[EMBOSS] Cannot configure, auto* tools problem?

[Martín Sarachu]

Dear list,

when running 'configure' I'm getting some errors...

> # ./configure --prefix=/usr/local/emboss
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether build environment is sane... yes
> checking for gawk... gawk
> checking whether make sets $(MAKE)... yes
> checking build system type... i686-pc-linux-gnu
> checking host system type... i686-pc-linux-gnu
> checking for style of include used by make... GNU
> checking for gcc... gcc
> checking for C compiler default output... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ANSI C... none needed
> checking dependency style of gcc... gcc3
> checking for ld used by GCC... /usr/bin/ld
> checking if the linker (/usr/bin/ld) is GNU ld... yes
> checking for /usr/bin/ld option to reload object files... -r
> checking for BSD-compatible nm... /usr/bin/nm -B
> checking whether ln -s works... yes
> checking how to recognise dependant libraries... pass_all
> checking command to parse /usr/bin/nm -B output... ok
> checking how to run the C preprocessor... gcc -E
> checking for egrep... grep -E
> checking for ANSI C header files... yes
> checking for sys/types.h... yes
> checking for sys/stat.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for memory.h... yes
> checking for strings.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... yes
> checking for unistd.h... yes
> checking dlfcn.h usability... yes
> checking dlfcn.h presence... yes
> checking for dlfcn.h... yes
> checking for ranlib... ranlib
> checking for strip... strip
> checking for objdir... .libs
> checking for gcc option to produce PIC... -fPIC
> checking if gcc PIC flag -fPIC works... yes
> checking if gcc static flag -static works... yes
> checking if gcc supports -c -o file.o... yes
> checking if gcc supports -c -o file.lo... yes
> checking if gcc supports -fno-rtti -fno-exceptions... yes
> checking whether the linker (/usr/bin/ld) supports shared libraries... yes
> checking how to hardcode library paths into programs... immediate
> checking whether stripping libraries is possible... yes
> checking dynamic linker characteristics... GNU/Linux ld.so
> checking if libtool supports shared libraries... yes
> checking whether to build shared libraries... yes
> checking whether to build static libraries... yes
> checking whether -lc should be explicitly linked in... no
> creating libtool
> checking for gawk... (cached) gawk
> checking for gcc... (cached) gcc
> checking whether we are using the GNU C compiler... (cached) yes
> checking whether gcc accepts -g... (cached) yes
> checking for gcc option to accept ANSI C... (cached) none needed
> checking dependency style of gcc... (cached) gcc3
> checking how to run the C preprocessor... gcc -E
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether ln -s works... yes
> checking whether make sets $(MAKE)... (cached) yes
> checking for ranlib... (cached) ranlib
> checking for X... libraries /usr/X11R6/lib, headers /usr/X11R6/include
> checking for gethostbyname... yes
> checking for connect... yes
> checking for remove... yes
> checking for shmat... yes
> checking for IceConnectionNumber in -lICE... yes
> checking for dirent.h that defines DIR... yes
> checking for library containing opendir... none required
> checking for ANSI C header files... (cached) yes
> checking for unistd.h... (cached) yes
> checking for an ANSI C-conforming const... yes
> checking for pid_t... yes
> checking for size_t... yes
> checking whether struct tm is in sys/time.h or time.h... time.h
> checking whether getpgrp requires zero arguments... yes
> checking for strftime... yes
> checking for unistd.h... (cached) yes
> checking vfork.h usability... no
> checking vfork.h presence... no
> checking for vfork.h... no
> checking for fork... yes
> checking for vfork... yes
> checking for working fork... yes
> checking for working vfork... (cached) yes
> checking for vprintf... yes
> checking for _doprnt... no
> checking for memmove... yes
> ./configure: LF_EMBOSS_PATH_XLIB: command not found  << HERE
> checking for gethostbyname in -lc... yes
> checking for socket in -lc... yes
> checking for main in -lm... yes
> ./configure: CHECK_PNGDRIVER: command not found  << HERE
> ./configure: CHECK_JAVA: command not found  << HERE
> ./configure: CHECK_JAVAOS: command not found  << HERE
> ./configure: CHECK_AUTH: command not found  << HERE
> checking for purify... no
> ./configure: CHECK_THREADS: command not found  << HERE
> configure: creating ./config.status
> config.status: creating plplot/Makefile
> config.status: creating plplot/lib/Makefile
> config.status: creating nucleus/Makefile
> config.status: creating ajax/Makefile
> config.status: creating emboss/Makefile
> config.status: creating emboss/acd/Makefile
> config.status: creating test/Makefile
> config.status: creating test/data/Makefile
> config.status: creating test/embl/Makefile
> config.status: creating test/genbank/Makefile
> config.status: creating test/gb/Makefile
> config.status: creating test/pir/Makefile
> config.status: creating test/swiss/Makefile
> config.status: creating test/swnew/Makefile
> config.status: creating test/wormpep/Makefile
> config.status: creating emboss/data/Makefile
> config.status: creating emboss/data/AAINDEX/Makefile
> config.status: creating emboss/data/CODONS/Makefile
> config.status: creating emboss/data/REBASE/Makefile
> config.status: creating emboss/data/PRINTS/Makefile
> config.status: creating emboss/data/PROSITE/Makefile
> config.status: creating doc/Makefile
> config.status: creating doc/manuals/Makefile
> config.status: creating doc/tutorials/Makefile
> config.status: creating doc/programs/Makefile
> config.status: creating doc/programs/html/Makefile
> config.status: creating doc/programs/text/Makefile
> config.status: creating jemboss/Makefile
> config.status: creating jemboss/api/Makefile
> config.status: creating jemboss/api/org/Makefile
> config.status: creating jemboss/api/org/emboss/Makefile
> config.status: creating jemboss/api/org/emboss/jemboss/Makefile
> config.status: creating jemboss/api/org/emboss/jemboss/gui/Makefile
> config.status: creating jemboss/api/org/emboss/jemboss/gui/filetree/Makefile
> config.status: creating jemboss/api/org/emboss/jemboss/gui/form/Makefile
> config.status: creating jemboss/api/org/emboss/jemboss/gui/sequenceChooser/Makefile
> config.status: creating jemboss/api/org/emboss/jemboss/gui/startup/Makefile
> config.status: creating jemboss/api/org/emboss/jemboss/parser/Makefile
> config.status: creating jemboss/api/org/emboss/jemboss/parser/acd/Makefile
> config.status: creating jemboss/api/org/emboss/jemboss/programs/Makefile
> config.status: creating jemboss/api/org/emboss/jemboss/soap/Makefile
> config.status: creating jemboss/images/Makefile
> config.status: creating jemboss/lib/Makefile
> config.status: creating jemboss/lib/axis/Makefile
> config.status: creating jemboss/org/Makefile
> config.status: creating jemboss/org/emboss/Makefile
> config.status: creating jemboss/org/emboss/jemboss/Makefile
> config.status: creating jemboss/org/emboss/jemboss/gui/Makefile
> config.status: creating jemboss/org/emboss/jemboss/gui/filetree/Makefile
> config.status: creating jemboss/org/emboss/jemboss/gui/form/Makefile
> config.status: creating jemboss/org/emboss/jemboss/gui/startup/Makefile
> config.status: creating jemboss/org/emboss/jemboss/gui/sequenceChooser/Makefile
> config.status: creating jemboss/org/emboss/jemboss/parser/Makefile
> config.status: creating jemboss/org/emboss/jemboss/parser/acd/Makefile
> config.status: creating jemboss/org/emboss/jemboss/programs/Makefile
> config.status: creating jemboss/org/emboss/jemboss/server/Makefile
> config.status: creating jemboss/org/emboss/jemboss/soap/Makefile
> config.status: creating jemboss/resources/Makefile
> config.status: creating jemboss/utils/Makefile
> config.status: creating Makefile
> config.status: executing depfiles commands
> #

