Your message dated Sat, 27 Jun 2015 17:34:24 +0000
with message-id <e1z8tzk-0002r3...@franck.debian.org>
and subject line Bug#789985: fixed in r-bioc-shortread 1.26.0-1
has caused the Debian Bug report #789985,
regarding FTBFS: IRanges_defines.h: fatal error: S4Vectors_defines.h: No such
file or directory
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
789985: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=789985
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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)
--- End Message ---
--- Begin Message ---
Source: r-bioc-shortread
Source-Version: 1.26.0-1
We believe that the bug you reported is fixed in the latest version of
r-bioc-shortread, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 789...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated r-bioc-shortread package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Sat, 27 Jun 2015 19:18:04 +0200
Source: r-bioc-shortread
Binary: r-bioc-shortread
Architecture: source amd64
Version: 1.26.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Description:
r-bioc-shortread - GNU R classes and methods for high-throughput short-read
sequenci
Closes: 789985
Changes:
r-bioc-shortread (1.26.0-1) unstable; urgency=medium
.
* New upstream version
Closes: #789985
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--- End Message ---
