[EMBOSS] problem installing EMBOSS-3.0.0 in FC4

Thu Dec 15 16:10:26 UTC 2005

is it possible that you are missing some of the graphics components that are
dependencies for installing emboss? does the output of the configure process
show any components "not found". one way to find out if this is a problem
would be to configure the emboss install without using some of the graphics
components. 
in the configure -help for instance:

--with-pngdriver=DIR    root directory path of png/gd/zlib installation
defaults to /usr
--without-pngdriver     to disable pngdriver usage completely

good luck
-- 

Iain Drummond, Ph.D.
Assistant Professor
Department of Medicine, Harvard Medical School and
Nephrology Division, Massachusetts General Hospital

Mailing address:
Nephrology Division / MGH 149-8000
149 13th St. 
Charlestown, MA 02129

Tel: 617 726 5647
Fax: 617 726 5669

idrummond at partners.org
idrummon at receptor.mgh.harvard.edu

Lab Home Page:
http://danio.mgh.harvard.edu

> From: Iris Vargas Jentzsch <imj15 at student.canterbury.ac.nz>
> Date: Thu, 15 Dec 2005 12:41:01 +1300
> To: emboss at emboss.open-bio.org
> Subject: [EMBOSS] problem installing EMBOSS-3.0.0 in FC4
> 
> Hello everybody,
> 
> I need some help here. My recent tries to install EMBOSS-3.0.0 have been
> mostly unsuccessfull. I am working with a Fedora Core 4 Linux
> installation. After ./configure when I issue the command make, at the
> beginning it seems to work fine but it gets to some point in
> /pkg/EMBOSS-3.0.0/emboss/data after installing the libraries I guess,
> where it can¹t go further. Here are the messages I get, I did cut a huge
> part in the middle that seemed to have no error messages (although it
> seemed to be the same over and over again... however if someone needs
> the whole long message I can post it.
> 
> [root at localhost EMBOSS-3.0.0]# make
> Making all in plplot
> make[1]: Entering directory `/pkg/EMBOSS-3.0.0/plplot'
> Making all in lib
> make[2]: Entering directory `/pkg/EMBOSS-3.0.0/plplot/lib'
> make[2]: Nothing to be done for `all'.
> make[2]: Leaving directory `/pkg/EMBOSS-3.0.0/plplot/lib'
> make[2]: Entering directory `/pkg/EMBOSS-3.0.0/plplot'
> if /bin/sh ../libtool --tag=CC --mode=compile gcc -DPACKAGE_NAME=\"\"
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
> -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"3.0.0\"
> -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_STDINT_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 -DPLD_png=1 -I. -I. -I/usr/X11R6/include
> -I./ -I/usr/include/gd -DPREFIX=\"/usr/local\"
> -DEMBOSS_TOP=\"/pkg/EMBOSS-3.0.0\" -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64
> -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DLENDIAN -DNO_AUTH -O2 -MT
> pdfutils.lo -MD -MP -MF ".deps/pdfutils.Tpo" -c -o pdfutils.lo pdfutils.c; \
> then mv -f ".deps/pdfutils.Tpo" ".deps/pdfutils.Plo"; else rm -f
> ".deps/pdfutils.Tpo"; exit 1; fi
> mkdir .libs
> .
> .
> .
> .
> .
> gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
> -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\"
> -DVERSION=\"3.0.0\" -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_STDINT_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
> -DPLD_png=1 -I. -I. -I../plplot -I/usr/X11R6/include -I./ -I../ajax
> -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> -D_LARGEFILE64_SOURCE -DLENDIAN -DNO_AUTH -O2 -MT embword.lo -MD -MP -MF
> .deps/embword.Tpo -c embword.c -fPIC -DPIC -o .libs/embword.o
> gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
> -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\"
> -DVERSION=\"3.0.0\" -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_STDINT_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