then when doing 'make'...

> # make
> Making all in plplot
> make[1]: Entering directory `/home/work/EMBOSS/test/plplot'
> Making all in lib
> make[2]: Entering directory `/home/work/EMBOSS/test/plplot/lib'
> make[2]: Nothing to be done for `all'.
> make[2]: Leaving directory `/home/work/EMBOSS/test/plplot/lib'
> make[2]: Entering directory `/home/work/EMBOSS/test/plplot'
> source='pdfutils.c' object='pdfutils.lo' libtool=yes \
> depfile='.deps/pdfutils.Plo' tmpdepfile='.deps/pdfutils.TPlo' \
> depmode=gcc3 /bin/sh ../depcomp \
> /bin/sh ../libtool --mode=compile gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"2.6.0\" -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  -I. -I. -I/usr/X11R6/include -I./ -I/usr/include/gd    -g -O2 -c -o pdfutils.lo `test -f pdfutils.c || echo './'`pdfutils.c
> ../libtool: s%^.*/%%: No such file or directory
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> ../libtool: -e: command not found
> : compile: cannot determine name of library object from `'
> make[2]: *** [pdfutils.lo] Error 1
> make[2]: Leaving directory `/home/work/EMBOSS/test/plplot'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory `/home/work/EMBOSS/test/plplot'
> make: *** [all-recursive] Error 1
> #

The system is a Redhat 7.3, autoconf 2.13 RPM, automake 1.4p5 RPM
Any hints of what is the problem?
Thanks.

Regards,

martin

-- 
Martín Sarachu
mad at biol.unlp.edu.ar
EMBNet Argentina
http://www.ar.embnet.org