[Debian-med-packaging] Bug#591130: (Was: Bug#558852: Need some help with EMBOSS, that links to too many libraries.)

Andreas Tille andreas at an3as.eu
Wed Aug 11 11:33:46 UTC 2010

On Tue, Aug 10, 2010 at 09:58:12PM +0900, Charles Plessy wrote:
> Since version 6.3, EMBOSS depends on MySQL and PostgreSQL. This gives it the
> capacity to use remote databases, in particular from ENSEMBL, and although I
> did not have time to test this feature, I think that it is important enough to
> be enabled by default. However, as long as the linking problem explained above
> is not solved, it makes the embassy-* packages build-depend on libpq-dev and
> libmysqlclient-dev, which really looks wrong.

... at least it is probably badly implemented by upstream.  From the build

checking for mysql_config... no
checking for pg_config... no
Not configuring for PostgreSQL

/bin/bash ../libtool --tag=CC   --mode=link gcc    -g -O2 -g -Wall -O2 -I/usr/include/eplplot -I/usr/include/ajax -I/usr/include/ajax/epcre -I/usr/include/nucleus  -O2  -D__amd64__     -o cathparse cathparse.o
-L/usr/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre -leexpat -lezlib -leplplot -lX11  -lm  -lgd -lpng -lz -lm
libtool: link: cannot find the library `/usr/lib/libmysqlclient.la' or unhandled argument `/usr/lib/libmysqlclient.la'

The configure script is realisiing that there is no mysql support but
libtools tries to link against it anyway.

However, after adding libmysqlclient-dev to the Build-Depends (which is
IMHO a reasonable means to handle this problem for the moment) I get:

Making all in src
make[2]: Entering directory `/tmp/buildd/embassy-domainatrix-0.1.0+20100721/src'
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"DOMAINATRIX\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_STRDUP=1 -DHAVE_STRSTR=1 -DHAVE_STRCHR=1 -DHAVE_ERAND48=1 -DHAVE_MEMMOVE=1 -DPLD_xwin=1 -DHAVE_LIBM=1 -DPLD_png=1 -DHAVE_MYSQL=1 -I. -I/usr/include -I/usr/include/eplplot -I/usr/include/ezlib -I/usr/include/eexpat -I/usr/include/epcre  -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE  -DLENDIAN -DNO_AUTH    -g -O2 -g -Wall -O2 -I/usr/include/eplplot -I/usr/include/ajax -I/usr/include/ajax/epcre -I/usr/include/nucleus  -O2  -D__amd64__ -I/usr/include/mysql  -c cathparse.c
/bin/bash ../libtool --tag=CC   --mode=link gcc    -g -O2 -g -Wall -O2 -I/usr/include/eplplot -I/usr/include/ajax -I/usr/include/ajax/epcre -I/usr/include/nucleus  -O2  -D__amd64__ -I/usr/include/mysql   -rdynamic -L/usr/lib/mysql -lmysqlclient  -o cathparse cathparse.o -L/usr/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre -leexpat -lezlib -leplplot -lX11  -lm  -lgd -lpng -lz -lm
libtool: link: gcc -g -O2 -g -Wall -O2 -I/usr/include/eplplot -I/usr/include/ajax -I/usr/include/ajax/epcre -I/usr/include/nucleus -O2 -D__amd64__ -I/usr/include/mysql -rdynamic -o cathparse cathparse.o  -L/usr/lib/mysql -L/usr/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre -leexpat -lezlib /usr/lib/libeplplot.so /usr/lib/libexpat.so /usr/lib/libmysqlclient.so -lpthread -lcrypt -lnsl -lpq /usr/lib/libgd.so -lXpm -lX11 /usr/lib/libjpeg.so -lfontconfig /usr/lib/libfreetype.so -lpng12 -lpng -lz -lm
/usr/bin/ld: cannot find -leexpat

However, there is no such library in Debian which fits this
string.  Do we have another even more grave problem?

Kind regards



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