Hi!
I have installed EMBOSS previously without any issues on our server running on
RedHat Enterprise Linux, using the ./configure and make commands, updating the
version with every new release. Recently however our system crashed and the OS
and other software/libraries had to be re-installed. Now, when I tried to
install EMBOSS using the same commands I get the following errors. Could anyone
help with the problem? Am I missing some libraries?
_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 -DLT_OBJDIR=\".libs/\" -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1
-DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_FORK=1
-DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1
-DHAVE_MEMMOVE=1 -DPLD_xwin=1 -DHAVE_LIBM=1 -DPLD_png=1 -DHAVE_MYSQL=1
-DHAVE_POSTGRESQL=1 -I. -I../plplot -I/usr/X11R6/include -I./ -I../ajax
-I../ajax/pcre -I../ajax/expat -I../ajax/zlib -I../ajax/core -I../ajax/graphics
-I../ajax/ensembl -I../ajax/ajaxdb -I../ajax/acd -DAJ_LinuxLF
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DLENDIAN -O2
-I/usr/X11R6/include -DNO_AUTH -I/usr/include/mysql -I/usr/include -MT
embshow.lo -MD -MP -MF .deps/embshow.Tpo -c embshow.c -fPIC -DPIC -o
.libs/embshow.o
libtool: compile: gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\"
-DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\"
-DPACKAGE_URL=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"6.3.0\" -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 -DLT_OBJDIR=\".libs/\" -DHAVE_DIRENT_H=1
-DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1
-DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1
-DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DPLD_xwin=1 -DHAVE_LIBM=1 -DPLD_png=1
-DHAVE_MYSQL=1 -DHAVE_POSTGRESQL=1 -I. -I../plplot -I/usr/X11R6/include -I./
-I../ajax -I../ajax/pcre -I../ajax/expat -I../ajax/zlib -I../ajax/core
-I../ajax/graphics -I../ajax/ensembl -I../ajax/ajaxdb -I../ajax/acd
-DAJ_LinuxLF -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE
-DLENDIAN -O2 -I/usr/X11R6/include -D!
NO_AUTH -I/usr/include/mysql -I/usr/include -MT embshow.lo -MD -MP -MF
.deps/embshow.Tpo -c embshow.c -o embshow.o >/dev/null 2>&1
mv -f .deps/embshow.Tpo .deps/embshow.Plo
/bin/sh ../libtool --tag=CC --mode=compile gcc -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
-DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"EMBOSS\"
-DVERSION=\"6.3.0\" -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
-DLT_OBJDIR=\".libs/\" -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1
-DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_FORK=1 -DHAVE_VFORK=1
-DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1
-DPLD_xwin=1 -DHAVE_LIBM=1 -DPLD_png=1 -DHAVE_MYSQL=1 -DHAVE_POSTGRESQL=1 -I.
-I../plplot -I/usr/X11R6/include -I./ -I../ajax -I../ajax/pcre -I../ajax/expat
-I../ajax/zlib -I../ajax/core -I../ajax/graphics -I../ajax/ensembl
-I../ajax/ajaxdb -I../ajax/acd -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DLENDIAN!
-O2 -I/usr/X11R6/include -DNO_AUTH -I/usr/include/mysql -I/usr/include
-MT embword.lo -MD -MP -MF .deps/embword.Tpo -c -o embword.lo embword.c
libtool: compile: gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\"
-DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\"
-DPACKAGE_URL=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"6.3.0\" -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 -DLT_OBJDIR=\".libs/\" -DHAVE_DIRENT_H=1
-DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1
-DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1
-DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DPLD_xwin=1 -DHAVE_LIBM=1 -DPLD_png=1
-DHAVE_MYSQL=1 -DHAVE_POSTGRESQL=1 -I. -I../plplot -I/usr/X11R6/include -I./
-I../ajax -I../ajax/pcre -I../ajax/expat -I../ajax/zlib -I../ajax/core
-I../ajax/graphics -I../ajax/ensembl -I../ajax/ajaxdb -I../ajax/acd
-DAJ_LinuxLF -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE
-DLENDIAN -O2 -I/usr/X11R6/include -D!
NO_AUTH -I/usr/include/mysql -I/usr/include -MT embword.lo -MD -MP -MF
.deps/embword.Tpo -c embword.c -fPIC -DPIC -o .libs/embword.o
libtool: compile: gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\"
-DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\"
-DPACKAGE_URL=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"6.3.0\" -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 -DLT_OBJDIR=\".libs/\" -DHAVE_DIRENT_H=1
-DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1
-DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1
-DHAVE_VPRINTF=1 -DHAVE_MEMMOVE=1 -DPLD_xwin=1 -DHAVE_LIBM=1 -DPLD_png=1
-DHAVE_MYSQL=1 -DHAVE_POSTGRESQL=1 -I. -I../plplot -I/usr/X11R6/include -I./
-I../ajax -I../ajax/pcre -I../ajax/expat -I../ajax/zlib -I../ajax/core
-I../ajax/graphics -I../ajax/ensembl -I../ajax/ajaxdb -I../ajax/acd
-DAJ_LinuxLF -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE
-DLENDIAN -O2 -I/usr/X11R6/include -D!
