Your message dated Fri, 28 Oct 2011 15:06:01 +0000
with message-id <[email protected]>
and subject line Bug#643465: fixed in readseq 1-9
has caused the Debian Bug report #643465,
regarding readseq: FTBFS: readseq.c:338:3: 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.)
--
643465: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=643465
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: readseq
Version: 1-8
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 -o readseq -I/usr/include/ncbi -g -O2 -fstack-protector
> --param=ssp-buffer-size=4 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
> -Werror=format-security -Wall -DNCBI -I/usr/include/ncbi -DARB readseq.c
> ureadseq.c ureadasn.c -lncbi -lncbiobj -lncbicdr -lncbiacc -lncbitool
> -lncbimmdb -lncbiid1 -lnetcli -lm
> readseq.c:184:0: warning: ignoring #pragma segment readseq [-Wunknown-pragmas]
> readseq.c: In function 'formatstr':
> readseq.c:267:27: warning: return discards 'const' qualifier from pointer
> target type [enabled by default]
> readseq.c:269:31: warning: return discards 'const' qualifier from pointer
> target type [enabled by default]
> readseq.c:273:8: warning: return discards 'const' qualifier from pointer
> target type [enabled by default]
> readseq.c: In function 'parseformat':
> readseq.c:288:5: warning: suggest parentheses around comparison in operand of
> '|' [-Wparentheses]
> readseq.c: In function 'usage':
> readseq.c:338:3: error: format not a string literal and no format arguments
> [-Werror=format-security]
> readseq.c: In function 'readopt':
> readseq.c:497:14: warning: unused variable 'slen' [-Wunused-variable]
> readseq.c: In function 'Nlm_Main':
> readseq.c:936:13: warning: format '%d' expects argument of type 'int', but
> argument 4 has type 'long int' [-Wformat]
> readseq.c:938:13: warning: format '%d' expects argument of type 'int', but
> argument 3 has type 'long int' [-Wformat]
> readseq.c:981:17: warning: format '%d' expects argument of type 'int', but
> argument 3 has type 'long int' [-Wformat]
> readseq.c:981:17: warning: format '%d' expects argument of type 'int', but
> argument 4 has type 'long int' [-Wformat]
> readseq.c:981:17: warning: format '%X' expects argument of type 'unsigned
> int', but argument 5 has type 'long unsigned int' [-Wformat]
> readseq.c:991:15: error: format not a string literal and no format arguments
> [-Werror=format-security]
> readseq.c:998:19: warning: format '%d' expects argument of type 'int', but
> argument 3 has type 'long int' [-Wformat]
> readseq.c:998:19: warning: format '%d' expects argument of type 'int', but
> argument 4 has type 'long int' [-Wformat]
> readseq.c:999:19: warning: format '%d' expects argument of type 'int', but
> argument 3 has type 'long int' [-Wformat]
> readseq.c:999:19: warning: format '%d' expects argument of type 'int', but
> argument 4 has type 'long int' [-Wformat]
> readseq.c:1118:19: warning: format '%d' expects argument of type 'int', but
> argument 4 has type 'long int' [-Wformat]
> readseq.c:1118:19: warning: format '%d' expects argument of type 'int', but
> argument 6 has type 'long unsigned int' [-Wformat]
> readseq.c:1133:5: warning: format '%d' expects argument of type 'int', but
> argument 4 has type 'long int' [-Wformat]
> readseq.c:1134:5: warning: format '%d' expects argument of type 'int', but
> argument 4 has type 'long int' [-Wformat]
> readseq.c:1158:9: warning: format '%d' expects argument of type 'int', but
> argument 4 has type 'long int' [-Wformat]
> readseq.c:734:51: warning: variable 'progname' set but not used
> [-Wunused-but-set-variable]
> readseq.c:783:11: warning: ignoring return value of 'tmpnam', declared with
> attribute warn_unused_result [-Wunused-result]
> readseq.c:801:9: warning: ignoring return value of 'gets', declared with
> attribute warn_unused_result [-Wunused-result]
> readseq.c:865:11: warning: ignoring return value of 'gets', declared with
> attribute warn_unused_result [-Wunused-result]
> readseq.c:911:13: warning: ignoring return value of 'gets', declared with
> attribute warn_unused_result [-Wunused-result]
> readseq.c:937:20: warning: ignoring return value of 'freopen', declared with
> attribute warn_unused_result [-Wunused-result]
> readseq.c: In function 'chooseFormat':
> readseq.c:429:12: warning: ignoring return value of 'fgets', declared with
> attribute warn_unused_result [-Wunused-result]
> cc1: some warnings being treated as errors
>
> ureadseq.c:30:0: warning: ignoring #pragma segment ureadseq
