Date: Mon, 01 Nov 2004 20:48:49 +0100 From: Pav Lucistnik <pav@FreeBSD.org> To: Fernan Aguero <fernan@iib.unsam.edu.ar> Cc: linimon@FreeBSD.org Subject: Re: need help porting biology/EMBOSS Message-ID: <1099338529.51833.4.camel@hood.oook.cz> In-Reply-To: <20041101193658.GD94558@iib.unsam.edu.ar> References: <20041101193658.GD94558@iib.unsam.edu.ar>
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V po, 01. 11. 2004 v 20:36, Fernan Aguero p=ED=B9e:
> 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).
>=20
> 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.
>=20
>=20
> 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=3D'contacts.c' object=3D'contacts.o' libtool=3Dno \^M
> depfile=3D'.deps/contacts.Po' tmpdepfile=3D'.deps/contacts.TPo' \^M
> depmode=3Dgcc /bin/sh ../depcomp \^M=20
> gcc -DPACKAGE_NAME=3D\"\" -DPACKAGE_TARNAME=3D\"\" -DPACKAGE_VERSION=3D\"=
\" -DPACKAGE_STRING=3D\"\" -DPACKAGE_BUGREPORT=3D\"\" -DPACKAGE=3D\"DOMAINA=
TRIX\" -DVERSION=3D\"1.0.0\" -DSTDC_HEADERS=3D1 -DHAVE_SYS_TYPES_H=3D1 -DHA=
VE_SYS_STAT_H=3D1 -DHAVE_STDLIB_H=3D1 -DHAVE_STRING_H=3D1 -DHAVE_MEMORY_H=
=3D1 -DHAVE_STRINGS_H=3D1 -DHAVE_INTTYPES_H=3D1 -DHAVE_UNISTD_H=3D1 -DHAVE_=
DLFCN_H=3D1 -DHAVE_DIRENT_H=3D1 -DSTDC_HEADERS=3D1 -DHAVE_UNISTD_H=3D1 -DGE=
TPGRP_VOID=3D1 -DHAVE_STRFTIME=3D1 -DHAVE_UNISTD_H=3D1 -DHAVE_FORK=3D1 -DHA=
VE_VFORK=3D1 -DHAVE_WORKING_VFORK=3D1 -DHAVE_WORKING_FORK=3D1 -DHAVE_VPRINT=
F=3D1 -DHAVE_MEMMOVE=3D1 -DHAVE_LIBM=3D1 -I. -I. -I/usr/local/include -DA=
J_FreeBSDLF -DLENDIAN -DNO_AUTH -O2 -c contacts.c^M=20
> 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=20
> 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=20
> gmake: *** [all-recursive] Error 1^M
> *** Error code 2^M
If you need to add additional directories to header files search patch,
use -I/path/to/directory switch to gcc.
> Building DOMAINATRIX outside of the ports system:
> pi# cd work/EMBOSS-2.9.0/EMBASSY/DOMAINATRIX-1.0.0/
> pi# ./configure && (g)make
> ... ...=20
> Making all in src
> source=3D'contacts.c' object=3D'contacts.o' libtool=3Dno depfile=3D'.dep=
s/contacts.Po' tmpdepfile=3D'.deps/contacts.TPo' depmode=3Dgcc /bin/bash .=
./depcomp gcc -DPACKAGE_NAME=3D\"\" -DPACKAGE_TARNAME=3D\"\" -DPACKAGE_VER=
SION=3D\"\" -DPACKAGE_STRING=3D\"\" -DPACKAGE_BUGREPORT=3D\"\" -DPACKAGE=3D=
\"DOMAINATRIX\" -DVERSION=3D\"1.0.0\" -DSTDC_HEADERS=3D1 -DHAVE_SYS_TYPES_H=
=3D1 -DHAVE_SYS_STAT_H=3D1 -DHAVE_STDLIB_H=3D1 -DHAVE_STRING_H=3D1 -DHAVE_M=
EMORY_H=3D1 -DHAVE_STRINGS_H=3D1 -DHAVE_INTTYPES_H=3D1 -DHAVE_UNISTD_H=3D1 =
-DHAVE_DLFCN_H=3D1 -DHAVE_DIRENT_H=3D1 -DSTDC_HEADERS=3D1 -DHAVE_UNISTD_H=
=3D1 -DGETPGRP_VOID=3D1 -DHAVE_STRFTIME=3D1 -DHAVE_UNISTD_H=3D1 -DHAVE_FORK=
=3D1 -DHAVE_VFORK=3D1 -DHAVE_WORKING_VFORK=3D1 -DHAVE_WORKING_FORK=3D1 -DHA=
VE_VPRINTF=3D1 -DHAVE_MEMMOVE=3D1 -DHAVE_LIBM=3D1 -I. -I. -I../../../plplot=
-I../../../ajax -I../../../nucleus -DAJ_FreeBSDLF -DLENDIAN -DNO_AUTH =
-O2 -c contacts.c
> /bin/bash ../libtool --mode=3Dlink gcc -O2 -o contacts contacts.o ..=
/../../nucleus/libnucleus.la ../../../ajax/libajaxg.la ../../../ajax/libaja=
x.la ../../../plplot/libplplot.la -L/usr/X11R6/lib -lX11 -liconv -lm
> mkdir .libs
> gcc -O2 -o .libs/contacts contacts.o ../../../nucleus/.libs/libnucleus.s=
o ../../../ajax/.libs/libajaxg.so ../../../ajax/.libs/libajax.so ../../../p=
lplot/.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
To add a directory to linker search path, use -L/path/to/directory.
libiconv lives in ${LOCALBASE}/lib, so -L${LOCALBASE}/lib would cure
this problem (note that ${LOCALBASE} variable is only available in ports
framework Makefiles, so you can't use it in standalone build).
> 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.
Depends on how you think the EMBASSY stuff is important. If you think
2.9.0 port without EMBASSY stuff is more useful than 2.4.1 port with
EMBASSY, you can just detach EMBASSY from build for now.
> Should I submit it as a new PR? Or as a followup to the
> latest (still open) ports/68950?
As you care, I'm in small preference of followup.
--=20
Pav Lucistnik <pav@oook.cz>
<pav@FreeBSD.org>
God is real unless declared integer.
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