NO_AUTH -I/usr/include/mysql -I/usr/include -MT embword.lo -MD -MP -MF
.deps/embword.Tpo -c embword.c -o embword.o >/dev/null 2>&1
mv -f .deps/embword.Tpo .deps/embword.Plo
/bin/sh ../libtool --tag=CC --mode=link gcc -O2 -I/usr/X11R6/include
-DNO_AUTH -I/usr/include/mysql -I/usr/include -version-info 6:3:0
-L/usr/lib/mysql -lmysqlclient -lz -lcrypt -lnsl -lm -L/usr/lib -lssl -lcrypto
-L/usr/lib -lpq -o libnucleus.la -rpath /usr/local/lib 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 embpatlist.lo embprop.lo embpdb.lo embread.lo embsig.lo
embshow.lo embword.lo -lm -lgd -lpng -lz -lm
libtool: link: 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/embpatlist.o .libs/embprop.o .libs/embpdb.o
.libs/embread.o .libs/embsig.o .libs/embshow.o .libs/embword.o
-L/usr/lib/mysql -lmysqlclient -lcrypt -lnsl -L/usr/lib -lssl -lcrypto -lpq
-lgd -lpng -lz -lm -Wl,-soname -Wl,libnucleus.so.6 -o
.libs/libnucleus.so.6.0.3
libtool: link: (cd ".libs" && rm -f "libnucleus.so.6" && ln -s
"libnucleus.so.6.0.3" "libnucleus.so.6")
libtool: link: (cd ".libs" && rm -f "libnucleus.so" && ln -s
"libnucleus.so.6.0.3" "libnucleus.so")
libtool: link: 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 embpatlist.o embprop.o
embpdb.o embread.o embsig.o embshow.o embword.o
libtool: link: ranlib .libs/libnucleus.a
libtool: link: ( cd ".libs" && rm -f "libnucleus.la" && ln -s
"../libnucleus.la" "libnucleus.la" )
make[1]: Leaving directory `/usr/local/EMBOSS-6.3.0/nucleus'
Making all in emboss
make[1]: Entering directory `/usr/local/EMBOSS-6.3.0/emboss'
Making all in acd
make[2]: Entering directory `/usr/local/EMBOSS-6.3.0/emboss/acd'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/usr/local/EMBOSS-6.3.0/emboss/acd'
Making all in data
make[2]: Entering directory `/usr/local/EMBOSS-6.3.0/emboss/data'
Making all in AAINDEX
make[3]: Entering directory `/usr/local/EMBOSS-6.3.0/emboss/data/AAINDEX'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/usr/local/EMBOSS-6.3.0/emboss/data/AAINDEX'
Making all in CODONS
make[3]: Entering directory `/usr/local/EMBOSS-6.3.0/emboss/data/CODONS'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/usr/local/EMBOSS-6.3.0/emboss/data/CODONS'
Making all in REBASE
make[3]: Entering directory `/usr/local/EMBOSS-6.3.0/emboss/data/REBASE'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/usr/local/EMBOSS-6.3.0/emboss/data/REBASE'
Making all in PRINTS
make[3]: Entering directory `/usr/local/EMBOSS-6.3.0/emboss/data/PRINTS'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/usr/local/EMBOSS-6.3.0/emboss/data/PRINTS'
Making all in PROSITE
make[3]: Entering directory `/usr/local/EMBOSS-6.3.0/emboss/data/PROSITE'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/usr/local/EMBOSS-6.3.0/emboss/data/PROSITE'
Making all in JASPAR_CORE
make[3]: Entering directory `/usr/local/EMBOSS-6.3.0/emboss/data/JASPAR_CORE'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/usr/local/EMBOSS-6.3.0/emboss/data/JASPAR_CORE'
Making all in JASPAR_FAM
make[3]: Entering directory `/usr/local/EMBOSS-6.3.0/emboss/data/JASPAR_FAM'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/usr/local/EMBOSS-6.3.0/emboss/data/JASPAR_FAM'
Making all in JASPAR_PHYLOFACTS
make[3]: Entering directory
`/usr/local/EMBOSS-6.3.0/emboss/data/JASPAR_PHYLOFACTS'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory
`/usr/local/EMBOSS-6.3.0/emboss/data/JASPAR_PHYLOFACTS'
Making all in JASPAR_CNE
make[3]: Entering directory `/usr/local/EMBOSS-6.3.0/emboss/data/JASPAR_CNE'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/usr/local/EMBOSS-6.3.0/emboss/data/JASPAR_CNE'
Making all in JASPAR_POLII
make[3]: Entering directory `/usr/local/EMBOSS-6.3.0/emboss/data/JASPAR_POLII'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/usr/local/EMBOSS-6.3.0/emboss/data/JASPAR_POLII'
Making all in JASPAR_SPLICE
make[3]: Entering directory `/usr/local/EMBOSS-6.3.0/emboss/data/JASPAR_SPLICE'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/usr/local/EMBOSS-6.3.0/emboss/data/JASPAR_SPLICE'
Making all in JASPAR_PBM
make[3]: Entering directory `/usr/local/EMBOSS-6.3.0/emboss/data/JASPAR_PBM'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/usr/local/EMBOSS-6.3.0/emboss/data/JASPAR_PBM'
Making all in JASPAR_PBM_HLH
make[3]: Entering directory `/usr/local/EMBOSS-6.3.0/emboss/data/JASPAR_PBM_HLH'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/usr/local/EMBOSS-6.3.0/emboss/data/JASPAR_PBM_HLH'
Making all in JASPAR_PBM_HOMEO
make[3]: Entering directory
`/usr/local/EMBOSS-6.3.0/emboss/data/JASPAR_PBM_HOMEO'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory
`/usr/local/EMBOSS-6.3.0/emboss/data/JASPAR_PBM_HOMEO'
make[3]: Entering directory `/usr/local/EMBOSS-6.3.0/emboss/data'
make[3]: Nothing to be done for `all-am'.