> [-Wunknown-pragmas]
> ureadseq.c: In function 'readLINALL':
> ureadseq.c:520:7: warning: unused variable 'i' [-Wunused-variable]
> ureadseq.c: In function 'readUWGCG':
> ureadseq.c:613:3: warning: suggest parentheses around assignment used as
> truth value [-Wparentheses]
> ureadseq.c:614:3: warning: suggest parentheses around assignment used as
> truth value [-Wparentheses]
> ureadseq.c: In function 'readOlsen':
> ureadseq.c:658:9: warning: suggest parentheses around assignment used as
> truth value [-Wparentheses]
> ureadseq.c:669:5: warning: suggest parentheses around assignment used as
> truth value [-Wparentheses]
> ureadseq.c: In function 'readMSF':
> ureadseq.c:713:11: warning: unused variable 'atseq' [-Wunused-variable]
> ureadseq.c: In function 'readPAUPinterleaved':
> ureadseq.c:776:11: warning: unused variable 'atseq' [-Wunused-variable]
> ureadseq.c: In function 'seqFileFormatFp':
> ureadseq.c:1535:5: warning: format '%d' expects argument of type 'int *', but
> argument 3 has type 'long int *' [-Wformat]
> ureadseq.c:1535:5: warning: format '%d' expects argument of type 'int *', but
> argument 4 has type 'long int *' [-Wformat]
> ureadseq.c:1262:13: warning: unused variable 'foundDNA' [-Wunused-variable]
> ureadseq.c: In function 'writeSeq':
> ureadseq.c:1784:3: warning: format '%d' expects argument of type 'int', but
> argument 3 has type 'long int' [-Wformat]
> ureadseq.c:1813:7: warning: format '%d' expects argument of type 'int', but
> argument 4 has type 'long int' [-Wformat]
> ureadseq.c:1814:7: warning: format '%d' expects argument of type 'int', but
> argument 4 has type 'long int' [-Wformat]
> ureadseq.c:1814:7: warning: format '%X' expects argument of type 'unsigned
> int', but argument 5 has type 'long unsigned int' [-Wformat]
> ureadseq.c:1828:7: warning: format '%d' expects argument of type 'int', but
> argument 4 has type 'long int' [-Wformat]
> ureadseq.c:1828:7: warning: format '%X' expects argument of type 'unsigned
> int', but argument 5 has type 'long unsigned int' [-Wformat]
> ureadseq.c:1838:7: warning: format '%d' expects argument of type 'int', but
> argument 3 has type 'long int' [-Wformat]
> ureadseq.c:1848:7: warning: format '%d' expects argument of type 'int', but
> argument 4 has type 'long int' [-Wformat]
> ureadseq.c:1848:7: warning: format '%X' expects argument of type 'unsigned
> int', but argument 5 has type 'long unsigned int' [-Wformat]
> ureadseq.c:1857:7: warning: format '%d' expects argument of type 'int', but
> argument 4 has type 'long int' [-Wformat]
> ureadseq.c:1857:7: warning: format '%X' expects argument of type 'unsigned
> int', but argument 5 has type 'long unsigned int' [-Wformat]
> ureadseq.c:1858:7: warning: format '%d' expects argument of type 'int', but
> argument 3 has type 'long int' [-Wformat]
> ureadseq.c:1869:7: warning: format '%d' expects argument of type 'int', but
> argument 4 has type 'long int' [-Wformat]
> ureadseq.c:1869:7: warning: format '%d' expects argument of type 'int', but
> argument 5 has type 'long unsigned int' [-Wformat]
> ureadseq.c:1878:7: warning: format '%d' expects argument of type 'int', but
> argument 4 has type 'long int' [-Wformat]
> ureadseq.c:1878:7: warning: format '%X' expects argument of type 'unsigned
> int', but argument 5 has type 'long unsigned int' [-Wformat]
> ureadseq.c:1884:7: warning: format '%d' expects argument of type 'int', but
> argument 4 has type 'long int' [-Wformat]
> ureadseq.c:1884:7: warning: format '%X' expects argument of type 'unsigned
> int', but argument 5 has type 'long unsigned int' [-Wformat]
> ureadseq.c:1915:7: warning: format '%d' expects argument of type 'int', but
> argument 4 has type 'long int' [-Wformat]
> ureadseq.c:1937:7: warning: format '%d' expects argument of type 'int', but
> argument 4 has type 'long int' [-Wformat]
> ureadseq.c:1937:7: warning: format '%X' expects argument of type 'unsigned
> int', but argument 5 has type 'long unsigned int' [-Wformat]
> ureadseq.c:1954:9: warning: format '%d' expects argument of type 'int', but
> argument 4 has type 'long int' [-Wformat]
> ureadseq.c:1954:9: warning: format '%X' expects argument of type 'unsigned
> int', but argument 5 has type 'long unsigned int' [-Wformat]
> ureadseq.c:1961:21: warning: format '%d' expects argument of type 'int', but
> argument 4 has type 'long int' [-Wformat]
> ureadseq.c:1961:21: warning: format '%d' expects argument of type 'int', but
> argument 5 has type 'long unsigned int' [-Wformat]
