Merge remote-tracking branch 'origin/master' into core-updates

1 files changed, 64 insertions, 27 deletions

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b191c8b4ae..6210a4b3f1 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -798,14 +798,14 @@ closely reconstructs the mutational profile.")
 (define-public r-nmf
   (package
     (name "r-nmf")
-    (version "0.22.0")
+    (version "0.23.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "NMF" version))
        (sha256
         (base32
-         "0b2ls3x1nkrnam45hagpys624nzxj3v7kxnp0q216yakvx5h57cq"))))
+         "0ls7q9yc9l1z10jphq5a11wkfgcxc3gm3sfjj376zx3vnc0wl30g"))))
     (properties `((upstream-name . "NMF")))
     (build-system r-build-system)
     (propagated-inputs
@@ -826,6 +826,8 @@ closely reconstructs the mutational profile.")
        ("r-reshape2" ,r-reshape2)
        ("r-rngtools" ,r-rngtools)
        ("r-stringr" ,r-stringr)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
     (home-page "http://renozao.github.io/NMF")
     (synopsis "Algorithms and framework for nonnegative matrix factorization")
     (description
@@ -1502,14 +1504,14 @@ browser.")
 (define-public r-oligoclasses
   (package
     (name "r-oligoclasses")
-    (version "1.50.0")
+    (version "1.50.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "oligoClasses" version))
        (sha256
         (base32
-         "05jy9qz3ir4maxackr1xqlfi1czhy1qd22wwibjdhfh5dp534cpn"))))
+         "1d8c3i8v8kcm1afgpz6zc1iysip7993y8456cqxl37f7n6n0ax67"))))
     (properties `((upstream-name . "oligoClasses")))
     (build-system r-build-system)
     (propagated-inputs
@@ -1537,14 +1539,14 @@ packages.")
 (define-public r-oligo
   (package
     (name "r-oligo")
-    (version "1.52.0")
+    (version "1.52.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "oligo" version))
        (sha256
         (base32
-         "102szyiicws4c6l3k282236ml1m1vl9zmars4q1kdjfnvsyclfc4"))))
+         "1gpvr33pwzz1glzajcipvjcplb7yxvjj00q0ybqcc3wa47bhfkwd"))))
     (properties `((upstream-name . "oligo")))
     (build-system r-build-system)
     (inputs `(("zlib" ,zlib)))
@@ -3622,14 +3624,14 @@ information about samples and features can be added to the plot.")
 (define-public r-gosemsim
   (package
     (name "r-gosemsim")
-    (version "2.14.0")
+    (version "2.14.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "GOSemSim" version))
        (sha256
         (base32
-         "0mg4d8whq90iyl2jjj5dx3kyar17yqn00jvia3b4a8lhmjw8l1hk"))))
+         "0v4q9xr1cm5xr08pgbzrss41kh3yz7xyh31n55l0sjmr1629ykln"))))
     (properties `((upstream-name . "GOSemSim")))
     (build-system r-build-system)
     (propagated-inputs
@@ -3810,14 +3812,14 @@ All the visualization methods are developed based on ggplot2 graphics.")
 (define-public r-clusterprofiler
   (package
     (name "r-clusterprofiler")
-    (version "3.16.0")
+    (version "3.16.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "clusterProfiler" version))
        (sha256
         (base32
-         "0m7919gzrd2fddb4kcznwpshhab1ha2yppnkxg11zmh40wcdawyi"))))
+         "11zsgb8wbdv8r4c04iczz4aala4yw4ai7rz8igdzz87c0940nxkb"))))
     (properties
      `((upstream-name . "clusterProfiler")))
     (build-system r-build-system)
@@ -3832,6 +3834,7 @@ All the visualization methods are developed based on ggplot2 graphics.")
        ("r-magrittr" ,r-magrittr)
        ("r-plyr" ,r-plyr)
        ("r-qvalue" ,r-qvalue)
+       ("r-rlang" ,r-rlang)
        ("r-rvcheck" ,r-rvcheck)
        ("r-tidyr" ,r-tidyr)))
     (native-inputs
@@ -4087,7 +4090,8 @@ Affymetrix arrays.")
     (properties `((upstream-name . "abseqR")))
     (build-system r-build-system)
     (inputs
-     `(("pandoc" ,ghc-pandoc)))
+     `(("pandoc" ,pandoc)
+       ("pandoc-citeproc" ,pandoc-citeproc)))
     (propagated-inputs
      `(("r-biocparallel" ,r-biocparallel)
        ("r-biocstyle" ,r-biocstyle)
@@ -4287,14 +4291,14 @@ Bioconductor.")
 (define-public r-motifstack
   (package
     (name "r-motifstack")
-    (version "1.32.0")
+    (version "1.32.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "motifStack" version))
        (sha256
         (base32
-         "008f2mjcyyiz84ilrsldpqwvxy2lp93hjggrq4nrqwi78nyx3ls5"))))
+         "02vmkgn36n5xpmizy33znlzgmi3w5hnhsibgisbnhwwgxpkrwpcd"))))
     (properties `((upstream-name . "motifStack")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5236,14 +5240,14 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID
 (define-public r-rbowtie2
   (package
     (name "r-rbowtie2")
-    (version "1.10.0")
+    (version "1.10.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rbowtie2" version))
        (sha256
         (base32
-         "1z2dn0q3wcw8b9ibx388kh7p5km16i71sw9miqj3daw7g0v5bxp3"))))
+         "19v7wfvrd53j618c1xbiqnlsf2kxw697myryx0vb9s2aspknyzz7"))))
     (properties `((upstream-name . "Rbowtie2")))
     (build-system r-build-system)
     (inputs
@@ -5314,14 +5318,14 @@ Infinium HumanMethylation 450k assay.")
