Your message dated Sun, 02 Oct 2011 04:34:03 +0000
with message-id <[email protected]>
and subject line Bug#643444: fixed in ncbi-tools6 6.1.20110713-2
has caused the Debian Bug report #643444,
regarding ncbi-tools6: FTBFS: pgppop.c:2997:5: error: format not a string
literal and no format arguments [-Werror=format-security]
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 [email protected]
immediately.)
--
643444: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=643444
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: ncbi-tools6
Version: 6.1.20110713-1
Severity: serious
Tags: wheezy sid
User: [email protected]
Usertags: qa-ftbfs-20110923 qa-ftbfs hardening-format-security hardening
Justification: FTBFS on amd64
Hi,
During a rebuild of all packages in sid, your package failed to build on
amd64.
Relevant part:
> gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4
> -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -Werror=format-security -Wall
> -D_PNG -fPIC -I../include -DWIN_MOTIF pgppop.c
> pgppop.c:305:4: warning: missing braces around initializer [-Wmissing-braces]
> pgppop.c:305:4: warning: (near initialization for 'DDV_PaletteRGB[0]')
> [-Wmissing-braces]
> pgppop.c: In function 'DDV_WWW_get_CDS_minus':
> pgppop.c:574:9: warning: variable 'bGiForProductOk' set but not used
> [-Wunused-but-set-variable]
> pgppop.c:572:5: warning: variable 'numivals2' set but not used
> [-Wunused-but-set-variable]
> pgppop.c: In function 'DDV_WWW_get_CDS_plus':
> pgppop.c:696:9: warning: variable 'bGiForProductOk' set but not used
> [-Wunused-but-set-variable]
> pgppop.c: In function 'GetClrFromClrGlobal':
> pgppop.c:1322:4: warning: dereferencing type-punned pointer will break
> strict-aliasing rules [-Wstrict-aliasing]
> pgppop.c:1322:4: warning: dereferencing type-punned pointer will break
> strict-aliasing rules [-Wstrict-aliasing]
> pgppop.c: In function 'DDV_DisplayTopScale':
> pgppop.c:1545:7: warning: unused variable 'szBlank' [-Wunused-variable]
> pgppop.c: In function 'DDV_GetBLASTCompLine_1':
> pgppop.c:1981:21: warning: array subscript has type 'char' [-Wchar-subscripts]
> pgppop.c:1981:21: warning: array subscript has type 'char' [-Wchar-subscripts]
> pgppop.c: In function 'DDV_GetFullGapFASTAforIdxAli':
> pgppop.c:2997:5: error: format not a string literal and no format arguments
> [-Werror=format-security]
> pgppop.c: In function 'DDV_DisplayDefaultAlign':
> pgppop.c:3414:13: warning: unused variable 'sabp' [-Wunused-variable]
> pgppop.c: In function 'DDV_ShowSeqAlign':
> pgppop.c:3757:10: warning: unused variable 'szPopSetAuth' [-Wunused-variable]
> pgppop.c:3755:10: warning: unused variable 'szPopSetName' [-Wunused-variable]
> pgppop.c: In function 'DDV_PrintPopSetSummary':
> pgppop.c:3928:9: warning: variable 'bPairwise' set but not used
> [-Wunused-but-set-variable]
> pgppop.c: At top level:
> ../include/objentgene.h:176:33: warning: 'Method_methodFree' declared
> 'static' but never defined [-Wunused-function]
> ../include/objentgene.h:177:33: warning: 'Method_methodAsnRead' declared
> 'static' but never defined [-Wunused-function]
> ../include/objentgene.h:178:24: warning: 'Method_methodAsnWrite' declared
> 'static' but never defined [-Wunused-function]
> ../include/asnprt.h:12:15: warning: 'asnfilename' defined but not used
> [-Wunused-variable]
> ../include/asnprt.h:59:23: warning: 'avn' defined but not used
> [-Wunused-variable]
> ../include/asnprt.h:60:19: warning: 'at' defined but not used
> [-Wunused-variable]
> ../include/asnprt.h:61:21: warning: 'amp' defined but not used
> [-Wunused-variable]
> ../include/objalignloc.h:80:27: warning: 'Loc_locFree' declared 'static' but
> never defined [-Wunused-function]
> ../include/objalignloc.h:81:27: warning: 'Loc_locAsnRead' declared 'static'
> but never defined [-Wunused-function]
> ../include/objalignloc.h:82:24: warning: 'Loc_locAsnWrite' declared 'static'
> but never defined [-Wunused-function]
> pgppop.c:559:13: warning: 'DDV_WWW_get_CDS_minus' defined but not used
> [-Wunused-function]
> pgppop.c:2086:13: warning: 'DDV_HideMaskedLetters' defined but not used
> [-Wunused-function]
> pgppop.c:2861:13: warning: 'DDV_GetGappedSequence' defined but not used
> [-Wunused-function]
> pgppop.c:2908:13: warning: 'DDV_PrintFastaGappedSequence' defined but not
> used [-Wunused-function]
> cc1: some warnings being treated as errors
>
> make[2]: *** [pgppop.o] Error 1
The full build log is available from:
http://people.debian.org/~lucas/logs/2011/09/23/ncbi-tools6_6.1.20110713-1_lsid64.buildlog
This happened because since dpkg 1.16.0 [0], hardening flags are enabled
under various conditions.
