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
log:
...
checking for mysql_config... no
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
Andreas.
--
http://fam-tille.de
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