Your message dated Thu, 26 Nov 2009 12:18:26 +0000
with message-id <e1nddio-0006wy...@ries.debian.org>
and subject line Bug#552830: fixed in readseq 1-8
has caused the Debian Bug report #552830,
regarding readseq: FTBFS: ureadseq.c:145: error: conflicting types for 'getline'
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.)
--
552830: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=552830
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: readseq
Version: 1-7
Severity: serious
User: debian...@lists.debian.org
Usertags: qa-ftbfs-20091028 qa-ftbfs
Justification: FTBFS on amd64
Hi,
During a rebuild of all packages in sid, your package failed to build on
amd64.
In eglibc <= 2.9, getline was only defined if _GNU_SOURCE was defined.
In eglibc 2.10, getline is always defined (since it became a standard in
POSIX2008). The problem is that your package already has a function
named getline(), which now conflicts with glibc's. You need to rename
your function to something else.
Ubuntu already fixed many occurences of your problem, so it is possible
that an Ubuntu patch is available for your package. Look at the PTS to
find out.
Relevant part:
> gcc -o readseq -I/usr/include/ncbi -g -O2 -g -Wall -O2 -DNCBI
> -I/usr/include/ncbi -DARB readseq.c ureadseq.c ureadasn.c -lncbi -lncbiobj
> -lncbicdr -lncbiacc -lncbitool -lncbimmdb -lncbiid1 -lnetcli -lm
> readseq.c:184: warning: ignoring #pragma segment readseq
> readseq.c: In function 'formatstr':
> readseq.c:267: warning: return discards qualifiers from pointer target type
> readseq.c:269: warning: return discards qualifiers from pointer target type
> readseq.c:273: warning: return discards qualifiers from pointer target type
> readseq.c: In function 'parseformat':
> readseq.c:288: warning: suggest parentheses around comparison in operand of |
> readseq.c: In function 'readopt':
> readseq.c:497: warning: unused variable 'slen'
> readseq.c: In function 'Nlm_Main':
> readseq.c:936: warning: format '%d' expects type 'int', but argument 4 has
> type 'long int'
> readseq.c:938: warning: format '%d' expects type 'int', but argument 3 has
> type 'long int'
> readseq.c:981: warning: format '%d' expects type 'int', but argument 3 has
> type 'long int'
> readseq.c:981: warning: format '%d' expects type 'int', but argument 4 has
> type 'long int'
> readseq.c:981: warning: format '%X' expects type 'unsigned int', but argument
> 5 has type 'long unsigned int'
> readseq.c:998: warning: format '%d' expects type 'int', but argument 3 has
> type 'long int'
> readseq.c:998: warning: format '%d' expects type 'int', but argument 4 has
> type 'long int'
> readseq.c:999: warning: format '%d' expects type 'int', but argument 3 has
> type 'long int'
> readseq.c:999: warning: format '%d' expects type 'int', but argument 4 has
> type 'long int'
> readseq.c:1118: warning: format '%d' expects type 'int', but argument 4 has
> type 'long int'
> readseq.c:1118: warning: format '%d' expects type 'int', but argument 6 has
> type 'long unsigned int'
> readseq.c:1133: warning: format '%d' expects type 'int', but argument 4 has
> type 'long int'
> readseq.c:1134: warning: format '%d' expects type 'int', but argument 4 has
> type 'long int'
> readseq.c:1158: warning: format '%d' expects type 'int', but argument 4 has
> type 'long int'
> readseq.c:777: warning: 'fout' may be used uninitialized in this function
> readseq.c:777: warning: 'fin' may be used uninitialized in this function
> readseq.c:737: warning: 'ftmp' may be used uninitialized in this function
> readseq.c:734: warning: 'seq' may be used uninitialized in this function
