GNU bug report logs - #61656
[PATCH 00/24] Update some Bioconductor packages

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: guix-patches <at> gnu.org
Cc: Simon Tournier <zimon.toutoune <at> gmail.com>
Subject: [PATCH 00/24] Update some Bioconductor packages
Date: Mon, 20 Feb 2023 16:59:51 +0100

Hi,

Noting that the recent CRAN update breaks r-cytolib, here is a fix by
updating.  So let also take the opportunity for an update of Bioconductor.

Cheers,
simon


Simon Tournier (24):
  gnu: r-cytolib: Update to 2.10.1.
  gnu: r-annotationforge: Update to 1.40.1.
  gnu: r-bsgenome: Update to 1.66.3.
  gnu: r-deseq2: Update to 1.38.3.
  gnu: r-edger: Update to 3.40.2.
  gnu: r-genefilter: Update to 1.80.3.
  gnu: r-genomeinfodb: Update to 1.34.9.
  gnu: r-genomicfeatures: Update to 1.50.4.
  gnu: r-impute: Update to 1.72.3.
  gnu: r-limma: Update to 3.54.1.
  gnu: r-stringdb: Update to 2.10.1.
  gnu: r-variantannotation: Update to 1.44.1.
  gnu: r-oligo: Update to 1.62.2.
  gnu: r-interactionset: Update to 1.26.1.
  gnu: r-dnacopy: Update to 1.72.3.
  gnu: r-lpsymphony: Update to 1.26.3.
  gnu: r-massspecwavelet: Update to 1.64.1.
  gnu: r-biocfilecache: Update to 2.6.1.
  gnu: r-variancepartition: Update to 1.28.4.
  gnu: r-preprocesscore: Update to 1.60.2.
  gnu: r-scuttle: Update to 1.8.4.
  gnu: r-scran: Update to 1.26.2.
  gnu: r-gviz: Update to 1.42.1.
  gnu: r-tximeta: Update to 1.16.1.

 gnu/packages/bioconductor.scm | 99 +++++++++++++++++------------------
 1 file changed, 48 insertions(+), 51 deletions(-)


base-commit: 53e27f8abf1163e29fb5fc17af38b90a67a18138
-- 
2.38.1

Message #8 received at 61656 <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: 61656 <at> debbugs.gnu.org
Cc: Simon Tournier <zimon.toutoune <at> gmail.com>
Subject: [PATCH 23/24] gnu: r-gviz: Update to 1.42.1.
Date: Mon, 20 Feb 2023 19:54:10 +0100

* gnu/packages/bioconductor.scm (r-gviz): Update to 1.42.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b31480574c..a4a4238187 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -18039,14 +18039,14 @@ (define-public r-gqtlstats
 (define-public r-gviz
   (package
     (name "r-gviz")
-    (version "1.42.0")
+    (version "1.42.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Gviz" version))
        (sha256
         (base32
-         "09j94kk3dd3bbfw6a2l14i7vd4rh11g9lxhw4zsm15vg71cm1lv9"))))
+         "01qs60sdh7c8cxkv3qbfcfwpjhab88j872va50fi95xsqnmj5isa"))))
     (properties `((upstream-name . "Gviz")))
     (build-system r-build-system)
     (propagated-inputs
-- 
2.38.1

Message #11 received at 61656 <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: 61656 <at> debbugs.gnu.org
Cc: Simon Tournier <zimon.toutoune <at> gmail.com>
Subject: [PATCH 22/24] gnu: r-scran: Update to 1.26.2.
Date: Mon, 20 Feb 2023 19:54:09 +0100

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

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 38fecc114a..b31480574c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -17520,14 +17520,14 @@ (define-public r-scater
 (define-public r-scran
   (package
     (name "r-scran")
-    (version "1.26.1")
+    (version "1.26.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scran" version))
        (sha256
         (base32
-         "1sqc8pf1qzm24kf1l45da12wbzv0nxsy6l3v9fc8srmnvk37p04p"))))
+         "0r80k4dsk609l9ha1jl64yhpwnf0x37i28k9largqsffsl6hw0fy"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-beachmat
-- 
2.38.1

