From 8e54aafa3903b9bbf898170a86e4544db0ad23d3 Mon Sep 17 00:00:00 2001
From: zimoun <zimon.toutoune@gmail.com>
Date: Mon, 13 Sep 2021 16:20:27 +0200
Subject: gnu: Add r-simplifyenrichment.

* gnu/packages/bioconductor.scm (r-simplifyenrichment): New variable.
---
 gnu/packages/bioconductor.scm | 39 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 25202410e5..062867b2ab 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4236,6 +4236,45 @@ purposes.  The package also contains legacy support for early single-end,
 ungapped alignment formats.")
     (license license:artistic2.0)))
 
+(define-public r-simplifyenrichment
+  (package
+    (name "r-simplifyenrichment")
+    (version "1.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "simplifyEnrichment" version))
+       (sha256
+        (base32
+         "0rqa414kvyjjmj4932zk39rqa14z13b57rkrxdrf16jmq2r437vh"))))
+    (properties
+     `((upstream-name . "simplifyEnrichment")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-circlize" ,r-circlize)
+       ("r-clue" ,r-clue)
+       ("r-cluster" ,r-cluster)
+       ("r-complexheatmap" ,r-complexheatmap)
+       ("r-digest" ,r-digest)
+       ("r-getoptlong" ,r-getoptlong)
+       ("r-go-db" ,r-go-db)
+       ("r-gosemsim" ,r-gosemsim)
+       ("r-matrix" ,r-matrix)
+       ("r-org-hs-eg-db" ,r-org-hs-eg-db)
+       ("r-proxyc" ,r-proxyc)
+       ("r-slam" ,r-slam)
+       ("r-tm" ,r-tm)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/jokergoo/simplifyEnrichment")
+    (synopsis "Simplify functional enrichment results")
+    (description "This package provides a new clustering algorithm, binary
+cut, for clustering similarity matrices of functional terms is implemeted in
+this package.  It also provides functionalities for visualizing, summarizing
+and comparing the clusterings.")
+    (license license:expat)))
+
 (define-public r-trajectoryutils
   (package
     (name "r-trajectoryutils")
-- 
cgit v1.2.3


From ca962b5ba99c53bb91a2f82a4ecedf27d1e59f44 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 23 Sep 2021 14:46:30 +0200
Subject: gnu: Add r-omnipathr.

* gnu/packages/bioconductor.scm (r-omnipathr): New variable.
---
 gnu/packages/bioconductor.scm | 51 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 51 insertions(+)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 062867b2ab..e163d33b11 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -14641,6 +14641,57 @@ with a nested autoregressive correlated error structure for the effect of
 interest on transformed methylation proportions.")
     (license license:expat)))
 
+(define-public r-omnipathr
+  (package
+    (name "r-omnipathr")
+    (version "3.0.4")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "OmnipathR" version))
+       (sha256
+        (base32 "0rbq3h3cp5dgpy5ifmbnfm6z8w4jv45wjzyl1f4qacgrbyf2l30a"))))
+    (properties `((upstream-name . "OmnipathR")))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'set-HOME
+           (lambda _ (setenv "HOME" "/tmp"))))))
+    (propagated-inputs
+     `(("r-checkmate" ,r-checkmate)
+       ("r-curl" ,r-curl)
+       ("r-digest" ,r-digest)
+       ("r-dplyr" ,r-dplyr)
+       ("r-httr" ,r-httr)
+       ("r-igraph" ,r-igraph)
+       ("r-jsonlite" ,r-jsonlite)
+       ("r-later" ,r-later)
+       ("r-logger" ,r-logger)
+       ("r-magrittr" ,r-magrittr)
+       ("r-progress" ,r-progress)
+       ("r-purrr" ,r-purrr)
+       ("r-rappdirs" ,r-rappdirs)
+       ("r-readr" ,r-readr)
+       ("r-readxl" ,r-readxl)
+       ("r-rlang" ,r-rlang)
+       ("r-stringr" ,r-stringr)
+       ("r-tibble" ,r-tibble)
+       ("r-tidyr" ,r-tidyr)
+       ("r-tidyselect" ,r-tidyselect)
+       ("r-xml2" ,r-xml2)
+       ("r-yaml" ,r-yaml)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page "https://saezlab.github.io/OmnipathR/")
+    (synopsis "OmniPath web service client and more")
+    (description
+     "This package provides a client for the OmniPath web service and many
+other resources.  It also includes functions to transform and pretty print
+some of the downloaded data, functions to access a number of other resources.
+Furthermore, OmnipathR features a close integration with the NicheNet method
+for ligand activity prediction from transcriptomics data.")
+    (license license:expat)))
+
 (define-public r-biscuiteer
   (package
     (name "r-biscuiteer")
-- 
cgit v1.2.3