> readseq.c:732: warning: 'seqlen0' may be used uninitialized in this function
> readseq.c:731: warning: 'nlines' may be used uninitialized in this function
> readseq.c:734: warning: 'cp' may be used uninitialized in this function
> ureadseq.c:30: warning: ignoring #pragma segment ureadseq
> ureadseq.c:145: error: conflicting types for 'getline'
> /usr/include/stdio.h:651: error: previous declaration of 'getline' was here
> ureadseq.c: In function 'readLINALL':
> ureadseq.c:520: warning: unused variable 'i'
> ureadseq.c: In function 'readUWGCG':
> ureadseq.c:613: warning: suggest parentheses around assignment used as truth
> value
> ureadseq.c:614: warning: suggest parentheses around assignment used as truth
> value
> ureadseq.c: In function 'readOlsen':
> ureadseq.c:658: warning: suggest parentheses around assignment used as truth
> value
> ureadseq.c:669: warning: suggest parentheses around assignment used as truth
> value
> ureadseq.c: In function 'readMSF':
> ureadseq.c:713: warning: unused variable 'atseq'
> ureadseq.c: In function 'readPAUPinterleaved':
> ureadseq.c:776: warning: unused variable 'atseq'
> ureadseq.c: In function 'seqFileFormatFp':
> ureadseq.c:1535: warning: format '%d' expects type 'int *', but argument 3
> has type 'long int *'
> ureadseq.c:1535: warning: format '%d' expects type 'int *', but argument 4
> has type 'long int *'
> ureadseq.c:1262: warning: unused variable 'foundDNA'
> ureadseq.c: In function 'writeSeq':
> ureadseq.c:1784: warning: format '%d' expects type 'int', but argument 3 has
> type 'long int'
> ureadseq.c:1813: warning: format '%d' expects type 'int', but argument 4 has
> type 'long int'
> ureadseq.c:1814: warning: format '%d' expects type 'int', but argument 4 has
> type 'long int'
> ureadseq.c:1814: warning: format '%X' expects type 'unsigned int', but
> argument 5 has type 'long unsigned int'
> ureadseq.c:1828: warning: format '%d' expects type 'int', but argument 4 has
> type 'long int'
> ureadseq.c:1828: warning: format '%X' expects type 'unsigned int', but
> argument 5 has type 'long unsigned int'
> ureadseq.c:1838: warning: format '%10d' expects type 'int', but argument 3
> has type 'long int'
> ureadseq.c:1848: warning: format '%d' expects type 'int', but argument 4 has
> type 'long int'
> ureadseq.c:1848: warning: format '%X' expects type 'unsigned int', but
> argument 5 has type 'long unsigned int'
> ureadseq.c:1857: warning: format '%d' expects type 'int', but argument 4 has
> type 'long int'
> ureadseq.c:1857: warning: format '%X' expects type 'unsigned int', but
> argument 5 has type 'long unsigned int'
> ureadseq.c:1858: warning: format '%d' expects type 'int', but argument 3 has
> type 'long int'
> ureadseq.c:1869: warning: format '%d' expects type 'int', but argument 4 has
> type 'long int'
> ureadseq.c:1869: warning: format '%d' expects type 'int', but argument 5 has
> type 'long unsigned int'
> ureadseq.c:1878: warning: format '%d' expects type 'int', but argument 4 has
> type 'long int'
> ureadseq.c:1878: warning: format '%X' expects type 'unsigned int', but
> argument 5 has type 'long unsigned int'
> ureadseq.c:1884: warning: format '%d' expects type 'int', but argument 4 has
> type 'long int'
> ureadseq.c:1884: warning: format '%X' expects type 'unsigned int', but
> argument 5 has type 'long unsigned int'
> ureadseq.c:1915: warning: format '%d' expects type 'int', but argument 4 has
> type 'long int'
> ureadseq.c:1937: warning: format '%6d' expects type 'int', but argument 4 has
> type 'long int'
> ureadseq.c:1937: warning: format '%8X' expects type 'unsigned int', but
