[PATCH 00/24] Update some Bioconductor packages

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2 participants
  • Ricardo Wurmus
  • Simon Tournier
Owner
unassigned
Submitted by
Simon Tournier
Severity
normal

Debbugs page

Simon Tournier wrote 2 years ago
(address . guix-patches@gnu.org)(name . Simon Tournier)(address . zimon.toutoune@gmail.com)
20230220155951.240333-1-zimon.toutoune@gmail.com
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
Simon Tournier wrote 2 years ago
[PATCH 23/24] gnu: r-gviz: Update to 1.42.1.
(address . 61656@debbugs.gnu.org)(name . Simon Tournier)(address . zimon.toutoune@gmail.com)
20230220185411.377212-23-zimon.toutoune@gmail.com
* gnu/packages/bioconductor.scm (r-gviz): Update to 1.42.1.
---
gnu/packages/bioconductor.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (23 lines)
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
Simon Tournier wrote 2 years ago
[PATCH 22/24] gnu: r-scran: Update to 1.26.2.
(address . 61656@debbugs.gnu.org)(name . Simon Tournier)(address . zimon.toutoune@gmail.com)
20230220185411.377212-22-zimon.toutoune@gmail.com
* gnu/packages/bioconductor.scm (r-scran): Update to 1.26.2.
---
gnu/packages/bioconductor.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (23 lines)
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
Simon Tournier wrote 2 years ago
[PATCH 02/24] gnu: r-annotationforge: Update to 1.40.1.
(address . 61656@debbugs.gnu.org)(name . Simon Tournier)(address . zimon.toutoune@gmail.com)
20230220185411.377212-2-zimon.toutoune@gmail.com
* gnu/packages/bioconductor.scm (r-annotationforge): Update to 1.40.1.
---
gnu/packages/bioconductor.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (23 lines)
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
Simon Tournier wrote 2 years ago
[PATCH 01/24] gnu: r-cytolib: Update to 2.10.1.
(address . 61656@debbugs.gnu.org)(name . Simon Tournier)(address . zimon.toutoune@gmail.com)
20230220185411.377212-1-zimon.toutoune@gmail.com
* 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(-)

