idwhx50w3nzkwdpk79315b")))) + "01mx46a82vd3gz705pj0kk4wpxg683s8jqxchzjia3gz00b4qw52")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) @@ -8137,13 +8137,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-edger (package (name "r-edger") - (version "3.32.0") + (version "3.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "0dkjd6li270icy1x5qbzpakk9bx712mdm5k32lrr3yrggq92jhjg")))) + "1gaic8qf6a6sy0bmydh1xzf52w0wnq31aanpvw3a30pfsi218bcp")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -8340,13 +8340,13 @@ annotation data packages using SQLite data storage.") (define-public r-biomart (package (name "r-biomart") - (version "2.46.0") + (version "2.46.3") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "1zpdm8nw1d0m31pdmzw1dccbd6iczfhiklhm4d325zkzf3jrkvxf")))) + "0gwmd0ykpv0gyh34c56g5m12lil20fvig49f3ih1jxrxf3q4wmq7")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -8475,13 +8475,13 @@ tab-delimited (tabix) files.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.16.0") + (version "0.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "1564wnradxw15nsnv6w2wd3xngcs3xa1mlibbq3hygi5fcx4fk3g")))) + "1d75zrhha1v7dhbvjp6a4iap441l5k268w0jjxklpqywbqns7l3d")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) @@ -9771,13 +9771,13 @@ number detection tools.") (define-public r-methylkit (package (name "r-methylkit") - (version "1.16.0") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 - "11pmn191n0ga28x1w20cm2cmw8kddl29q6h2xfjjba5bspp2g613")))) + "1c9b11gfh3cc37iwym9rgsba3mh2xkp78a1gvnjqhzlkiz667mn3")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs @@ -10111,14 +10111,14 @@ structure (pcaRes) to provide a common interface to the PCA results.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.16.0") + (version "2.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "0cvcdmq1glifga5qwv9j3lgj31dcrcc6ql4kkk83jy4y43v2zxlx")))) + "0hxzs9zzljywqxr7q388hshpy1pdryhl0zkwffqbxpf5pcf92d3h")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs @@ -10430,14 +10430,14 @@ microarrays or GRanges for sequencing data.") (define-public r-gage (package (name "r-gage") - (version "2.40.0") + (version "2.40.1") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "0xm50wgjjjymv71mbv1clnhx4m12nrd1pc6vfplpdqr5q49v3yd5")))) + "1iawa03dy4bl333my69d4sk7d74cjzfg5dpcxga6q5dglan4sp8r")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) |