Message #14 received at 61656 <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: 61656 <at> debbugs.gnu.org
Cc: Simon Tournier <zimon.toutoune <at> gmail.com>
Subject: [PATCH 02/24] gnu: r-annotationforge: Update to 1.40.1.
Date: Mon, 20 Feb 2023 19:53:49 +0100

* gnu/packages/bioconductor.scm (r-annotationforge): Update to 1.40.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9b1235ab79..aff6cf00dd 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5054,14 +5054,14 @@ (define-public r-annotationfilter
 (define-public r-annotationforge
   (package
     (name "r-annotationforge")
-    (version "1.40.0")
+    (version "1.40.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "AnnotationForge" version))
        (sha256
         (base32
-         "15shh8rmcx69g3zd256720vh0c3qbly5zrvwm463dws41cjla48x"))))
+         "16wdcl56d5i8wrmin610kzs9ldy7h9w5fbnysjb1crkcgbikq1yy"))))
     (properties
      `((upstream-name . "AnnotationForge")))
     (build-system r-build-system)
-- 
2.38.1

Message #17 received at 61656 <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: 61656 <at> debbugs.gnu.org
Cc: Simon Tournier <zimon.toutoune <at> gmail.com>
Subject: [PATCH 01/24] gnu: r-cytolib: Update to 2.10.1.
Date: Mon, 20 Feb 2023 19:53:48 +0100

* gnu/packages/bioconductor.scm (r-cytolib): Update to 2.10.1.
[propagated-inputs]: Remove r-rcpp, r-rcpparmadillo and r-rcppparallel.
---
 gnu/packages/bioconductor.scm | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4b5ec7db28..9b1235ab79 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13952,23 +13952,20 @@ (define-public r-cycombine
 (define-public r-cytolib
   (package
     (name "r-cytolib")
-    (version "2.10.0")
+    (version "2.10.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "cytolib" version))
        (sha256
         (base32
-         "1y06x7z3p938kfvjx6zqab9hh1xzlrlhdxczyprx7lsd34ylz46n"))))
+         "0rgqlqasil75b03c8c4nyg71ybysrsbqb0bwk6hbnaw8rljxdmi5"))))
     (properties `((upstream-name . "cytolib")))
     (build-system r-build-system)
     (native-inputs
      (list r-knitr))
     (propagated-inputs
      (list r-bh
-           r-rcpp
-           r-rcpparmadillo
-           r-rcppparallel
            r-rhdf5lib
            r-rprotobuflib))
     (home-page "https://bioconductor.org/packages/cytolib/")
-- 
2.38.1

Message #20 received at 61656 <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: 61656 <at> debbugs.gnu.org
Cc: Simon Tournier <zimon.toutoune <at> gmail.com>
Subject: [PATCH 06/24] gnu: r-genefilter: Update to 1.80.3.
Date: Mon, 20 Feb 2023 19:53:53 +0100

* gnu/packages/bioconductor.scm (r-genefilter): Update to 1.80.3.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 66d389e778..18b6eccf31 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6012,14 +6012,14 @@ (define-public r-gage
 (define-public r-genefilter
   (package
     (name "r-genefilter")
-    (version "1.80.2")
+    (version "1.80.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "genefilter" version))
        (sha256
         (base32
-         "0f25z0hqmrkimv14j03pgjsxpq5rz9ymk151rlg4j4vpc06n73cq"))))
+         "047p84qxfqqm0d0ik7fxcs37fmg0yazsn9rz7h4g24cksb45p689"))))
     (build-system r-build-system)
     (native-inputs
      (list gfortran r-knitr))
-- 
2.38.1

Message #23 received at 61656 <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: 61656 <at> debbugs.gnu.org
Cc: Simon Tournier <zimon.toutoune <at> gmail.com>
Subject: [PATCH 08/24] gnu: r-genomicfeatures: Update to 1.50.4.
Date: Mon, 20 Feb 2023 19:53:55 +0100

* gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.50.4.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f00d57112a..fbd0f3bcc1 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6162,13 +6162,13 @@ (define-public r-genomicalignments
 (define-public r-genomicfeatures
   (package
     (name "r-genomicfeatures")
-    (version "1.50.3")
+    (version "1.50.4")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomicFeatures" version))
               (sha256
                (base32
-                "14pn7lngayascj5k84g2g748assbivpiakss247cdj9ngzx5sfwz"))))
+                "1qsr433nh225pk5ngsrjrf2rfv7ynq4c8qsjfjr7khy2z9czlg6n"))))
     (properties
      `((upstream-name . "GenomicFeatures")))
     (build-system r-build-system)
-- 
2.38.1

Message #26 received at 61656 <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: 61656 <at> debbugs.gnu.org
Cc: Simon Tournier <zimon.toutoune <at> gmail.com>
Subject: [PATCH 21/24] gnu: r-scuttle: Update to 1.8.4.
Date: Mon, 20 Feb 2023 19:54:08 +0100

* gnu/packages/bioconductor.scm (r-scuttle): Update to 1.8.4.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ab2b9cd433..38fecc114a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -17440,14 +17440,14 @@ (define-public r-singler
 (define-public r-scuttle
   (package
     (name "r-scuttle")
-    (version "1.8.3")
+    (version "1.8.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "scuttle" version))
        (sha256
         (base32
-         "1wgh28rj8m5dz89s9y4rzfy68d8ign6pcnnwj9g7h4sc3jfsg56i"))))
+         "04257gl995r575md1n3h2gy502yi6c8x3352l96mib7rdv4yg53f"))))
     (properties `((upstream-name . "scuttle")))
     (build-system r-build-system)
     (propagated-inputs
-- 
2.38.1

Message #29 received at 61656 <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: 61656 <at> debbugs.gnu.org
Cc: Simon Tournier <zimon.toutoune <at> gmail.com>
Subject: [PATCH 05/24] gnu: r-edger: Update to 3.40.2.
Date: Mon, 20 Feb 2023 19:53:52 +0100

* gnu/packages/bioconductor.scm (r-edger): Update to 3.40.2.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e2b8e689b8..66d389e778 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5887,13 +5887,13 @@ (define-public r-edaseq
 (define-public r-edger
   (package
     (name "r-edger")
-    (version "3.40.1")
+    (version "3.40.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "edgeR" version))
               (sha256
                (base32
-                "1a0rmczlqmqmip2ix28m4iwcpfj04p6nrcl562bjgaifvgyjqhzg"))))
+                "0ds34b135qd63dh3cxkp8b28270m50bn1njwr49b8svgcgzz9x09"))))
     (properties `((upstream-name . "edgeR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
2.38.1

Message #32 received at 61656 <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: 61656 <at> debbugs.gnu.org
Cc: Simon Tournier <zimon.toutoune <at> gmail.com>
Subject: [PATCH 04/24] gnu: r-deseq2: Update to 1.38.3.
Date: Mon, 20 Feb 2023 19:53:51 +0100

* gnu/packages/bioconductor.scm (r-deseq2): Update to 1.38.3.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 3828b7ba4c..e2b8e689b8 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5655,14 +5655,14 @@ (define-public r-deseq
 (define-public r-deseq2
   (package
     (name "r-deseq2")
-    (version "1.38.2")
+    (version "1.38.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DESeq2" version))
        (sha256
         (base32
-         "1m81yvcl63h5m7kbbxpjk7hzygxmn4l9mlgqrdmnnls56183h3b4"))))
+         "0kryg9jb6zl4zj1wx09rmljqlhr5vdbcmdnri4q91jpggsaj9nxm"))))
     (properties `((upstream-name . "DESeq2")))
     (build-system r-build-system)
     (propagated-inputs
-- 
2.38.1

Message #35 received at 61656 <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: 61656 <at> debbugs.gnu.org
Cc: Simon Tournier <zimon.toutoune <at> gmail.com>
Subject: [PATCH 03/24] gnu: r-bsgenome: Update to 1.66.3.
Date: Mon, 20 Feb 2023 19:53:50 +0100