Toggle diff (32 lines)
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
Simon Tournier wrote 2 years ago
[PATCH 06/24] gnu: r-genefilter: Update to 1.80.3.
(address . 61656@debbugs.gnu.org)(name . Simon Tournier)(address . zimon.toutoune@gmail.com)
20230220185411.377212-6-zimon.toutoune@gmail.com
* gnu/packages/bioconductor.scm (r-genefilter): Update to 1.80.3.
---
gnu/packages/bioconductor.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (23 lines)
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
Simon Tournier wrote 2 years ago
[PATCH 08/24] gnu: r-genomicfeatures: Update to 1.50.4.
(address . 61656@debbugs.gnu.org)(name . Simon Tournier)(address . zimon.toutoune@gmail.com)
20230220185411.377212-8-zimon.toutoune@gmail.com
* gnu/packages/bioconductor.scm (r-genomicfeatures): Update to 1.50.4.
---
gnu/packages/bioconductor.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (22 lines)
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
Simon Tournier wrote 2 years ago
[PATCH 21/24] gnu: r-scuttle: Update to 1.8.4.
(address . 61656@debbugs.gnu.org)(name . Simon Tournier)(address . zimon.toutoune@gmail.com)
20230220185411.377212-21-zimon.toutoune@gmail.com
* gnu/packages/bioconductor.scm (r-scuttle): Update to 1.8.4.
---
gnu/packages/bioconductor.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (23 lines)
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
Simon Tournier wrote 2 years ago
[PATCH 05/24] gnu: r-edger: Update to 3.40.2.
(address . 61656@debbugs.gnu.org)(name . Simon Tournier)(address . zimon.toutoune@gmail.com)
20230220185411.377212-5-zimon.toutoune@gmail.com
* gnu/packages/bioconductor.scm (r-edger): Update to 3.40.2.
---
gnu/packages/bioconductor.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (22 lines)
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
Simon Tournier wrote 2 years ago
[PATCH 04/24] gnu: r-deseq2: Update to 1.38.3.
(address . 61656@debbugs.gnu.org)(name . Simon Tournier)(address . zimon.toutoune@gmail.com)
20230220185411.377212-4-zimon.toutoune@gmail.com
* gnu/packages/bioconductor.scm (r-deseq2): Update to 1.38.3.
---
gnu/packages/bioconductor.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (23 lines)
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
Simon Tournier wrote 2 years ago
[PATCH 03/24] gnu: r-bsgenome: Update to 1.66.3.
(address . 61656@debbugs.gnu.org)(name . Simon Tournier)(address . zimon.toutoune@gmail.com)
20230220185411.377212-3-zimon.toutoune@gmail.com
* gnu/packages/bioconductor.scm (r-bsgenome): Update to 1.66.3.
---
gnu/packages/bioconductor.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (22 lines)
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
Simon Tournier wrote 2 years ago
[PATCH 07/24] gnu: r-genomeinfodb: Update to 1.34.9.
(address . 61656@debbugs.gnu.org)(name . Simon Tournier)(address . zimon.toutoune@gmail.com)
20230220185411.377212-7-zimon.toutoune@gmail.com
* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.34.9.
---
gnu/packages/bioconductor.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (22 lines)
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
Simon Tournier wrote 2 years ago
[PATCH 11/24] gnu: r-stringdb: Update to 2.10.1.
(address . 61656@debbugs.gnu.org)(name . Simon Tournier)(address . zimon.toutoune@gmail.com)
20230220185411.377212-11-zimon.toutoune@gmail.com
* gnu/packages/bioconductor.scm (r-stringdb): Update to 2.10.1.
---
gnu/packages/bioconductor.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (22 lines)
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
Simon Tournier wrote 2 years ago
[PATCH 24/24] gnu: r-tximeta: Update to 1.16.1.
(address . 61656@debbugs.gnu.org)(name . Simon Tournier)(address . zimon.toutoune@gmail.com)
20230220185411.377212-24-zimon.toutoune@gmail.com
* gnu/packages/bioconductor.scm (r-tximeta): Update to 1.16.1.
---
gnu/packages/bioconductor.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (23 lines)
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
Simon Tournier wrote 2 years ago
[PATCH 12/24] gnu: r-variantannotation: Update to 1.44.1.
(address . 61656@debbugs.gnu.org)(name . Simon Tournier)(address . zimon.toutoune@gmail.com)
20230220185411.377212-12-zimon.toutoune@gmail.com
* gnu/packages/bioconductor.scm (r-variantannotation): Update to 1.44.1.
---
gnu/packages/bioconductor.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (22 lines)
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
Simon Tournier wrote 2 years ago
[PATCH 10/24] gnu: r-limma: Update to 3.54.1.
(address . 61656@debbugs.gnu.org)(name . Simon Tournier)(address . zimon.toutoune@gmail.com)