> -DPLD_png=1 -I. -I. -I../plplot -I/usr/X11R6/include -I./ -I../ajax
> -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
> -D_LARGEFILE64_SOURCE -DLENDIAN -DNO_AUTH -O2 -MT embword.lo -MD -MP -MF
> .deps/embword.Tpo -c embword.c -o embword.o >/dev/null 2>&1
> /bin/sh ../libtool --tag=CC --mode=link gcc -O2 -o libnucleus.la -rpath
> /usr/local/lib -version-info 3:0:0 embaln.lo embcom.lo embcons.lo
> embdata.lo embdbi.lo embdmx.lo embdomain.lo embest.lo embexit.lo
> embgroup.lo embiep.lo embindex.lo embinit.lo embmat.lo embmisc.lo
> embmol.lo embnmer.lo embpat.lo embprop.lo embpdb.lo embread.lo embsig.lo
> embshow.lo embword.lo
> gcc -shared .libs/embaln.o .libs/embcom.o .libs/embcons.o
> .libs/embdata.o .libs/embdbi.o .libs/embdmx.o .libs/embdomain.o
> .libs/embest.o .libs/embexit.o .libs/embgroup.o .libs/embiep.o
> .libs/embindex.o .libs/embinit.o .libs/embmat.o .libs/embmisc.o
> .libs/embmol.o .libs/embnmer.o .libs/embpat.o .libs/embprop.o
> .libs/embpdb.o .libs/embread.o .libs/embsig.o .libs/embshow.o
> .libs/embword.o -Wl,-soname -Wl,libnucleus.so.3 -o .libs/libnucleus.so.3.0.0
> (cd .libs && rm -f libnucleus.so.3 && ln -s libnucleus.so.3.0.0
> libnucleus.so.3)
> (cd .libs && rm -f libnucleus.so && ln -s libnucleus.so.3.0.0 libnucleus.so)
> ar cru .libs/libnucleus.a embaln.o embcom.o embcons.o embdata.o embdbi.o
> embdmx.o embdomain.o embest.o embexit.o embgroup.o embiep.o embindex.o
> embinit.o embmat.o embmisc.o embmol.o embnmer.o embpat.o embprop.o
> embpdb.o embread.o embsig.o embshow.o embword.o
> ranlib .libs/libnucleus.a
> creating libnucleus.la
> (cd .libs && rm -f libnucleus.la && ln -s ../libnucleus.la libnucleus.la)
> make[1]: Leaving directory `/pkg/EMBOSS-3.0.0/nucleus'
> Making all in emboss
> make[1]: Entering directory `/pkg/EMBOSS-3.0.0/emboss'
> Making all in acd
> make[2]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/acd'
> make[2]: Nothing to be done for `all'.
> make[2]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/acd'
> Making all in data
> make[2]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data'
> Making all in AAINDEX
> make[3]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data/AAINDEX'
> make[3]: Nothing to be done for `all'.
> make[3]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data/AAINDEX'
> Making all in CODONS
> make[3]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data/CODONS'
> make[3]: Nothing to be done for `all'.
> make[3]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data/CODONS'
> Making all in REBASE
> make[3]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data/REBASE'
> make[3]: Nothing to be done for `all'.
> make[3]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data/REBASE'
> Making all in PRINTS
> make[3]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data/PRINTS'
> make[3]: Nothing to be done for `all'.
> make[3]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data/PRINTS'
> Making all in PROSITE
> make[3]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data/PROSITE'
> make[3]: Nothing to be done for `all'.
> make[3]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data/PROSITE'
> make[3]: Entering directory `/pkg/EMBOSS-3.0.0/emboss/data'
> make[3]: *** No rule to make target `EBLOSUMN', needed by `all-am'. Stop.
> make[3]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data'
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss/data'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory `/pkg/EMBOSS-3.0.0/emboss'
> make: *** [all-recursive] Error 1
> 
> 
> I¹ll appreciate very much if you can give me a hand with this. Thank you!
> 
> Iris
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