gnu: Fix typos in descriptions.

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

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 71ff6ae..2b0303b 100644 (file)
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3196,7 +3196,7 @@ sequencing tag position and orientation.")
 (define-public mafft
   (package
     (name "mafft")
-    (version "7.305")
+    (version "7.310")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -3205,7 +3205,7 @@ sequencing tag position and orientation.")
               (file-name (string-append name "-" version ".tgz"))
               (sha256
                (base32
-                "0ziim7g58n3z8gppsa713f5fxprl60ldj3xck186z0n9dpp06i8r"))))
+                "0gbsaz6z2qa307kd7wfb06c3y4ikmv1hsdvlns11f6zq4w1z9pwc"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; no automated tests, though there are tests in the read me
@@ -4041,7 +4041,7 @@ extremely diverse sets of genomes.")
 (define-public raxml
   (package
     (name "raxml")
-    (version "8.2.9")
+    (version "8.2.10")
     (source
      (origin
        (method url-fetch)
@@ -4052,7 +4052,7 @@ extremely diverse sets of genomes.")
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "1pv8p2fy67y21a9y4cm7xpvxqjwz2v4201flfjshdq1p8j52rqf7"))))
+         "13s7aspfdcfr6asynwdg1x6vznys6pzap5f8wsffbnnwpkkg9ya8"))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; There are no tests.
@@ -5356,40 +5356,18 @@ information as possible.")
 (define-public r-vegan
   (package
     (name "r-vegan")
-    (version "2.4-2")
+    (version "2.4-3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "vegan" version))
        (sha256
         (base32
-         "12wf64izrpq9z3ix7mgm5421mq0xsm8dw5qblvcrz452nfhjf5w9"))))
+         "15zcxfix2d854897k1lr0sfmj2n00339nlsppcr3zrb238lb2mi5"))))
     (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'revert-test-deletion
-           ;; The distributed sources do not include tests with the CRAN
-           ;; package.  Here we revert the commit
-           ;; `591d0e8ba1deaaf82445474ec6619c0b43db4e63' which deletes these
-           ;; tests.  There are plans to not delete tests in future as
-           ;; documented at https://github.com/vegandevs/vegan/issues/181.
-           (lambda* (#:key inputs #:allow-other-keys)
-             (zero?
-              (system* "patch" "-R" "-p1" "-i"
-                       (assoc-ref inputs "r-vegan-delete-tests-patch"))))))))
     (native-inputs
      `(("gfortran" ,gfortran)
-       ("r-knitr" ,r-knitr)
-       ("r-vegan-delete-tests-patch"
-        ,(origin
-           (method url-fetch)
-           (uri (string-append
-                 "https://github.com/vegandevs/vegan/commit/"
-                 "591d0e8ba1deaaf82445474ec6619c0b43db4e63.patch"))
-           (sha256
-            (base32
-             "0b1bi7y4jjdl3ph721vm9apm51dr2z9piwvhy4355sf2b4kyyj5a"))))))
+       ("r-knitr" ,r-knitr)))
     (propagated-inputs
      `(("r-cluster" ,r-cluster)
        ("r-lattice" ,r-lattice)
@@ -5428,7 +5406,7 @@ data types as well.")
     (home-page
      "http://bioconductor.org/packages/annotate")
     (synopsis "Annotation for microarrays")
-    (description "This package provides R enviroments for the annotation of
+    (description "This package provides R environments for the annotation of
 microarrays.")
     (license license:artistic2.0)))
 
