need help porting biology/EMBOSS

[Fernan Aguero]

Hi!

biology/emboss have been stale for a while, with several
updates waiting in line in GNATS

http://www.freebsd.org/cgi/query-pr.cgi?pr=48786 (update to
2.6.0, obsoleted by
http://www.freebsd.org/cgi/query-pr.cgi?pr=68950 (update to
2.8.0) now also obsolete, since EMBOSS is at 2.9.0 (see
emboss.sf.net).

I'm CCing Choe Cheng-Dae, author of ports/68950, and also
the committers that got involved in either one or both of
the previous PRs to see if I can get some help from you and
get this update now finished.

I've a working port of EMBOSS-2.9.0 (see
http://genoma.unsam.edu.ar/~fernan/freebsd/emboss), however
the problem lies in building the contributed EMBASSY stuff.

I believe that the problems should be trivial to fix, but
I'm just not understanding what they are ... I guess that it
has something to do with the environment because the error
changes if the build is done from within the ports system
(using the port's Makefile) or from a standalone run of
./configure && make.

Output for one of the contributed packages (DOMAINATRIX) is
appended below. In the first case, see that the missing file
'emboss.h' is present under ${WRKSRC}/nucleus (which is
correctly included in the second case, now failing for
-liconv).  I've not tested all of them, but I got the same
results with the nex one (EMNU).

A diff of the two config.log files shows very little,
except perhaps for SHELL which is /bin/sh when run from
ports, but /bin/bash otherwise.


Building for EMBASSY:DOMAINATRIX^M
Making all in src^M
gmake[1]: Entering directory `/home/fernan/misc/freebsd-ports/emboss/work/EMBOSS-2.9.0/EMBASSY/DOMAINATRIX-1.0.0/src'^M
gmake[2]: Entering directory `/home/fernan/misc/freebsd-ports/emboss/work/EMBOSS-2.9.0/EMBASSY/DOMAINATRIX-1.0.0/src'^M
source='contacts.c' object='contacts.o' libtool=no \^M
depfile='.deps/contacts.Po' tmpdepfile='.deps/contacts.TPo' \^M
depmode=gcc /bin/sh ../depcomp \^M 
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"DOMAINATRIX\" -DVERSION=\"1.0.0\" -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_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1  -I. -I. -I/usr/local/include  -DAJ_FreeBSDLF  -DLENDIAN -DNO_AUTH  -O2 -c contacts.c^M 
contacts.c:291: emboss.h: No such file or directory^M
gmake[2]: *** [contacts.o] Error 1^M
gmake[2]: Leaving directory `/home/fernan/misc/freebsd-ports/emboss/work/EMBOSS-2.9.0/EMBASSY/DOMAINATRIX-1.0.0/src'^M 
gmake[1]: *** [all-recursive] Error 1^M
gmake[1]: Leaving directory `/home/fernan/misc/freebsd-ports/emboss/work/EMBOSS-2.9.0/EMBASSY/DOMAINATRIX-1.0.0/src'^M 
gmake: *** [all-recursive] Error 1^M
*** Error code 2^M

Building DOMAINATRIX outside of the ports system:
pi# cd work/EMBOSS-2.9.0/EMBASSY/DOMAINATRIX-1.0.0/
pi# ./configure && (g)make
... ... 
Making all in src
source='contacts.c' object='contacts.o' libtool=no  depfile='.deps/contacts.Po' tmpdepfile='.deps/contacts.TPo'  depmode=gcc /bin/bash ../depcomp  gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"DOMAINATRIX\" -DVERSION=\"1.0.0\" -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_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_UNISTD_H=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1 -I. -I. -I../../../plplot -I../../../ajax -I../../../nucleus   -DAJ_FreeBSDLF  -DLENDIAN -DNO_AUTH  -O2 -c contacts.c
/bin/bash ../libtool --mode=link gcc  -O2    -o contacts  contacts.o ../../../nucleus/libnucleus.la ../../../ajax/libajaxg.la ../../../ajax/libajax.la ../../../plplot/libplplot.la -L/usr/X11R6/lib -lX11 -liconv -lm
mkdir .libs
gcc -O2 -o .libs/contacts contacts.o  ../../../nucleus/.libs/libnucleus.so ../../../ajax/.libs/libajaxg.so ../../../ajax/.libs/libajax.so ../../../plplot/.libs/libplplot.so -L/usr/X11R6/lib -lX11 -liconv -lm -Wl,--rpath -Wl,/usr/local/lib
/usr/libexec/elf/ld: cannot find -liconv
*** Error code 1


If anyone can give me a hand with this, all the better. If
not I guess I'll be submitting the port without the EMBASSY
stuff until I (or someone else) can fix the issue. At least
this way we all can have an up to date EMBOSS port, though
lacking the optional stuff.

Should I submit it as a new PR? Or as a followup to the
latest (still open) ports/68950?

Fernan

-- 
Fernán Agüero | Instituto de Investigaciones Biotecnológicas
email         | fernan at { iib.unsam.edu.ar , mail.retina.ar }
wwww          | http://genoma.unsam.edu.ar/~fernan
phone, fax    | +54 11 { 4580-7255 ext 310, 4752-9639 }