Your message dated Mon, 19 May 2014 23:34:37 +0000
with message-id <[email protected]>
and subject line Bug#748395: fixed in emboss 6.6.0+dfsg-1
has caused the Debian Bug report #748395,
regarding Misaligned array access caused by conflicting declarations
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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--
748395: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=748395
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: emboss
Version: 6.6.0-1
Usertags: goto-cc
During a rebuild of all packages in a clean sid chroot (and cowbuilder+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.
[...]
libtool: link: gcc -shared -fPIC -DPIC .libs/pdfutils.o .libs/plargs.o
.libs/plbox.o .libs/plcont.o .libs/plcore.o .libs/plctrl.o .libs/plcvt.o
.libs/pldtik.o .libs/plfill.o .libs/plhist.o .libs/plline.o .libs/plmap.o
.libs/plot3d.o .libs/plpage.o .libs/plsdef.o .libs/plshade.o .libs/plsym.o
.libs/pltick.o .libs/plvpor.o .libs/plwind.o .libs/plstripc.o .libs/hpgl.o
.libs/impress.o .libs/ljiip.o .libs/ljii.o .libs/null.o .libs/data.o
.libs/pbm.o .libs/plbuf.o .libs/plmeta.o .libs/ps.o .libs/tek.o .libs/xfig.o
.libs/xwin.o .libs/gd.o .libs/pdf.o .libs/svg.o .libs/plimage.o .libs/plstdio.o
.libs/plvect.o /usr/lib/x86_64-linux-gnu/libexpat.so
-L/usr/lib/x86_64-linux-gnu -lmysqlclient -lpthread -ldl -lpq -lhpdf -lgd -lpng
-lz -lm -O2 -Wl,-z -Wl,relro -Wl,-soname -Wl,libeplplot.so.3 -o
.libs/libeplplot.so.3.2.7
error: conflicting types for variable "hershey_to_unicode_lookup_table"
old definition in module plcore file plplotP.h line 385
struct Hershey_to_Unicode_table []
new definition in module plsym file plhershey-unicode.h line 50
const Hershey_to_Unicode_table [980l]
reason for conflict at padding in types listed below (array/array):
char [3l]
char [7l]
make[4]: *** [libeplplot.la] Error 64
make[4]: Leaving directory
`/srv/jenkins-slave/workspace/sid-goto-cc-emboss/emboss-6.6.0/plplot'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory
`/srv/jenkins-slave/workspace/sid-goto-cc-emboss/emboss-6.6.0/plplot'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory
`/srv/jenkins-slave/workspace/sid-goto-cc-emboss/emboss-6.6.0'
dh_auto_build: make -j1 AJAX_FIXED_ROOT=\"/usr/share/EMBOSS\"
CPPFLAGS=-D_FORTIFY_SOURCE=2 CFLAGS=-g -O2 -fstack-protector
--param=ssp-buffer-size=4 -Wformat -Werror=format-security LDFLAGS=-lexpat
-L/usr/lib/x86_64-linux-gnu -lmysqlclient -lpthread -lz -lm -ldl -lpq
-Wl,-z,relro returned exit code 2
make[1]: *** [override_dh_auto_build] Error 2
make[1]: Leaving directory
`/srv/jenkins-slave/workspace/sid-goto-cc-emboss/emboss-6.6.0'
make: *** [build] Error 2
Review the full (conflicting) declarations here:
http://sources.debian.net/src/emboss/6.6.0-1/plplot/plplotP.h?hl=381#L377
http://sources.debian.net/src/emboss/6.6.0-1/plplot/plhershey-unicode.h?hl=46#L42
As plcore.c (via plcore.h) solely includes plplotP.h, all accesses in this code
will be misaligned with arbitrary consequences.
Best,
Michael
PS.: As this bug appears to be entirely within an embedded code copy of plplot,
maybe it's about time to get rid of that.
pgpqD4HWm7lg6.pgp
Description: PGP signature
--- End Message ---
--- Begin Message ---
Source: emboss
Source-Version: 6.6.0+dfsg-1
We believe that the bug you reported is fixed in the latest version of
emboss, 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 emboss 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])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Mon, 19 May 2014 20:52:12 +0200
Source: emboss
Binary: emboss emboss-data emboss-doc emboss-test emboss-lib jemboss
Architecture: source amd64 all
Version: 6.6.0+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
emboss - european molecular biology open software suite
emboss-data - data files for the EMBOSS package
emboss-doc - documentation for EMBOSS
emboss-lib - EMBOSS Libraries
emboss-test - test files for the EMBOSS package
jemboss - graphical user interface to EMBOSS
Closes: 748395
Changes:
emboss (6.6.0+dfsg-1) unstable; urgency=medium
.
[ Andreas Tille ]
* debian/copyright: Add Upstream-Contact to report bugs
.
[ Gert Wollny ]
* Add patch to pad Hershey_to_Unicode_table consistently (Closes: #748395)
.
[ Andreas Tille ]
* cme fix dpkg-control:
- drop very old library versions from conflicts / replaces list
* remove explicite quilt dependency which is not needed
* debian/copyright: Exclude invariant GFDL 1.1 files which are related to
quite outdated EMBOSS 2.5.0
* debian/emboss-doc.doc-base.emboss-admin: removed
* debian/patches/remove_non-free_doc.patch: Cleanup Makefile.am from non-free
docs
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