> argument 5 has type 'long unsigned int'
> ureadseq.c:1954: warning: format '%6d' expects type 'int', but argument 4 has
> type 'long int'
> ureadseq.c:1954: warning: format '%8X' expects type 'unsigned int', but
> argument 5 has type 'long unsigned int'
> ureadseq.c:1961: warning: format '%6d' expects type 'int', but argument 4 has
> type 'long int'
> ureadseq.c:1961: warning: format '%5d' expects type 'int', but argument 5 has
> type 'long unsigned int'
> ureadseq.c:1972: warning: format '%d' expects type 'int', but argument 4 has
> type 'long int'
> ureadseq.c:1972: warning: format '%X' expects type 'unsigned int', but
> argument 5 has type 'long unsigned int'
> ureadseq.c:1979: warning: format '%4d' expects type 'int', but argument 3 has
> type 'long int'
> ureadseq.c:2002: warning: format '%d' expects type 'int', but argument 4 has
> type 'long int'
> ureadseq.c:2002: warning: format '%X' expects type 'unsigned int', but
> argument 5 has type 'long unsigned int'
> ureadseq.c:2043: warning: format '%-9d' expects type 'int', but argument 3
> has type 'long int'
> ureadasn.c:19: warning: ignoring #pragma segment ureadasn
> ureadasn.c: In function 'listASNSeqs':
> ureadasn.c:189: warning: passing argument 1 of 'AsnIoOpen' discards
> qualifiers from pointer target type
> ureadasn.c: In function 'readASNSeq':
> ureadasn.c:261: warning: passing argument 1 of 'AsnIoOpen' discards
> qualifiers from pointer target type
> make[1]: *** [build] Error 1
The full build log is available from:
http://people.debian.org/~lucas/logs/2009/10/28/readseq_1-7_lsid64.buildlog
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.
--
| Lucas Nussbaum
| lu...@lucas-nussbaum.net http://www.lucas-nussbaum.net/ |
| jabber: lu...@nussbaum.fr GPG: 1024D/023B3F4F |
--- End Message ---
--- Begin Message ---
Source: readseq
Source-Version: 1-8
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_1-8.diff.gz
to main/r/readseq/readseq_1-8.diff.gz
readseq_1-8.dsc
to main/r/readseq/readseq_1-8.dsc
readseq_1-8_i386.deb
to main/r/readseq/readseq_1-8_i386.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 552...@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 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 ftpmas...@debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Format: 1.8
Date: Thu, 26 Nov 2009 12:31:49 +0100
Source: readseq
Binary: readseq
Architecture: source i386
Version: 1-8
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Description:
readseq - [Biology] Conversion between sequence formats
Closes: 552830
Changes:
readseq (1-8) unstable; urgency=low
.
[ Charles Plessy ]
* DM-Upload-Allowed: Yes
.
[ Andreas Tille ]
* Added Vcs-Browser, Vcs-Svn
* Standards-Version: 3.8.3 (added README.source)
* Debhelper 7
* Switch to quilt
* debian/patches/552830.patch: Patch from Ruben Molina <rmol...@udea.edu.co>
to fix build problem (thanks to Ruben), changed one last remaining of
getline myself
Closes: #552830
Checksums-Sha1:
e55f42d0a6ec4a401190cd9864426e744ca16162 1270 readseq_1-8.dsc
53837e4d8a8579573a6a30f80553ffd7e70af36e 15443 readseq_1-8.diff.gz
8331a8f6f942209e74a3357274bf6edc0af2de7a 57030 readseq_1-8_i386.deb
Checksums-Sha256:
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readseq_1-8.dsc
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readseq_1-8_i386.deb
Files:
21445f39d7ed3f5c0e1c7d51d29be290 1270 science optional readseq_1-8.dsc
842457a9b9b3a51c689d4d4fa359a314 15443 science optional readseq_1-8.diff.gz
1fddaac9b14598716ff4e1c8d2830719 57030 science optional readseq_1-8_i386.deb
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--- End Message ---
