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

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Your message dated Mon, 23 Dec 2019 19:32:05 +0100
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and subject line Re: [bug#38674] [PATCH] gnu: tophat: Build with GCC 5
has caused the debbugs.gnu.org bug report #38674,
regarding [PATCH] gnu: tophat: Build with GCC 5
to be marked as done.

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-- 
38674: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=38674
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> --- Begin Message ---
>
>
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> Subject: 
>
> [PATCH] gnu: tophat: Build with GCC 5
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>
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> Date: 
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> Thu, 19 Dec 2019 19:53:31 +0100
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>
>
> * 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 <address@hidden>
>  ;;; Copyright © 2018 Joshua Sierles, Nextjournal <address@hidden>
>  ;;; Copyright © 2018 Gábor Boskovits <address@hidden>
> -;;; Copyright © 2018 Mădălin Ionel Patrașcu <address@hidden>
> +;;; Copyright © 2018, 2019 Mădălin Ionel Patrașcu <address@hidden>
>  ;;; Copyright © 2019 Maxim Cournoyer <address@hidden>
>  ;;; Copyright © 2019 Brian Leung <address@hidden>
>  ;;;
> @@ -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
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> --- End Message ---
> --- Begin Message ---
>
>
>
> Subject: 
>
> Re: [bug#38674] [PATCH] gnu: tophat: Build with GCC 5
>
>
>
>
> Date: 
>
> Mon, 23 Dec 2019 19:32:05 +0100
>
>
>
>
> User-agent: 
>
> Gnus/5.13 (Gnus v5.13) Emacs/26.3 (gnu/linux)
>
>
>
>
> Hi,
>
> Mădălin Ionel Patrașcu <address@hidden> 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’.
>
>
> --- End Message ---