Hi,
thanks for this bug report. I guess some other r-bioc-* packages are
similarly affected. There is a transition to a new version of these
packages ongoing and the problem will be dealt with soon.
Kind regards
Andreas.
On Thu, Jun 25, 2015 at 08:30:04PM +0000, Chris West (Faux) wrote:
> Package: r-bioc-shortread
> Version: 1.22.0-1
> Severity: serious
> Justification: fails to build from source (but built successfully in the past)
> User: reproducible-bui...@lists.alioth.debian.org
> Usertags: ftbfs
>
> Dear Maintainer,
>
> The package fails to build:
>
> config.status: creating src/Makevars
> ** libs
> make[1]: Entering directory '/tmp/buildd/r-bioc-shortread-1.22.0/src'
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
> -I"/usr/lib/R/site-library/IRanges/include"
> -I"/usr/lib/R/site-library/XVector/include"
> -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -fpic -g -O2
> -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2
> -g -c Biostrings_stubs.c -o Biostrings_stubs.o
> In file included from
> /usr/lib/R/site-library/Biostrings/include/Biostrings_defines.h:18:0,
> from
> /usr/lib/R/site-library/Biostrings/include/Biostrings_interface.h:114,
> from
> /usr/lib/R/site-library/Biostrings/include/_Biostrings_stubs.c:1,
> from Biostrings_stubs.c:1:
> /usr/lib/R/site-library/IRanges/include/IRanges_defines.h:18:31: fatal error:
> S4Vectors_defines.h: No such file or directory
> #include "S4Vectors_defines.h"
> ^
> compilation terminated.
> /usr/lib/R/etc/Makeconf:134: recipe for target 'Biostrings_stubs.o' failed
>
>
> Maybe this is a bug in r-bioc-biostrings, or r-bioc-iranges?
>
> The same bug affects at least r-bioc-genomicalignments, r-bioc-rtracklayer,
> and r-bioc-variantannotation.
> (all same maintainer)
>
> Full build log:
> https://reproducible.debian.net/rb-pkg/testing/amd64/r-bioc-shortread.html
>
> -- System Information:
> Debian Release: stretch/sid
> APT prefers unstable
> APT policy: (500, 'unstable'), (1, 'experimental')
> Architecture: amd64 (x86_64)
>
> Kernel: Linux 3.19.0-21-generic (SMP w/8 CPU cores)
> Locale: LANG=en_GB.UTF-8, LC_CTYPE=en_GB.UTF-8 (charmap=UTF-8)
> Shell: /bin/sh linked to /bin/dash
> Init: systemd (via /run/systemd/system)
>
> _______________________________________________
> Debian-med-packaging mailing list
> debian-med-packag...@lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
>
--
http://fam-tille.de
--
To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org
with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