From 708fe49523de255df3898e78b3ae5a865218c0da Mon Sep 17 00:00:00 2001
From: Tobias Geerinckx-Rice <me@tobias.gr>
Date: Mon, 27 Sep 2021 16:32:55 +0200
Subject: gnu: r-simplifyenrichment: Fix typo in description.
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* gnu/packages/bioconductor.scm (r-simplifyenrichment)[description]:
Fix ‘implemeted’ typo.
---
 gnu/packages/bioconductor.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e163d33b11..4ec4e78791 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4270,7 +4270,7 @@ ungapped alignment formats.")
     (home-page "https://github.com/jokergoo/simplifyEnrichment")
     (synopsis "Simplify functional enrichment results")
     (description "This package provides a new clustering algorithm, binary
-cut, for clustering similarity matrices of functional terms is implemeted in
+cut, for clustering similarity matrices of functional terms is implemented in
 this package.  It also provides functionalities for visualizing, summarizing
 and comparing the clusterings.")
     (license license:expat)))
-- 
cgit v1.2.3


From e8aab58d0c8f091ea30891d5927f04e99b8abb08 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Sep 2021 23:28:02 +0200
Subject: gnu: r-affxparser: Update to 1.64.1.

* gnu/packages/bioconductor.scm (r-affxparser): Update to 1.64.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4ec4e78791..bf102e01f7 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1971,14 +1971,14 @@ CDF file formats.")
 (define-public r-affxparser
   (package
     (name "r-affxparser")
-    (version "1.64.0")
+    (version "1.64.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affxparser" version))
        (sha256
         (base32
-         "0n3yyrglzqzw0wqxl9igqvkj8qslw6yjkym3vcq0c93kkg7vk01l"))))
+         "0lr0kmp087j2g4i5kd7rh8a038ymp6z82861lyql2fwk5dh80043"))))
     (properties `((upstream-name . "affxparser")))
     (build-system r-build-system)
     (home-page "https://github.com/HenrikBengtsson/affxparser")
-- 
cgit v1.2.3


From 77a5fdd51c8d06442e3b89703926e01c23ae5d12 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Sep 2021 23:28:12 +0200
Subject: gnu: r-biocparallel: Update to 1.26.2.

* gnu/packages/bioconductor.scm (r-biocparallel): Update to 1.26.2.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index bf102e01f7..5016d6a38b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2272,13 +2272,13 @@ powerful online queries from gene annotation to database mining.")
 (define-public r-biocparallel
   (package
     (name "r-biocparallel")
-    (version "1.26.1")
+    (version "1.26.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BiocParallel" version))
               (sha256
                (base32
-                "1jx1wm47s64ywfddrg8kqzz4xpcmfjwrzbxhvlmys7pf2hzj4gbh"))))
+                "1y459cygq21f3igsdlxz1zlyad8qbl2qlr5h2d2dpnvblykvf48i"))))
     (properties
      `((upstream-name . "BiocParallel")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 0ac7b8b6ad07db72833e5f547a7a0950fe1604c9 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Sep 2021 23:28:13 +0200
Subject: gnu: r-edger: Update to 3.34.1.

* gnu/packages/bioconductor.scm (r-edger): Update to 3.34.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 5016d6a38b..923618a49a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2795,13 +2795,13 @@ global-scaling and full-quantile normalization.")
 (define-public r-edger
   (package
     (name "r-edger")
-    (version "3.34.0")
+    (version "3.34.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "edgeR" version))
               (sha256
                (base32
-                "1ikl9y6hj2p92nrb1ydxy2410b3wrax83rfy2imaj0vgfmhsgx6g"))))
+                "0f6apsjq6cn794840ls9y2n0hix1gyhvkdgxch1v22qr4sq0c86k"))))
     (properties `((upstream-name . "edgeR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 7c6046a6db0266ff01da30c44cd7e48109522107 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Sep 2021 23:28:13 +0200
Subject: gnu: r-genomeinfodb: Update to 1.28.4.

* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.28.4.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 923618a49a..a25863661b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3024,13 +3024,13 @@ genomic intervals.  In addition, it can use BAM or BigWig files as input.")
 (define-public r-genomeinfodb
   (package
     (name "r-genomeinfodb")
-    (version "1.28.1")
+    (version "1.28.4")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomeInfoDb" version))
               (sha256
                (base32
-                "1ga8yrn7j1wn9wdsvf4ws6n2987yk1yxz22v2jzaszfikhjh1sp8"))))
+                "0fjpgvpvyvl8cqgh2annib6h0c5li3aqz1ajfh5z5k5d0avdm4w0"))))
     (properties
      `((upstream-name . "GenomeInfoDb")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 43ac163bdfd2cfc102edf360d34339ceaca19156 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Sep 2021 23:28:13 +0200
Subject: gnu: r-genomicfeatures: Update to 1.44.2.

* gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.44.2.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a25863661b..f766ebd858 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3087,13 +3087,13 @@ alignments.")
 (define-public r-genomicfeatures
   (package
     (name "r-genomicfeatures")
-    (version "1.44.1")
+    (version "1.44.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicFeatures" version))
               (sha256
                (base32
-                "0byizkq18kkyq3n604f38z4mikhi3szsrfrlz22wdq2ldq3nzkis"))))
+                "091p8xnf2xkqhind81vyv1rmy2fz2b3qalcbrsw4qnp24vgdv2am"))))
     (properties
      `((upstream-name . "GenomicFeatures")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 4fb187b79eb795fae9cd4ac57e76bf238860b362 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Sep 2021 23:28:13 +0200
Subject: gnu: r-diffbind: Update to 3.2.7.

* gnu/packages/bioconductor.scm (r-diffbind): Update to 3.2.7.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f766ebd858..e98ccb7f91 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4890,14 +4890,14 @@ signal in the input, that lead to spurious peaks during peak calling.")
 (define-public r-diffbind
   (package
     (name "r-diffbind")
-    (version "3.2.5")
+    (version "3.2.7")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DiffBind" version))
        (sha256
         (base32
-         "1rp4sgx58g1lq5brpx07wffllhvsqq1097vrjiaksbih08338nih"))))
+         "01jfxcj5c0088vvsi3pz8fs0ka6n12l2j8s1d0rpqwa1y0444x7z"))))
     (properties `((upstream-name . "DiffBind")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From ce23a074f0e6837ad0a45cf6eeb92f5f8247e9e8 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Sep 2021 23:28:13 +0200
Subject: gnu: r-chippeakanno: Update to 3.26.4.

* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.26.4.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e98ccb7f91..6085db6c36 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5136,14 +5136,14 @@ determining dependencies between variables, code improvement suggestions.")
 (define-public r-chippeakanno
   (package
     (name "r-chippeakanno")
-    (version "3.26.3")
+    (version "3.26.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChIPpeakAnno" version))
        (sha256
         (base32
-         "07dvg3r4kghkqhh1a8rw149hgfswmzdh9cvnam8c82006cpmi74s"))))
+         "1iqzm7pifl9zrw3s06i6h85n1p01pd06vh1a93izyfhgybxn262d"))))
     (properties `((upstream-name . "ChIPpeakAnno")))
     (build-system r-build-system)
     (propagated-inputs
-- 
cgit v1.2.3


From 538618552b7e5455cf1abad8b3b59c5200a95b09 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Sep 2021 23:28:13 +0200
Subject: gnu: r-matrixgenerics: Update to 1.4.3.

