[Debian-med-packaging] Bug#552830: readseq: FTBFS: ureadseq.c:145: error: conflicting types for 'getline'

Wed Oct 28 10:35:00 UTC 2009

Source: readseq
Version: 1-7
Severity: serious
User: debian-qa at 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
| lucas at lucas-nussbaum.net   http://www.lucas-nussbaum.net/ |
| jabber: lucas at nussbaum.fr             GPG: 1024D/023B3F4F |