> ureadseq.c:1972:7: warning: format '%d' expects argument of type 'int', but
> argument 4 has type 'long int' [-Wformat]
> ureadseq.c:1972:7: warning: format '%X' expects argument of type 'unsigned
> int', but argument 5 has type 'long unsigned int' [-Wformat]
> ureadseq.c:1979:2: warning: format '%d' expects argument of type 'int', but
> argument 3 has type 'long int' [-Wformat]
> ureadseq.c:2002:7: warning: format '%d' expects argument of type 'int', but
> argument 4 has type 'long int' [-Wformat]
> ureadseq.c:2002:7: warning: format '%X' expects argument of type 'unsigned
> int', but argument 5 has type 'long unsigned int' [-Wformat]
> ureadseq.c:2043:9: warning: format '%d' expects argument of type 'int', but
> argument 3 has type 'long int' [-Wformat]
> In file included from /usr/include/string.h:642:0,
> from ureadseq.c:24:
> In function 'strcpy',
> inlined from 'writeSeq' at ureadseq.c:1925:13:
> /usr/include/x86_64-linux-gnu/bits/string3.h:105:3: warning: call to
> __builtin___strcpy_chk will always overflow destination buffer [enabled by
> default]
> ureadasn.c:19:0: warning: ignoring #pragma segment ureadasn
> [-Wunknown-pragmas]
> ureadasn.c: In function 'listASNSeqs':
> ureadasn.c:189:3: warning: passing argument 1 of 'AsnIoOpen' discards 'const'
> qualifier from pointer target type [enabled by default]
> /usr/include/ncbi/asn.h:354:29: note: expected 'Nlm_CharPtr' but argument is
> of type 'const char *'
> ureadasn.c: In function 'readASNSeq':
> ureadasn.c:261:3: warning: passing argument 1 of 'AsnIoOpen' discards 'const'
> qualifier from pointer target type [enabled by default]
> /usr/include/ncbi/asn.h:354:29: note: expected 'Nlm_CharPtr' but argument is
> of type 'const char *'
> ureadasn.c:262:36: warning: ignoring return value of 'fgets', declared with
> attribute warn_unused_result [-Wunused-result]
> ureadasn.c: In function 'listASNSeqs':
> ureadasn.c:190:36: warning: ignoring return value of 'fgets', declared with
> attribute warn_unused_result [-Wunused-result]
> In file included from /usr/include/stdio.h:930:0,
> from ureadasn.c:8:
> In function 'fgets',
> inlined from 'readASNSeq' at ureadasn.c:262:36:
> /usr/include/x86_64-linux-gnu/bits/stdio2.h:253:2: warning: call to
> '__fgets_chk_warn' declared with attribute warning: fgets called with bigger
> size than length of destination buffer [enabled by default]
> make[1]: *** [build] Error 1
The full build log is available from:
http://people.debian.org/~lucas/logs/2011/09/23/readseq_1-8_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: readseq
Source-Version: 1-9
We believe that the bug you reported is fixed in the latest version of
readseq, which is due to be installed in the Debian FTP archive:
readseq_1-9.debian.tar.gz
to main/r/readseq/readseq_1-9.debian.tar.gz
readseq_1-9.dsc
to main/r/readseq/readseq_1-9.dsc
readseq_1-9_amd64.deb
to main/r/readseq/readseq_1-9_amd64.deb
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 readseq 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: SHA1
Format: 1.8
Date: Fri, 28 Oct 2011 16:15:21 +0200
Source: readseq
Binary: readseq
Architecture: source amd64
Version: 1-9
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
readseq - Conversion between sequence formats
Closes: 643465
Changes:
readseq (1-9) unstable; urgency=low
.
* Remove [Biology] from description
* Standards-Version: 3.9.2 (no changes needed)
* debian/source/format: 3.0 (quilt)
* debian/get-orig-source: Make sure repackaging is binary reproducible
* Fixed Vcs fields
* Debhelper 8 (control+compat)
* debian/rules: switch to short dh syntax
* debian/patches/gcc-4.6_format-security.patch: Fix format-security issue
Closes: #643465
* debian/dirs: Create dirs used by dh_auto_install
Checksums-Sha1:
0df0638139bd5dca41ce7aecfd5c3d114b212e17 1326 readseq_1-9.dsc
b4a37223c283a5f0c628336dce4791495cd38664 17130 readseq_1-9.debian.tar.gz
81db346d51cf3d58d9c435c61f4d5356ed837a69 59526 readseq_1-9_amd64.deb
Checksums-Sha256:
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readseq_1-9.dsc
243e38878c230112e501bbcc61b5557f9172ad95fae10f69d80aea6401573066 17130
readseq_1-9.debian.tar.gz
0cb0b97b2a15948519d4ff2b9f066454eb6c5ce3df83a4a426982b195842c78f 59526
readseq_1-9_amd64.deb
Files:
0c135e2f18b4b3c278b53f31d46ff0ee 1326 science optional readseq_1-9.dsc
9e525ef69931624151946a82e08708eb 17130 science optional
readseq_1-9.debian.tar.gz
0be20852881d2208830636ca45745b76 59526 science optional readseq_1-9_amd64.deb
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--- End Message ---
