Your message dated Thu, 28 Jan 2016 10:40:17 +0000
with message-id <[email protected]>
and subject line Bug#812767: fixed in r-bioc-genefilter 1.52.0-2
has caused the Debian Bug report #812767,
regarding r-bioc-genefilter: conflicting declarations of function gf_distance
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
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--
812767: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=812767
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: r-bioc-genefilter
Version: 1.52.0-1
Usertags: goto-cc
During a rebuild of all Debian packages in a clean sid chroot (using cowbuilder
and pbuilder) the build failed with the following error. Please note that we
use our research compiler tool-chain (using tools from the cbmc package), which
permits extended reporting on type inconsistencies at link time.
g++ -shared -L/usr/lib/R/lib -Wl,-z,relro -o genefilter.so half_range_mode.o
init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o -lgfortran -lm -lquadmath
-L/usr/lib/R/lib -lR
file nd.c line 270: error: conflicting parameter counts of function
declarations `gf_distance'
old definition in module `init' file genefilter.h line 5
void (double *, double *, signed int *, signed int *, double *, signed int *,
signed int *)
new definition in module `nd' file nd.c line 270
void (double *x, signed int *nr, signed int *nc, signed int *g, double *d,
signed int *iRow, signed int *nInterest, signed int *nResults, signed int
*method, double *wval)
/usr/share/R/share/make/shlib.mk:6: recipe for target 'genefilter.so' failed
make[1]: *** [genefilter.so] Error 1
make[1]: Leaving directory
'/srv/jenkins-slave/workspace/sid-goto-cc-r-bioc-genefilter/r-bioc-genefilter-1.52.0/src'
It seems the declaration in genefilter.h and the definition in nd.c are highly
inconsistent as not only the number, but also the individual types do not match
up. This will cause misaligned stack accesses.
Best,
Michael
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--- End Message ---
--- Begin Message ---
Source: r-bioc-genefilter
Source-Version: 1.52.0-2
We believe that the bug you reported is fixed in the latest version of
r-bioc-genefilter, 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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated r-bioc-genefilter 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 [email protected])
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Hash: SHA256
Format: 1.8
Date: Thu, 28 Jan 2016 10:55:03 +0100
Source: r-bioc-genefilter
Binary: r-bioc-genefilter
Architecture: source amd64
Version: 1.52.0-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
r-bioc-genefilter - methods for filtering genes from microarray experiments
Closes: 812767
Changes:
r-bioc-genefilter (1.52.0-2) unstable; urgency=medium
.
* Apply upstream patch to fix conflicting declarations of function
gf_distance
Closes: #812767
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