* gnu/packages/bioconductor.scm (r-bsgenome): Update to 1.66.3.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index aff6cf00dd..3828b7ba4c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5409,13 +5409,13 @@ (define-public r-biovizbase
 (define-public r-bsgenome
   (package
     (name "r-bsgenome")
-    (version "1.66.2")
+    (version "1.66.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "BSgenome" version))
               (sha256
                (base32
-                "0p75c52sw464bdqz7dyda9h8k2wsxdpdxxhya5awh977xaly90pf"))))
+                "1ps7s6i9mv8ys8k2xw8fdkh2rl2n3kcf2q4zsz6kcz5qpav95ys6"))))
     (properties
      `((upstream-name . "BSgenome")))
     (build-system r-build-system)
-- 
2.38.1

Message #38 received at 61656 <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: 61656 <at> debbugs.gnu.org
Cc: Simon Tournier <zimon.toutoune <at> gmail.com>
Subject: [PATCH 07/24] gnu: r-genomeinfodb: Update to 1.34.9.
Date: Mon, 20 Feb 2023 19:53:54 +0100

* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.34.9.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 18b6eccf31..f00d57112a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6102,13 +6102,13 @@ (define-public r-genomation
 (define-public r-genomeinfodb
   (package
     (name "r-genomeinfodb")
-    (version "1.34.6")
+    (version "1.34.9")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GenomeInfoDb" version))
               (sha256
                (base32
-                "123kp69fmy5pbqh0j6qxdkvkm4g9pdwzms01i8qnix3m1b9j597w"))))
+                "0mn9ddm2xwc2b7zg0n9a056jcr61jv6v8jacxm3q8qmz6r30kfrb"))))
     (properties
      `((upstream-name . "GenomeInfoDb")))
     (build-system r-build-system)
-- 
2.38.1

Message #41 received at 61656 <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: 61656 <at> debbugs.gnu.org
Cc: Simon Tournier <zimon.toutoune <at> gmail.com>
Subject: [PATCH 11/24] gnu: r-stringdb: Update to 2.10.1.
Date: Mon, 20 Feb 2023 19:53:58 +0100

* gnu/packages/bioconductor.scm (r-stringdb): Update to 2.10.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 20a46feceb..65d1a9e249 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8192,13 +8192,13 @@ (define-public r-stager
 (define-public r-stringdb
   (package
     (name "r-stringdb")
-    (version "2.10.0")
+    (version "2.10.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "STRINGdb" version))
        (sha256
-        (base32 "1md79vx4270wgh07g3m1mypdki1b9d4a558zxplcalwppqh0dsmp"))))
+        (base32 "0qpss8fcf8ll47jv45ypsqd9jf7ajdiya7w4mw1wysk76spcwllm"))))
     (properties `((upstream-name . "STRINGdb")))
     (build-system r-build-system)
     (propagated-inputs
-- 
2.38.1

Message #44 received at 61656 <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: 61656 <at> debbugs.gnu.org
Cc: Simon Tournier <zimon.toutoune <at> gmail.com>
Subject: [PATCH 24/24] gnu: r-tximeta: Update to 1.16.1.
Date: Mon, 20 Feb 2023 19:54:11 +0100

* gnu/packages/bioconductor.scm (r-tximeta): Update to 1.16.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a4a4238187..f6bb6ab342 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -19542,14 +19542,14 @@ (define-public r-tricycle
 (define-public r-tximeta
   (package
     (name "r-tximeta")
-    (version "1.16.0")
+    (version "1.16.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "tximeta" version))
        (sha256
         (base32
-         "0v1s5ssinyrizpg2i88dn2ckzs4i16hjfg2pzxhal3ypsiw24qna"))))
+         "15qf8s9akl5qp5wklph5i61d96d9ifr5ijl796v1vafwrj4f3wpa"))))
     (properties `((upstream-name . "tximeta")))
     (build-system r-build-system)
     (propagated-inputs
-- 
2.38.1

Message #47 received at 61656 <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: 61656 <at> debbugs.gnu.org
Cc: Simon Tournier <zimon.toutoune <at> gmail.com>
Subject: [PATCH 12/24] gnu: r-variantannotation: Update to 1.44.1.
Date: Mon, 20 Feb 2023 19:53:59 +0100