20230220185411.377212-10-zimon.toutoune@gmail.com
* gnu/packages/bioconductor.scm (r-limma): Update to 3.54.1.
---
gnu/packages/bioconductor.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (22 lines)
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
Simon Tournier wrote 2 years ago
[PATCH 13/24] gnu: r-oligo: Update to 1.62.2.
(address . 61656@debbugs.gnu.org)(name . Simon Tournier)(address . zimon.toutoune@gmail.com)
20230220185411.377212-13-zimon.toutoune@gmail.com
* gnu/packages/bioconductor.scm (r-oligo): Update to 1.62.2.
---
gnu/packages/bioconductor.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (23 lines)
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
Simon Tournier wrote 2 years ago
[PATCH 15/24] gnu: r-dnacopy: Update to 1.72.3.
(address . 61656@debbugs.gnu.org)(name . Simon Tournier)(address . zimon.toutoune@gmail.com)
20230220185411.377212-15-zimon.toutoune@gmail.com
* gnu/packages/bioconductor.scm (r-dnacopy): Update to 1.72.3.
---
gnu/packages/bioconductor.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (23 lines)
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
Simon Tournier wrote 2 years ago
[PATCH 14/24] gnu: r-interactionset: Update to 1.26.1.
(address . 61656@debbugs.gnu.org)(name . Simon Tournier)(address . zimon.toutoune@gmail.com)
20230220185411.377212-14-zimon.toutoune@gmail.com
* gnu/packages/bioconductor.scm (r-interactionset): Update to 1.26.1.
---
gnu/packages/bioconductor.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (23 lines)
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
Simon Tournier wrote 2 years ago
[PATCH 16/24] gnu: r-lpsymphony: Update to 1.26.3.
(address . 61656@debbugs.gnu.org)(name . Simon Tournier)(address . zimon.toutoune@gmail.com)
20230220185411.377212-16-zimon.toutoune@gmail.com
* gnu/packages/bioconductor.scm (r-lpsymphony): Update to 1.26.3.
---
gnu/packages/bioconductor.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (23 lines)
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
Simon Tournier wrote 2 years ago
[PATCH 17/24] gnu: r-massspecwavelet: Update to 1.64.1.
(address . 61656@debbugs.gnu.org)(name . Simon Tournier)(address . zimon.toutoune@gmail.com)
20230220185411.377212-17-zimon.toutoune@gmail.com
* gnu/packages/bioconductor.scm (r-massspecwavelet): Update to 1.64.1.
---
gnu/packages/bioconductor.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (23 lines)
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
Simon Tournier wrote 2 years ago
[PATCH 18/24] gnu: r-biocfilecache: Update to 2.6.1.
(address . 61656@debbugs.gnu.org)(name . Simon Tournier)(address . zimon.toutoune@gmail.com)
20230220185411.377212-18-zimon.toutoune@gmail.com
* gnu/packages/bioconductor.scm (r-biocfilecache): Update to 2.6.1.
---
gnu/packages/bioconductor.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (23 lines)
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
Simon Tournier wrote 2 years ago
[PATCH 19/24] gnu: r-variancepartition: Update to 1.28.4.
(address . 61656@debbugs.gnu.org)(name . Simon Tournier)(address . zimon.toutoune@gmail.com)
20230220185411.377212-19-zimon.toutoune@gmail.com
* gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.28.4.
---
gnu/packages/bioconductor.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (23 lines)
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
Simon Tournier wrote 2 years ago
[PATCH 09/24] gnu: r-impute: Update to 1.72.3.
(address . 61656@debbugs.gnu.org)(name . Simon Tournier)(address . zimon.toutoune@gmail.com)
20230220185411.377212-9-zimon.toutoune@gmail.com
* gnu/packages/bioconductor.scm (r-impute): Update to 1.72.3.
---
gnu/packages/bioconductor.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (22 lines)
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
Simon Tournier wrote 2 years ago
[PATCH 20/24] gnu: r-preprocesscore: Update to 1.60.2.
(address . 61656@debbugs.gnu.org)(name . Simon Tournier)(address . zimon.toutoune@gmail.com)
20230220185411.377212-20-zimon.toutoune@gmail.com
* gnu/packages/bioconductor.scm (r-preprocesscore): Update to 1.60.2.
---
gnu/packages/bioconductor.scm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)

Toggle diff (23 lines)
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
Ricardo Wurmus wrote 2 years ago
Re: [bug#61656] [PATCH 00/24] Update some Bioconductor packages
(name . Simon Tournier)(address . zimon.toutoune@gmail.com)(address . 61656-done@debbugs.gnu.org)
87356vk02q.fsf@elephly.net
Hi Simon,

Toggle quote (3 lines)
> 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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