* gnu/packages/bioconductor.scm (r-matrixgenerics): Update to 1.4.3.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6085db6c36..ed3cd60bc1 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5190,13 +5190,13 @@ enrichedGO (addGeneIDs).")
 (define-public r-matrixgenerics
   (package
    (name "r-matrixgenerics")
-   (version "1.4.2")
+   (version "1.4.3")
    (source (origin
             (method url-fetch)
             (uri (bioconductor-uri "MatrixGenerics" version))
             (sha256
              (base32
-              "0kjsc5ghcplay4a74ffpwsf3kbp51x6rl5265gvlfchdwrawkzd2"))))
+              "1yir3rwhz5vf0pdn3fpvlc57c75k98gvv8gapajbvymz3lyghijv"))))
    (properties
     `((upstream-name . "MatrixGenerics")))
    (build-system r-build-system)
-- 
cgit v1.2.3


From 1359fc7fbd0e6d32c11b9424673fa9b5210131f2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Sep 2021 23:28:14 +0200
Subject: gnu: r-ggtree: Update to 3.0.4.

* gnu/packages/bioconductor.scm (r-ggtree): Update to 3.0.4.
[propagated-inputs]: Remove r-rvcheck; add r-ggfun and r-yulab-utils.
---
 gnu/packages/bioconductor.scm | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ed3cd60bc1..f9d0e0bd62 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5840,29 +5840,30 @@ platform for merging tree with associated data and converting file formats.")
 (define-public r-ggtree
   (package
     (name "r-ggtree")
-    (version "3.0.3")
+    (version "3.0.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ggtree" version))
        (sha256
         (base32
-         "02ydi5iyxwrvwfjmv8pbanmzpi1r99mc4gxl17fpq2jf1d1mk6g0"))))
+         "0xf4b9vfdyzzivwgw4ymapl5bb4k9p04mmr53822kxgfd5qrs1zx"))))
     (properties `((upstream-name . "ggtree")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-ape" ,r-ape)
        ("r-aplot" ,r-aplot)
        ("r-dplyr" ,r-dplyr)
+       ("r-ggfun" ,r-ggfun)
        ("r-ggplot2" ,r-ggplot2)
        ("r-magrittr" ,r-magrittr)
        ("r-purrr" ,r-purrr)
        ("r-rlang" ,r-rlang)
-       ("r-rvcheck" ,r-rvcheck)
        ("r-scales" ,r-scales)
        ("r-tidyr" ,r-tidyr)
        ("r-tidytree" ,r-tidytree)
-       ("r-treeio" ,r-treeio)))
+       ("r-treeio" ,r-treeio)
+       ("r-yulab-utils" ,r-yulab-utils)))
     (native-inputs `(("r-knitr" ,r-knitr)))
     (home-page "https://yulab-smu.top/treedata-book/")
     (synopsis "R package for visualization of trees and annotation data")
-- 
cgit v1.2.3


From a88e7abf2faab8e706474492f04fb5342be703e0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Sep 2021 23:28:14 +0200
Subject: gnu: r-clusterprofiler: Update to 4.0.5.

* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 4.0.5.
[propagated-inputs]: Remove r-rvcheck; add r-yulab-utils.
---
 gnu/packages/bioconductor.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f9d0e0bd62..646ce5ce19 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -7438,14 +7438,14 @@ All the visualization methods are developed based on ggplot2 graphics.")
 (define-public r-clusterprofiler
   (package
     (name "r-clusterprofiler")
-    (version "4.0.4")
+    (version "4.0.5")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "clusterProfiler" version))
        (sha256
         (base32
-         "161w9mn2plmymvzf1hkk9fwi3d9c26kbcpndyyrfcl6bg2nxr1s8"))))
+         "1dccrl2ffhgmv3iqlmpln7z86ahpf0j9ma194fnknsgi3cd9rhrl"))))
     (properties
      `((upstream-name . "clusterProfiler")))
     (build-system r-build-system)
@@ -7461,8 +7461,8 @@ All the visualization methods are developed based on ggplot2 graphics.")
        ("r-plyr" ,r-plyr)
        ("r-qvalue" ,r-qvalue)
        ("r-rlang" ,r-rlang)
-       ("r-rvcheck" ,r-rvcheck)
-       ("r-tidyr" ,r-tidyr)))
+       ("r-tidyr" ,r-tidyr)
+       ("r-yulab-utils" ,r-yulab-utils)))
     (native-inputs
      `(("r-knitr" ,r-knitr)))
     (home-page "https://guangchuangyu.github.io/software/clusterProfiler/")
-- 
cgit v1.2.3


From 3278daa726bd9eabe90c1b31ddc007351036c2b4 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Sep 2021 23:28:14 +0200
Subject: gnu: r-zinbwave: Update to 1.14.2.