* gnu/packages/bioconductor.scm (r-variantannotation): Update to 1.44.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 65d1a9e249..e8f4b246ad 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8461,13 +8461,13 @@ (define-public r-valr
 (define-public r-variantannotation
   (package
     (name "r-variantannotation")
-    (version "1.44.0")
+    (version "1.44.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "VariantAnnotation" version))
               (sha256
                (base32
-                "08rm27jcx6amawqdh59291r0qzkr5cdhbhm0xbjbd5mvdpp1icl8"))))
+                "13zim7dglsd5w39v22d2qa3d1h5dx33c1r4fz3vzri64kac0lhzx"))))
     (properties
      `((upstream-name . "VariantAnnotation")))
     (propagated-inputs
-- 
2.38.1

Message #50 received at 61656 <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: 61656 <at> debbugs.gnu.org
Cc: Simon Tournier <zimon.toutoune <at> gmail.com>
Subject: [PATCH 10/24] gnu: r-limma: Update to 3.54.1.
Date: Mon, 20 Feb 2023 19:53:57 +0100

* gnu/packages/bioconductor.scm (r-limma): Update to 3.54.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4c1a58abe2..20a46feceb 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6517,13 +6517,13 @@ (define-public r-lfa
 (define-public r-limma
   (package
     (name "r-limma")
-    (version "3.54.0")
+    (version "3.54.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "limma" version))
               (sha256
                (base32
-                "1jy75nbkhl0kgv4gw88acx58r9f1kywrd36405x6g05xy05bprma"))))
+                "0x6wkbw8v0hq9dfr433165jmii05rswjsm97dpxvyvxvya3sxqa1"))))
     (build-system r-build-system)
     (home-page "http://bioinf.wehi.edu.au/limma")
     (synopsis "Package for linear models for microarray and RNA-seq data")
-- 
2.38.1

Message #53 received at 61656 <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: 61656 <at> debbugs.gnu.org
Cc: Simon Tournier <zimon.toutoune <at> gmail.com>
Subject: [PATCH 13/24] gnu: r-oligo: Update to 1.62.2.
Date: Mon, 20 Feb 2023 19:54:00 +0100

* gnu/packages/bioconductor.scm (r-oligo): Update to 1.62.2.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e8f4b246ad..c2a6b6fd1f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8776,14 +8776,14 @@ (define-public r-oligoclasses
 (define-public r-oligo
   (package
     (name "r-oligo")
-    (version "1.62.1")
+    (version "1.62.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "oligo" version))
        (sha256
         (base32
-         "1rhzav57d092ip9qjsmskj3l8h4xyq8cpa2a2jl8g32fwh0dyvsz"))))
+         "19n0nvgyv2hzzcla93w2bzxvfdqg6walh0s1yykwl5b7ni4cazg9"))))
     (properties `((upstream-name . "oligo")))
     (build-system r-build-system)
     (inputs (list zlib))
-- 
2.38.1

Message #56 received at 61656 <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: 61656 <at> debbugs.gnu.org
Cc: Simon Tournier <zimon.toutoune <at> gmail.com>
Subject: [PATCH 15/24] gnu: r-dnacopy: Update to 1.72.3.
Date: Mon, 20 Feb 2023 19:54:02 +0100

* gnu/packages/bioconductor.scm (r-dnacopy): Update to 1.72.3.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0ddd184a4f..190fe23e0a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10193,14 +10193,14 @@ (define-public r-copynumber
 (define-public r-dnacopy
   (package
     (name "r-dnacopy")
-    (version "1.72.2")
+    (version "1.72.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "DNAcopy" version))
        (sha256
         (base32
-         "1f6ilfwhli7bdnr48y2ijdydvw7kjbyz701kgbsw3w7inr6x6ayr"))))
+         "1kxzrny19dqd9pqj27vzr15i071sl8ivznpfd6zlqhcymlcsq7nw"))))
     (properties `((upstream-name . "DNAcopy")))
     (build-system r-build-system)
     (native-inputs (list gfortran))
-- 
2.38.1

