gnu: r-annotationfilter: Update to 1.4.0.

[jackhill/guix/guix.git] / gnu / packages / bioinformatics.scm

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7318e16..fb2ce3c 100644 (file)
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7885,13 +7885,13 @@ genome data packages and support for efficient SNP representation.")
 (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)
@@ -7905,13 +7905,13 @@ microarray data, using nearest neighbor averaging.")
 (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)
@@ -7932,13 +7932,13 @@ reference point and sorted by a user defined feature.")
 (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)
@@ -8110,14 +8110,14 @@ annotations for the genome of the model mouse Mus musculus.")
 (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")
@@ -8356,14 +8356,14 @@ Biostrings objects.")
 (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
@@ -8408,13 +8408,13 @@ two-dimensional genome scans.")
 (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)
@@ -8450,14 +8450,14 @@ secondary structure and comparative analysis in R.")
 (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 @@ secondary structure and comparative analysis in R.")
     (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
@@ -8477,14 +8477,14 @@ of other R packages who wish to make use of HTSlib.")
 (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)
@@ -8599,18 +8599,19 @@ library implementing most of the pipeline's features.")
 (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)
@@ -8774,13 +8775,13 @@ kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
 (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")
@@ -8796,39 +8797,18 @@ of gene-level counts.")
 (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
@@ -8844,13 +8824,13 @@ the available RAM.")
 (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)