* gnu/packages/bioconductor.scm (r-zinbwave): Update to 1.14.2.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 646ce5ce19..6faeb9a5a1 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8890,14 +8890,14 @@ Currently only Affymetrix oligonucleotide analysis is supported.")
 (define-public r-zinbwave
   (package
     (name "r-zinbwave")
-    (version "1.14.1")
+    (version "1.14.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "zinbwave" version))
        (sha256
         (base32
-         "0xgjbk35wl1vjqyq4y5c7hna8hkgmf56xjaxcph9bs2q7mbdnqwf"))))
+         "1y8krazz2qdn0wn8ijjs2gn5dl5l960v6bijbkvh0r8066l7viky"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biocparallel" ,r-biocparallel)
-- 
cgit v1.2.3


From 494b7c4eca417eb29ff9603300b783d09bd653a7 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Sep 2021 23:28:14 +0200
Subject: gnu: r-cicero: Update to 1.10.1.

* gnu/packages/bioconductor.scm (r-cicero): Update to 1.10.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6faeb9a5a1..94ce2ddb4e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10216,14 +10216,14 @@ genes in the gene-set that are ranked above the leading edge).")
 (define-public r-cicero
   (package
     (name "r-cicero")
-    (version "1.10.0")
+    (version "1.10.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "cicero" version))
        (sha256
         (base32
-         "0kw16zf9004d1zlwsswhbcb7p77nabpd1fjagznff3zyan9fpdxf"))))
+         "1y34cm52bv1v2hr7sz8zjzxwd4wng7v75avz5wx45l0ld54z9l10"))))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-assertthat" ,r-assertthat)
-- 
cgit v1.2.3


From 74e218673113ab043c36ee5e933ec63ac0cd3a77 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Sep 2021 23:28:15 +0200
Subject: gnu: r-gdsfmt: Update to 1.28.1.

* gnu/packages/bioconductor.scm (r-gdsfmt): Update to 1.28.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 94ce2ddb4e..d311d96845 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10528,14 +10528,14 @@ metrics, with methods for objects produced by the @code{methylumi} and
 (define-public r-gdsfmt
   (package
     (name "r-gdsfmt")
-    (version "1.28.0")
+    (version "1.28.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gdsfmt" version))
        (sha256
         (base32
-         "119qdivd7vaaqkjb0nrwidi6g26hh8znhif3g4prqn7x5pl2clvy"))
+         "1w3z718q3bhh8bp71va9pbcd62pwbvgjw33ffg960jya40xssvc7"))
        (modules '((guix build utils)))
        ;; Remove bundled sources of zlib, lz4, and xz.  Don't attempt to build
        ;; them and link with system libraries instead.
-- 
cgit v1.2.3


From 3683f7f0a848e80ecd25f4114c846ab5c944eced Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Sep 2021 23:28:15 +0200
Subject: gnu: r-timeseriesexperiment: Update to 1.10.1.

* gnu/packages/bioconductor.scm (r-timeseriesexperiment): Update to 1.10.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d311d96845..bbddb0b290 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10751,14 +10751,14 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).")
 (define-public r-timeseriesexperiment
   (package
     (name "r-timeseriesexperiment")
-    (version "1.10.0")
+    (version "1.10.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "TimeSeriesExperiment" version))
        (sha256
         (base32
-         "10xgihjssnc6i03819p9gnzwfc7znanic514ar3yxzl3fhxy3yyy"))))
+         "1095a2ynxcf9xiac5cjzslcbmjnjpbby0vy7d84qagdiq1w6mrhn"))))
     (properties
      `((upstream-name . "TimeSeriesExperiment")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From c935b25a9e5e87083eb7a1f72ff0e9bcce639633 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Sep 2021 23:28:15 +0200
Subject: gnu: r-biocpkgtools: Update to 1.10.2.