Message #59 received at 61656 <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: 61656 <at> debbugs.gnu.org
Cc: Simon Tournier <zimon.toutoune <at> gmail.com>
Subject: [PATCH 14/24] gnu: r-interactionset: Update to 1.26.1.
Date: Mon, 20 Feb 2023 19:54:01 +0100

* gnu/packages/bioconductor.scm (r-interactionset): Update to 1.26.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index c2a6b6fd1f..0ddd184a4f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9512,14 +9512,14 @@ (define-public r-riboseqr
 (define-public r-interactionset
   (package
     (name "r-interactionset")
-    (version "1.26.0")
+    (version "1.26.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "InteractionSet" version))
        (sha256
         (base32
-         "14fb780f2g24ay28dy9xkmfziavbkj75v4vc2cmqbxfdsfp4yn0w"))))
+         "1nk8jhabbrirpyjd1wdy2fjk8y2qi1bsjmgqzh0qi1c83n0ccz5d"))))
     (properties
      `((upstream-name . "InteractionSet")))
     (build-system r-build-system)
-- 
2.38.1

Message #62 received at 61656 <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: 61656 <at> debbugs.gnu.org
Cc: Simon Tournier <zimon.toutoune <at> gmail.com>
Subject: [PATCH 16/24] gnu: r-lpsymphony: Update to 1.26.3.
Date: Mon, 20 Feb 2023 19:54:03 +0100

* gnu/packages/bioconductor.scm (r-lpsymphony): Update to 1.26.3.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 190fe23e0a..0e53d367ed 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10351,14 +10351,14 @@ (define-public r-karyoploter
 (define-public r-lpsymphony
   (package
     (name "r-lpsymphony")
-    (version "1.26.2")
+    (version "1.26.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "lpsymphony" version))
        (sha256
         (base32
-         "167zpf7k7gn7gw2cxkqx89y322qinyzjr1naracp5axj4q2qagm3"))))
+         "0iqc6km4pw50li2q35km8jpa0p3i6a6way910wcz56yd2jjbjyz5"))))
     (build-system r-build-system)
     (arguments
      (list
-- 
2.38.1

Message #65 received at 61656 <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: 61656 <at> debbugs.gnu.org
Cc: Simon Tournier <zimon.toutoune <at> gmail.com>
Subject: [PATCH 17/24] gnu: r-massspecwavelet: Update to 1.64.1.
Date: Mon, 20 Feb 2023 19:54:04 +0100

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

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0e53d367ed..0668712801 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13004,14 +13004,14 @@ (define-public r-xbseq
 (define-public r-massspecwavelet
   (package
     (name "r-massspecwavelet")
-    (version "1.64.0")
+    (version "1.64.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MassSpecWavelet" version))
        (sha256
         (base32
-         "0l86gwq073nbx973v99b0lr9cz0pb72c4asmgj5w16jykicrnxn9"))))
+         "0p8cd4r3c8va5gybs1vlm3kn7jcg1xg529hvvg27fybb3g91nvqg"))))
     (properties
      `((upstream-name . "MassSpecWavelet")))
     (build-system r-build-system)
-- 
2.38.1

Message #68 received at 61656 <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: 61656 <at> debbugs.gnu.org
Cc: Simon Tournier <zimon.toutoune <at> gmail.com>
Subject: [PATCH 18/24] gnu: r-biocfilecache: Update to 2.6.1.
Date: Mon, 20 Feb 2023 19:54:05 +0100

* gnu/packages/bioconductor.scm (r-biocfilecache): Update to 2.6.1.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0668712801..6536caf875 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -13361,14 +13361,14 @@ (define-public r-arrmnormalization
 (define-public r-biocfilecache
   (package
     (name "r-biocfilecache")
-    (version "2.6.0")
+    (version "2.6.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "BiocFileCache" version))
        (sha256
         (base32
-         "0skrvmkm6ch8gbpdi4wr59zk5vxzxs7cyqvz3jhki9d8w492wylg"))))
+         "16316a5pgyl5rppyviibf6z3k3m7xmvqyylf1kxdpg0avs6dk8w7"))))
     (properties `((upstream-name . "BiocFileCache")))
     (build-system r-build-system)
     (propagated-inputs
-- 
2.38.1

