Subject: bug#38674: closed (Re: [bug#38674] [PATCH] gnu: tophat: Build with GCC 5)

From: [email-masked] (GNU bug Tracking System)
Date: Mon, 23 Dec 2019 18:33:02 +0000

Your bug report

#38674: [PATCH] gnu: tophat: Build with GCC 5

which was filed against the guix-patches package, has been closed.

The explanation is attached below, along with your original report.
If you require more details, please reply to [email-masked].

-- 
38674: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=38674
GNU Bug Tracking System
Contact [email-masked] with problems

Subject: Re: [bug#38674] [PATCH] gnu: tophat: Build with GCC 5
From: Ludovic Courtès <[email-masked]>
To: Mădălin Ionel Patrașcu<[email-masked]>
Cc: [email-masked]
Date: Mon, 23 Dec 2019 19:32:05 +0100
List-Id: <debbugs-submit.debbugs.gnu.org>

Hi,

Mădălin Ionel Patrașcu <[email-masked]> skribis:

> * gnu/packages/python-xyz.scm (tophat)[native-inputs]: Add gcc-5.
> (tophat)[inputs]: Reorder alphabetically the dependencies.
> (tophat)[home-page]: Swapp to https.

Applied, thanks!

Ludo’.

Subject: [PATCH] gnu: tophat: Build with GCC 5
From: Mădălin Ionel Patrașcu<[email-masked]>
To: <[email-masked]>
Cc: Mădălin Ionel Patrașcu<[email-masked]>
Date: Thu, 19 Dec 2019 19:53:31 +0100
List-Id: <debbugs-submit.debbugs.gnu.org>

* gnu/packages/python-xyz.scm (tophat)[native-inputs]: Add gcc-5.
(tophat)[inputs]: Reorder alphabetically the dependencies.
(tophat)[home-page]: Swapp to https.
---
 gnu/packages/bioinformatics.scm | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 528b603476..0f6c120687 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11,7 +11,7 @@
 ;;; Copyright © 2017 Arun Isaac <[email-masked]>
 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <[email-masked]>
 ;;; Copyright © 2018 Gábor Boskovits <[email-masked]>
-;;; Copyright © 2018 Mădălin Ionel Patrașcu <[email-masked]>
+;;; Copyright © 2018, 2019 Mădălin Ionel Patrașcu <[email-masked]>
 ;;; Copyright © 2019 Maxim Cournoyer <[email-masked]>
 ;;; Copyright © 2019 Brian Leung <[email-masked]>
 ;;;
@@ -1615,7 +1615,7 @@ genome (2.9 GB for paired-end).")
                   #t))))
     (build-system gnu-build-system)
     (arguments
-     '(#:parallel-build? #f ; not supported
+     '(#:parallel-build? #f             ; not supported
        #:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'use-system-samtools
@@ -1639,16 +1639,18 @@ genome (2.9 GB for paired-end).")
                (("#include <bam.h>") "#include <samtools/bam.h>")
                (("#include <sam.h>") "#include <samtools/sam.h>"))
              #t)))))
+    (native-inputs
+     `(("gcc" ,gcc-5))) ;; doesn't build with later versions
     (inputs
      `(("boost" ,boost)
        ("bowtie" ,bowtie)
-       ("samtools" ,samtools-0.1)
        ("ncurses" ,ncurses)
-       ("python" ,python-2)
        ("perl" ,perl)
-       ("zlib" ,zlib)
-       ("seqan" ,seqan-1)))
-    (home-page "http://ccb.jhu.edu/software/tophat/index.shtml")
+       ("python" ,python-2)
+       ("samtools" ,samtools-0.1)
+       ("seqan" ,seqan-1)
+       ("zlib" ,zlib)))
+    (home-page "https://ccb.jhu.edu/software/tophat/index.shtml")
     (synopsis "Spliced read mapper for RNA-Seq data")
     (description
      "TopHat is a fast splice junction mapper for nucleotide sequence
-- 
2.24.1