* gnu/packages/bioconductor.scm (r-biocpkgtools): Update to 1.10.2.
[propagated-inputs]: Remove r-rex.
---
 gnu/packages/bioconductor.scm | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index bbddb0b290..9ca6bf621f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -11918,14 +11918,14 @@ gene selection, testing relationships, and so on.")
 (define-public r-biocpkgtools
   (package
     (name "r-biocpkgtools")
-    (version "1.10.1")
+    (version "1.10.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocPkgTools" version))
        (sha256
         (base32
-         "18a9mbzfmkipnv1cc9h3rhn9jxdp7nzywp0bz7hvmsaffv4p4skc"))))
+         "1sfp1nxlwbbbpx2iwvyk9p10jdy2vxhgn2b5fy5blayzjjlb3d80"))))
     (properties `((upstream-name . "BiocPkgTools")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11944,7 +11944,6 @@ gene selection, testing relationships, and so on.")
        ("r-magrittr" ,r-magrittr)
        ("r-rbgl" ,r-rbgl)
        ("r-readr" ,r-readr)
-       ("r-rex" ,r-rex)
        ("r-rlang" ,r-rlang)
        ("r-rvest" ,r-rvest)
        ("r-stringr" ,r-stringr)
-- 
cgit v1.2.3


From 425c53b5687253dd1d6f36119f7045b46542f30c Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Sep 2021 23:28:15 +0200
Subject: gnu: r-s4vectors: Update to 0.30.1.

* gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.30.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9ca6bf621f..426b194fdd 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12318,13 +12318,13 @@ routines.")
 (define-public r-s4vectors
   (package
     (name "r-s4vectors")
-    (version "0.30.0")
+    (version "0.30.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "S4Vectors" version))
               (sha256
                (base32
-                "0v5vxmg0a27ivgymmzfl595rcb1m3dz27r2wzbk1j97rlpwy1p4q"))))
+                "103sw0fmmm4f3hprrsn7dwg0kmmr9mcmb46dcwwb6p5np0al2sfx"))))
     (properties
      `((upstream-name . "S4Vectors")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From 0398a89fa1c1ab4d319a2e00d9e339148a6a8788 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 29 Sep 2021 23:28:15 +0200
Subject: gnu: r-delayedmatrixstats: Update to 1.14.3.

* gnu/packages/bioconductor.scm (r-delayedmatrixstats): Update to 1.14.3.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 426b194fdd..1e5777d6d9 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12973,14 +12973,14 @@ data in the column sparse format.")
 (define-public r-delayedmatrixstats
   (package
     (name "r-delayedmatrixstats")
-    (version "1.14.2")
+    (version "1.14.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DelayedMatrixStats" version))
        (sha256
         (base32
-         "1avzd3fj4am9klmlx03nwq2pvgx7646yjwha1gqf0cbx5hibxy02"))))
+         "1zxs2wjnsq9w1cl4andsd7y9xsdnl1an55khw9viaq758m7hhbcn"))))
     (properties
      `((upstream-name . "DelayedMatrixStats")))
     (build-system r-build-system)
-- 
cgit v1.2.3


From b28cd884b861f623d9691c58e4eb17ae5cf38117 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 30 Sep 2021 00:10:33 +0200
Subject: gnu: r-gdsfmt: Adjust bad substitution.

* gnu/packages/bioconductor.scm (r-gdsfmt)[source]: Include beginning-of-line
anchor in substitution regular expression.
---
 gnu/packages/bioconductor.scm | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

(limited to 'gnu/packages/bioconductor.scm')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1e5777d6d9..4cbffac000 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10548,7 +10548,7 @@ metrics, with methods for objects produced by the @code{methylumi} and
            (substitute* "src/Makevars"
              (("all: \\$\\(SHLIB\\)") "all:")
              (("\\$\\(SHLIB\\): liblzma.a") "")
-             (("(ZLIB|LZ4)/.*") "")
+             (("^	(ZLIB|LZ4)/.*") "")
              (("CoreArray/dVLIntGDS.cpp.*")
               "CoreArray/dVLIntGDS.cpp")
              (("CoreArray/dVLIntGDS.o.*")
@@ -10557,8 +10557,7 @@ metrics, with methods for objects produced by the @code{methylumi} and
               "PKG_LIBS = -llz4"))
            (substitute* "src/CoreArray/dStream.h"
              (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header)
-              (string-append "include <" header ">")))
-           #t))))
+              (string-append "include <" header ">")))))))
     (properties `((upstream-name . "gdsfmt")))
     (build-system r-build-system)
     (inputs
-- 
cgit v1.2.3