[Debian-med-packaging] Bug#1091047: phast: FTBFS: ./src/lib/feature/./src/lib/feature/phast_genepred.c:170:(.text+0xf85): undefined reference to `str_new'

[Lucas Nussbaum]

Source: phast
Version: 1.7+dfsg-1
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20241222 ftbfs-trixie

Hi,

During a rebuild of all packages in sid, your package failed to build
on amd64.


Relevant part (hopefully):
> /usr/bin/ld: /<<PKGBUILDDIR>>/src/dless/../../lib/libphast.a(phast_genepred.o): in function `gff_print_genepred':
> ./src/lib/feature/./src/lib/feature/phast_genepred.c:170:(.text+0xf85): undefined reference to `str_new'
> /usr/bin/ld: ./src/lib/feature/./src/lib/feature/phast_genepred.c:170:(.text+0xf92): undefined reference to `str_new'
> /usr/bin/ld: ./src/lib/feature/./src/lib/feature/phast_genepred.c:171:(.text+0xf9f): undefined reference to `str_new'
> /usr/bin/ld: ./src/lib/feature/./src/lib/feature/phast_genepred.c:171:(.text+0xfae): undefined reference to `str_new'
> /usr/bin/ld: ./src/lib/feature/./src/lib/feature/phast_genepred.c:183:(.text+0x1003): undefined reference to `str_clear'
> /usr/bin/ld: ./src/lib/feature/./src/lib/feature/phast_genepred.c:184:(.text+0x100b): undefined reference to `str_clear'
> /usr/bin/ld: ./src/lib/feature/./src/lib/feature/phast_genepred.c:185:(.text+0x1015): undefined reference to `str_clear'
> /usr/bin/ld: ./src/lib/feature/./src/lib/feature/phast_genepred.c:186:(.text+0x101f): undefined reference to `str_clear'
> /usr/bin/ld: ./src/lib/feature/./src/lib/feature/phast_genepred.c:188:(.text+0x102f): undefined reference to `lst_qsort'
> /usr/bin/ld: ./src/lib/feature/./src/lib/feature/phast_genepred.c:193:(.text+0x107c): undefined reference to `str_append_int'
> /usr/bin/ld: ./src/lib/feature/./src/lib/feature/phast_genepred.c:194:(.text+0x1089): undefined reference to `str_append_char'
> /usr/bin/ld: ./src/lib/feature/./src/lib/feature/phast_genepred.c:195:(.text+0x1096): undefined reference to `str_append_int'
> /usr/bin/ld: ./src/lib/feature/./src/lib/feature/phast_genepred.c:196:(.text+0x10a3): undefined reference to `str_append_char'
> /usr/bin/ld: ./src/lib/feature/./src/lib/feature/phast_genepred.c:192:(.text+0x1104): undefined reference to `str_equals_charstr'
> /usr/bin/ld: ./src/lib/feature/./src/lib/feature/phast_genepred.c:205:(.text+0x111d): undefined reference to `str_equals_charstr'
> /usr/bin/ld: ./src/lib/feature/./src/lib/feature/phast_genepred.c:209:(.text+0x1153): undefined reference to `str_append_int'
> /usr/bin/ld: ./src/lib/feature/./src/lib/feature/phast_genepred.c:210:(.text+0x1162): undefined reference to `str_append_char'
> /usr/bin/ld: ./src/lib/feature/./src/lib/feature/phast_genepred.c:211:(.text+0x1171): undefined reference to `str_append_int'
> /usr/bin/ld: ./src/lib/feature/./src/lib/feature/phast_genepred.c:212:(.text+0x1180): undefined reference to `str_append_char'
> /usr/bin/ld: ./src/lib/feature/./src/lib/feature/phast_genepred.c:202:(.text+0x11d2): undefined reference to `die'
> /usr/bin/ld: ./src/lib/feature/./src/lib/feature/phast_genepred.c:218:(.text+0x1202): undefined reference to `die'
> /usr/bin/ld: ./src/lib/feature/./src/lib/feature/phast_genepred.c:235:(.text+0x12a0): undefined reference to `str_free'
> /usr/bin/ld: ./src/lib/feature/./src/lib/feature/phast_genepred.c:236:(.text+0x12a8): undefined reference to `str_free'
> /usr/bin/ld: ./src/lib/feature/./src/lib/feature/phast_genepred.c:237:(.text+0x12b2): undefined reference to `str_free'
> /usr/bin/ld: ./src/lib/feature/./src/lib/feature/phast_genepred.c:201:(.text+0x12da): undefined reference to `str_equals'
> /usr/bin/ld: ./src/lib/feature/./src/lib/feature/phast_genepred.c:217:(.text+0x12fa): undefined reference to `str_equals'
> /usr/bin/ld: ./src/lib/feature/./src/lib/feature/phast_genepred.c:174:(.text+0x1359): undefined reference to `die'
> /usr/bin/ld: ./src/lib/feature/./src/lib/feature/phast_genepred.c:238:(.text+0x12ca): undefined reference to `str_free'
> /usr/bin/ld: ./src/lib/feature/./src/lib/feature/phast_genepred.c:183:(.text.unlikely+0x18): undefined reference to `str_clear'
> /usr/bin/ld: ./src/lib/feature/./src/lib/feature/phast_genepred.c:184:(.text.unlikely+0x20): undefined reference to `str_clear'
> /usr/bin/ld: ./src/lib/feature/./src/lib/feature/phast_genepred.c:185:(.text.unlikely+0x2a): undefined reference to `str_clear'
> /usr/bin/ld: ./src/lib/feature/./src/lib/feature/phast_genepred.c:186:(.text.unlikely+0x34): undefined reference to `str_clear'
> /<<PKGBUILDDIR>>/src/dless/../../lib/libphast.a(phast_gff.o): in function `gff_new_feature':
> ./src/lib/feature/./src/lib/feature/phast_gff.c:207:(collect2: error: ld returned 1 exit status


The full build log is available from:
http://qa-logs.debian.net/2024/12/22/phast_1.7+dfsg-1_unstable.log

All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20241222;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20241222&fusertaguser=lucas@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results

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!

If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects

If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.