GNU bug report logs - #47070
[PATCH 0/3] Fix 3 bioconductor packages (fail to retrieve upstream)

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

From: zimoun <zimon.toutoune <at> gmail.com>
To: guix-patches <at> gnu.org
Cc: rekado <at> elephly.net, zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 0/3] Fix 3 bioconductor packages (fail to retrieve upstream)
Date: Thu, 11 Mar 2021 15:44:22 +0100

Hi,

This 3 packages had been updated by Bioconductor and the tarballs are not on
Berlin, so they fail to build.  The patch set updates them to fetch the last
upstream versions.


Cheers,
simon


zimoun (3):
  gnu: r-circrnaprofiler: Update to 1.4.2.
  gnu: r-chemminer: Update to 3.42.2.
  gnu: r-bioassayr: Update to 1.28.2.

 gnu/packages/bioconductor.scm | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)


base-commit: 21b3b755151028647081fe96d2992b3743531d71
--
2.30.1

Message #8 received at 47070 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 47070 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 1/3] gnu: r-circrnaprofiler: Update to 1.4.2.
Date: Thu, 11 Mar 2021 15:46:59 +0100

* gnu/packages/bioconductor.scm (r-circrnaprofiler): Update to 1.4.2.
---
 gnu/packages/bioconductor.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ee83e00492..17ee5d63d8 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2,7 +2,7 @@
 ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado <at> elephly.net>
 ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel <at> gnu.org>
 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me <at> tobias.gr>
-;;; Copyright © 2019, 2020 Simon Tournier <zimon.toutoune <at> gmail.com>
+;;; Copyright © 2019, 2020, 2021 Simon Tournier <zimon.toutoune <at> gmail.com>
 ;;; Copyright © 2020 Peter Lo <peterloleungyau <at> gmail.com>
 ;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba <at> kadziolka.net>
@@ -7167,14 +7167,14 @@ accessibility data.")
 (define-public r-circrnaprofiler
   (package
     (name "r-circrnaprofiler")
-    (version "1.4.0")
+    (version "1.4.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "circRNAprofiler" version))
        (sha256
         (base32
-         "1rwpl9a5p5242aiapik0vf4ywqh7m6phzl8z8qmzcy0imbx7mpbn"))))
+         "0r1hfm3pc7c71irzmxmdwc27ns9hkymz4vhb4pqbli4xn37q7cg8"))))
     (properties
      `((upstream-name . "circRNAprofiler")))
     (build-system r-build-system)
-- 
2.30.1

Message #11 received at 47070 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 47070 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 2/3] gnu: r-chemminer: Update to 3.42.2.
Date: Thu, 11 Mar 2021 15:47:00 +0100

* gnu/packages/bioconductor.scm (r-chemminer): Update to 3.42.2.
---
 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 17ee5d63d8..3a9720adc6 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8269,14 +8269,14 @@ visualizing RNA-sequencing datasets and differentially expressed genes.")
 (define-public r-chemminer
   (package
     (name "r-chemminer")
-    (version "3.42.1")
+    (version "3.42.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ChemmineR" version))
        (sha256
         (base32
-         "1853w19042c53whdnrfg1v8f07wpswf2si8q4613yrcamzg2zjkx"))))
+         "10d8h6w24h4s7l02zzv6q46w3yiqsjizip7mf11cvkmd6p7qxfl9"))))
     (properties `((upstream-name . "ChemmineR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
2.30.1

Message #14 received at 47070 <at> debbugs.gnu.org (full text, mbox):

From: zimoun <zimon.toutoune <at> gmail.com>
To: 47070 <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 3/3] gnu: r-bioassayr: Update to 1.28.2.
Date: Thu, 11 Mar 2021 15:47:01 +0100

* gnu/packages/bioconductor.scm (r-bioassayr): Update to 1.28.2.
---
 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 3a9720adc6..6301f2f7c4 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8310,14 +8310,14 @@ structures.")
 (define-public r-bioassayr
   (package
     (name "r-bioassayr")
-    (version "1.28.0")
+    (version "1.28.2")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "bioassayR" version))
        (sha256
         (base32
-         "0vxnd8wnhjdfqh47nc6y1ffiy5r9a6n3g2hyk1r9bv6vhrd0ns3f"))))
+         "0ylnnm31jkmi8zz78kngqv36yn6i5lvjp1i27v59svw13m4r03g5"))))
     (properties `((upstream-name . "bioassayR")))
     (build-system r-build-system)
     (propagated-inputs
-- 
2.30.1

Message #19 received at 47070-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 47070-done <at> debbugs.gnu.org
Cc: zimoun <zimon.toutoune <at> gmail.com>
Subject: [PATCH 0/3] Fix 3 bioconductor packages (fail to retrieve upstream)
Date: Fri, 12 Mar 2021 14:42:05 +0100

Thank you, I pushed these to the “master” branch.

-- 
Ricardo

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