Date: Mon, 1 Nov 2004 16:36:58 -0300 From: Fernan Aguero <fernan@iib.unsam.edu.ar> To: FreeBSD Ports <ports@FreeBSD.ORG> Cc: linimon@FreeBSD.ORG Subject: need help porting biology/EMBOSS Message-ID: <20041101193658.GD94558@iib.unsam.edu.ar>
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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 }
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