Message #71 received at 61656 <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: 61656 <at> debbugs.gnu.org
Cc: Simon Tournier <zimon.toutoune <at> gmail.com>
Subject: [PATCH 19/24] gnu: r-variancepartition: Update to 1.28.4.
Date: Mon, 20 Feb 2023 19:54:06 +0100

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

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6536caf875..677a199dca 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -15246,14 +15246,14 @@ (define-public r-wavetiling
 (define-public r-variancepartition
   (package
     (name "r-variancepartition")
-    (version "1.28.1")
+    (version "1.28.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "variancePartition" version))
        (sha256
         (base32
-         "0ypw3ckaf4qll83rl2bjzfc7g2m4v0n2mq645ppyfga8wv8kwssy"))))
+         "1ii4r0c76b7rnisy4qba2cp5686j73s6b3s6pj66w91wq65dykpd"))))
     (properties
      `((upstream-name . "variancePartition")))
     (build-system r-build-system)
-- 
2.38.1

Message #74 received at 61656 <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: 61656 <at> debbugs.gnu.org
Cc: Simon Tournier <zimon.toutoune <at> gmail.com>
Subject: [PATCH 09/24] gnu: r-impute: Update to 1.72.3.
Date: Mon, 20 Feb 2023 19:53:56 +0100

* gnu/packages/bioconductor.scm (r-impute): Update to 1.72.3.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index fbd0f3bcc1..4c1a58abe2 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -6427,13 +6427,13 @@ (define-public r-rhtslib
 (define-public r-impute
   (package
     (name "r-impute")
-    (version "1.72.2")
+    (version "1.72.3")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "impute" version))
               (sha256
                (base32
-                "1k697pqlkrwmfszipl9irbzmwhk1vz97j3rh0k5nj2mrj3dr71mv"))))
+                "1qq80za9bkg0wqnlckvahnjz08xacwvpnflwnrmwr2xg0ifkis38"))))
     (native-inputs
      (list gfortran))
     (build-system r-build-system)
-- 
2.38.1

Message #77 received at 61656 <at> debbugs.gnu.org (full text, mbox):

From: Simon Tournier <zimon.toutoune <at> gmail.com>
To: 61656 <at> debbugs.gnu.org
Cc: Simon Tournier <zimon.toutoune <at> gmail.com>
Subject: [PATCH 20/24] gnu: r-preprocesscore: Update to 1.60.2.
Date: Mon, 20 Feb 2023 19:54:07 +0100

* gnu/packages/bioconductor.scm (r-preprocesscore): Update to 1.60.2.
---
 gnu/packages/bioconductor.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 677a199dca..ab2b9cd433 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -16802,14 +16802,14 @@ (define-public r-fourcseq
 (define-public r-preprocesscore
   (package
     (name "r-preprocesscore")
-    (version "1.60.1")
+    (version "1.60.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "preprocessCore" version))
        (sha256
         (base32
-         "1rwr31jp4dh3xcfx1kx8rz5xvyx1mrwy85hqrjrfr4m6h0qv28k1"))))
+         "0ikxikmz9dy09g726q1wygymm6z2imlgfiizkgh1cl4s0m35fbbd"))))
     (properties
      `((upstream-name . "preprocessCore")))
     (build-system r-build-system)
-- 
2.38.1

Message #82 received at 61656-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Simon Tournier <zimon.toutoune <at> gmail.com>
Cc: 61656-done <at> debbugs.gnu.org
Subject: Re: [bug#61656] [PATCH 00/24] Update some Bioconductor packages
Date: Fri, 24 Feb 2023 08:12:53 +0100

Hi Simon,

> Noting that the recent CRAN update breaks r-cytolib, here is a fix by
> updating.  So let also take the opportunity for an update of Bioconductor.

Thank you for noticing, fixing, and upgrading!

I applied them all.

-- 
Ricardo

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