@@ -5497,14 +5475,6 @@ high-throughput sequencing experiments.")
          "1walwkqryn1gnwz7zryr5764a0p6ia7ag4w6w9n8fskg8dkg0fqs"))))
     (properties `((upstream-name . "DESeq2")))
     (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'link-against-armadillo
-           (lambda _
-             (substitute* "src/Makevars"
-               (("PKG_LIBS =" prefix)
-                (string-append prefix "-larmadillo"))))))))
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
        ("r-biocgenerics" ,r-biocgenerics)
@@ -5532,14 +5502,14 @@ distribution.")
 (define-public r-annotationforge
   (package
     (name "r-annotationforge")
-    (version "1.16.0")
+    (version "1.16.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AnnotationForge" version))
        (sha256
         (base32
-         "02msyb9p3hywrryx00zpjkjl126mrv827i1ah1092s0cplm6xxvf"))))
+         "0l1g9hy88sh5g567svyfd8pnjvkyklkn6a3gjn8zalvh62qqjjq1"))))
     (properties
      `((upstream-name . "AnnotationForge")))
     (build-system r-build-system)
@@ -5671,14 +5641,14 @@ testing and other simple calculations.")
 (define-public r-shortread
   (package
     (name "r-shortread")
-    (version "1.32.0")
+    (version "1.32.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ShortRead" version))
        (sha256
         (base32
-         "0mjdlg92x5qw4x2djc4dv5lxwl7ai6ix56nnf86zr07jk8vc7yls"))))
+         "1m7lbfxs7xwcy9xs76zy5rky2mb96anvh457xfw60lh3kygwfpxc"))))
     (properties `((upstream-name . "ShortRead")))
     (build-system r-build-system)
     (inputs
@@ -5818,7 +5788,7 @@ track.  The database is exposed as a @code{TxDb} object.")
 (define-public vsearch
   (package
     (name "vsearch")
-    (version "2.4.2")
+    (version "2.4.3")
     (source
      (origin
        (method url-fetch)
@@ -5828,7 +5798,7 @@ track.  The database is exposed as a @code{TxDb} object.")
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32
-         "15zy2d9xvgbgdjlxvrhj8s5ga42p13k7a3xv015ingn0bi1p3n6w"))
+         "0hc110ycqpa54nr6x173qg7190hk08qp7yz7zzqxlsypqnpc5zzp"))
        (patches (search-patches "vsearch-unbundle-cityhash.patch"))
        (snippet
         '(begin
@@ -6256,13 +6226,13 @@ abnormal copy number.")
 (define-public r-s4vectors
   (package
     (name "r-s4vectors")
-    (version "0.12.1")
+    (version "0.12.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "S4Vectors" version))
               (sha256
                (base32
-                "0i36y3w36h3d8rmazxcrip4gvn54rd9av1wz4lygsprrjmylfhcc"))))
+                "0syx0qgipx97zsp3b8afhzamsr30835a2a99yb9wnq7b50g3v3p1"))))
     (properties
      `((upstream-name . "S4Vectors")))
     (build-system r-build-system)
@@ -6283,14 +6253,14 @@ S4Vectors package itself.")
 (define-public r-seqinr
   (package
     (name "r-seqinr")
-    (version "3.3-3")
+    (version "3.3-6")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "seqinr" version))
         (sha256
           (base32
-            "0rk4yba8km26c0rh1f4h474zsb5n6kjmqsi55bnzr6p8pymp18hj"))))
+            "13d0qxm2244wgdl2dy2s8vnrnf5fx4n47if9gkb49dqx6c0sx8s2"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ade4" ,r-ade4)
@@ -6308,13 +6278,13 @@ utilities for sequence data management under the ACNUC system.")
 (define-public r-iranges
   (package
     (name "r-iranges")
-    (version "2.8.1")
+    (version "2.8.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "IRanges" version))
               (sha256
                (base32
-                "0cryqnpqb3p6l9jjw27hyqd550sxlljls3ka7b9rb38hkji7b5hw"))))
+                "0x8h74ik3xwdnwrkn89hq5ll0qa1lp9jgzlbmpa02dpws7snfwyr"))))
     (properties
      `((upstream-name . "IRanges")))
     (build-system r-build-system)
@@ -6391,13 +6361,13 @@ CAGE.")
 (define-public r-variantannotation
   (package
     (name "r-variantannotation")
-    (version "1.20.2")
+    (version "1.20.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "VariantAnnotation" version))
               (sha256
                (base32
-                "165wda1d2jagd907pnra4m3sla66icyqxvd60xpv09jl5agd5mn9"))))
+                "10v8apgfw57nd4dxmdxdrijxpw135jpp2p8wrk3wjpb3hhfjp1qj"))))
     (properties
      `((upstream-name . "VariantAnnotation")))
     (inputs
@@ -6592,13 +6562,13 @@ powerful online queries from gene annotation to database mining.")
 (define-public r-biocparallel
   (package
     (name "r-biocparallel")
-    (version "1.8.1")
+    (version "1.8.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocParallel" version))
               (sha256
                (base32
-                "123i928rwi4h4sy4fpysv6pinw5nns0sm3myxi2ghqhm34ws8gyl"))))
+                "18zpa0vl375n9pvxsgbid1k96m17nqqgv1g1sfnlmm7kj34jxg6v"))))
     (properties
      `((upstream-name . "BiocParallel")))
     (build-system r-build-system)
@@ -6642,13 +6612,13 @@ biological sequences or sets of sequences.")
 (define-public r-rsamtools
   (package
     (name "r-rsamtools")
-    (version "1.26.1")
+    (version "1.26.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "Rsamtools" version))
               (sha256
                (base32
-                "0pf4f6brf4bl5zgjrah0f38qslazrs49ayqgyh0xfqgrh63yx4ck"))))
+                "118nsajgghi4cy3h0wi7777kc70a5j1fdyxv5n1dy01glix2z4qk"))))
     (properties
      `((upstream-name . "Rsamtools")))
     (build-system r-build-system)