[Debian-med-packaging] Bug#789985: FTBFS: IRanges_defines.h: fatal error: S4Vectors_defines.h: No such file or directory

[Andreas Tille]

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-builds at 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)
> 
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