[0] http://lists.debian.org/debian-devel-announce/2011/09/msg00001.html
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
About the archive rebuild: The rebuild was done on about 50 AMD64 nodes
of the Grid'5000 platform, using a clean chroot. Internet was not
accessible from the build systems.
--- End Message ---
--- Begin Message ---
Source: ncbi-tools6
Source-Version: 6.1.20110713-2
We believe that the bug you reported is fixed in the latest version of
ncbi-tools6, which is due to be installed in the Debian FTP archive:
blast2_2.2.25.20110713-2_amd64.deb
to main/n/ncbi-tools6/blast2_2.2.25.20110713-2_amd64.deb
libncbi6-dbg_6.1.20110713-2_amd64.deb
to main/n/ncbi-tools6/libncbi6-dbg_6.1.20110713-2_amd64.deb
libncbi6-dev_6.1.20110713-2_amd64.deb
to main/n/ncbi-tools6/libncbi6-dev_6.1.20110713-2_amd64.deb
libncbi6_6.1.20110713-2_amd64.deb
to main/n/ncbi-tools6/libncbi6_6.1.20110713-2_amd64.deb
libvibrant6-dev_6.1.20110713-2_amd64.deb
to main/n/ncbi-tools6/libvibrant6-dev_6.1.20110713-2_amd64.deb
libvibrant6a-dbg_6.1.20110713-2_amd64.deb
to main/n/ncbi-tools6/libvibrant6a-dbg_6.1.20110713-2_amd64.deb
libvibrant6a_6.1.20110713-2_amd64.deb
to main/n/ncbi-tools6/libvibrant6a_6.1.20110713-2_amd64.deb
ncbi-data_6.1.20110713-2_all.deb
to main/n/ncbi-tools6/ncbi-data_6.1.20110713-2_all.deb
ncbi-rrna-data_6.1.20110713-2_all.deb
to main/n/ncbi-tools6/ncbi-rrna-data_6.1.20110713-2_all.deb
ncbi-tools-bin_6.1.20110713-2_amd64.deb
to main/n/ncbi-tools6/ncbi-tools-bin_6.1.20110713-2_amd64.deb
ncbi-tools-x11_6.1.20110713-2_amd64.deb
to main/n/ncbi-tools6/ncbi-tools-x11_6.1.20110713-2_amd64.deb
ncbi-tools6_6.1.20110713-2.diff.gz
to main/n/ncbi-tools6/ncbi-tools6_6.1.20110713-2.diff.gz
ncbi-tools6_6.1.20110713-2.dsc
to main/n/ncbi-tools6/ncbi-tools6_6.1.20110713-2.dsc
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.
Aaron M. Ucko <[email protected]> (supplier of updated ncbi-tools6 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: Sat, 01 Oct 2011 22:08:13 -0400
Source: ncbi-tools6
Binary: libncbi6 libncbi6-dev libncbi6-dbg ncbi-data ncbi-rrna-data
ncbi-tools-bin ncbi-tools-x11 blast2 libvibrant6a libvibrant6-dev
libvibrant6a-dbg
Architecture: source amd64 all
Version: 6.1.20110713-2
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Aaron M. Ucko <[email protected]>
Description:
blast2 - Basic Local Alignment Search Tool
libncbi6 - NCBI libraries for biology applications
libncbi6-dbg - NCBI libraries for biology applications (debugging symbols)
libncbi6-dev - NCBI libraries for biology applications (development files)
libvibrant6-dev - NCBI libraries for graphic biology applications (development
file
libvibrant6a - NCBI libraries for graphic biology applications
libvibrant6a-dbg - NCBI libraries for graphic biology applications (unstripped)
ncbi-data - Platform-independent data for the NCBI toolkit
ncbi-rrna-data - large rRNA BLAST databases distributed with the NCBI toolkit
ncbi-tools-bin - NCBI libraries for biology applications (text-based utilities)
ncbi-tools-x11 - NCBI libraries for biology applications (X-based utilities)
Closes: 643444
Changes:
ncbi-tools6 (6.1.20110713-2) unstable; urgency=low
.
* api/alignmgr2.c, api/pgppop.c, api/txalign.c, desktop/seqpanel.c,
tools/spidey.c: avoid calling printf and the like with non-constant
strings, as caught by -Werror=format-security. (Closes: #643444.)
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