 (define-public r-biocfilecache
   (package
     (name "r-biocfilecache")
-    (version "1.12.0")
+    (version "1.12.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocFileCache" version))
        (sha256
         (base32
-         "02chrzwccmazi7rdfpyriizhbgxyxlmprlw32w05wk54as6wrxv8"))))
+         "02yayjyliaqxcwqa0n2ccmsfflskqzf0gvdibh2r3nz5bi66imkf"))))
     (properties `((upstream-name . "BiocFileCache")))
     (build-system r-build-system)
     (propagated-inputs
@@ -5376,14 +5380,14 @@ Gaussian distributions.")
 (define-public r-rbowtie
   (package
     (name "r-rbowtie")
-    (version "1.28.0")
+    (version "1.28.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rbowtie" version))
        (sha256
         (base32
-         "06y1qp915dlwjdi2fs3344sgya55pcv07f3i61y0cxb0bhbcgvrz"))))
+         "0589ggbfx6di42wvqyhnzgrhmb52swr3r5z22w6b8x0z2y7hl8b3"))))
     (properties `((upstream-name . "Rbowtie")))
     (build-system r-build-system)
     (inputs
@@ -5781,14 +5785,14 @@ annotations.")
 (define-public r-rsubread
   (package
     (name "r-rsubread")
-    (version "2.2.4")
+    (version "2.2.6")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Rsubread" version))
        (sha256
         (base32
-         "0yznfqgp5cbz68n3rrfvm752267da16kl538zdrb1g1aw9zdfqc6"))))
+         "04h79qhq93d8id0rr5xnj9vf82ygwxzdlnck78yv738xd0jjvnpm"))))
     (properties `((upstream-name . "Rsubread")))
     (build-system r-build-system)
     (inputs `(("zlib" ,zlib)))
@@ -7048,14 +7052,14 @@ arrays based on fast wavelet-based functional models.")
 (define-public r-variancepartition
   (package
     (name "r-variancepartition")
-    (version "1.18.2")
+    (version "1.18.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "variancePartition" version))
        (sha256
         (base32
-         "19bhkb8vd44m3nkznw075fx3y2p3a1bsazbhcfiqw9n4190k9bgv"))))
+         "1jrlhi2c5ibvq8a41g5hwdq4kk4rdd7m464rz5767zaaci7l2ay0"))))
     (properties
      `((upstream-name . "variancePartition")))
     (build-system r-build-system)
@@ -7762,14 +7766,14 @@ different graph related packages produced by Bioconductor.")
 (define-public r-experimenthub
   (package
     (name "r-experimenthub")
-    (version "1.14.0")
+    (version "1.14.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ExperimentHub" version))
        (sha256
         (base32
-         "18d6kjfavy5b769gpkblihdkz2nz2hsgyjki8mp1sywi0ik08ncd"))))
+         "1kgvprchz1fg8pl1irj62mk2gyb4jcc9iimpypv4c2iccy5bp84x"))))
     (properties `((upstream-name . "ExperimentHub")))
     (build-system r-build-system)
     (propagated-inputs
@@ -7955,14 +7959,14 @@ analytics on packages.")
 (define-public r-biocset
   (package
     (name "r-biocset")
-    (version "1.2.1")
+    (version "1.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocSet" version))
        (sha256
         (base32
-         "14dmkc878lskbm001kgjyqmrwnn6s032z4h64f617f1xd9zx9wrj"))))
+         "041hq3rp0kv7kjwcjjrksk8lw3sj6j1v3wdcr8z611k0g0z6p0cj"))))
     (properties `((upstream-name . "BiocSet")))
     (build-system r-build-system)
     (propagated-inputs
@@ -8116,3 +8120,36 @@ dimensional mass cytometry data.")
 Tool) analysis automatic by constructing a HTTP POST request according to
 user's input and automatically retrieving results from GREAT web server.")
     (license license:expat)))
+
+(define-public r-m3c
+  (package
+    (name "r-m3c")
+    (version "1.10.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "M3C" version))
+       (sha256
+        (base32
+         "0zq8lm4280p8h65i7myscwa4srs5ajh944xv6zni2f5sjyp7ij2y"))))
+    (properties `((upstream-name . "M3C")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-cluster" ,r-cluster)
+       ("r-corpcor" ,r-corpcor)
+       ("r-doparallel" ,r-doparallel)
+       ("r-dosnow" ,r-dosnow)
+       ("r-foreach" ,r-foreach)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-matrix" ,r-matrix)
+       ("r-matrixcalc" ,r-matrixcalc)
+       ("r-rtsne" ,r-rtsne)
+       ("r-umap" ,r-umap)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/M3C")
+    (synopsis "Monte Carlo reference-based consensus clustering")
+    (description
+     "M3C is a consensus clustering algorithm that uses a Monte Carlo
+simulation to eliminate overestimation of @code{K} and can reject the null
+hypothesis @code{K=1}.")
+    (license license:agpl3+)))