make[3]: Leaving directory `/usr/local/EMBOSS-6.3.0/emboss/data'
make[2]: Leaving directory `/usr/local/EMBOSS-6.3.0/emboss/data'
make[2]: Entering directory `/usr/local/EMBOSS-6.3.0/emboss'
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\"
-DPACKAGE=\"EMBOSS\" -DVERSION=\"6.3.0\" -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 -DLT_OBJDIR=\".libs/\" -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1
-DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_FORK=1
-DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1
-DHAVE_MEMMOVE=1 -DPLD_xwin=1 -DHAVE_LIBM=1 -DPLD_png=1 -DHAVE_MYSQL=1
-DHAVE_POSTGRESQL=1 -I. -I../nucleus -I../ajax/pcre -I../ajax/expat
-I../ajax/zlib -I../ajax/core -I../ajax/graphics -I../ajax/ensembl
-I../ajax/ajaxdb -I../ajax/acd -I../plplot -DAJ_LinuxLF -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DLENDIAN -O2
-I/usr/X11R6/include -DNO_AUTH -I/usr/include/mysql -I/usr/!
include -MT aaindexextract.o -MD -MP -MF .deps/aaindexextract.Tpo -c -o
aaindexextract.o aaindexextract.c
mv -f .deps/aaindexextract.Tpo .deps/aaindexextract.Po
/bin/sh ../libtool --tag=CC --mode=link gcc -O2 -I/usr/X11R6/include
-DNO_AUTH -I/usr/include/mysql -I/usr/include -L/usr/lib/mysql -lmysqlclient
-lz -lcrypt -lnsl -lm -L/usr/lib -lssl -lcrypto -L/usr/lib -lpq -o
aaindexextract aaindexextract.o ../nucleus/libnucleus.la ../ajax/acd/libacd.la
../ajax/ajaxdb/libajaxdb.la ../ajax/ensembl/libensembl.la
../ajax/graphics/libajaxg.la ../ajax/core/libajax.la ../ajax/zlib/libezlib.la
../ajax/expat/libeexpat.la ../ajax/pcre/libepcre.la ../plplot/libeplplot.la
-L/usr/X11R6/lib -lX11 -lm -lgd -lpng -lz -lm
libtool: link: gcc -O2 -I/usr/X11R6/include -DNO_AUTH -I/usr/include/mysql
-I/usr/include -o .libs/aaindexextract aaindexextract.o -L/usr/lib/mysql
-L/usr/lib ../nucleus/.libs/libnucleus.so ../ajax/acd/.libs/libacd.so
../ajax/ajaxdb/.libs/libajaxdb.so ../ajax/ensembl/.libs/libensembl.so
../ajax/graphics/.libs/libajaxg.so ../ajax/core/.libs/libajax.so
../ajax/zlib/.libs/libezlib.so ../ajax/expat/.libs/libeexpat.so
../ajax/pcre/.libs/libepcre.so ../plplot/.libs/libeplplot.so -lmysqlclient
-lcrypt -lnsl -lssl -lcrypto -lpq -L/usr/X11R6/lib -lX11 -lgd -lpng -lz -lm
-Wl,-rpath -Wl,/usr/local/lib
../ajax/core/.libs/libajax.so: undefined reference to `PQescapeStringConn'
collect2: ld returned 1 exit status
make[2]: *** [aaindexextract] Error 1
make[2]: Leaving directory `/usr/local/EMBOSS-6.3.0/emboss'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/usr/local/EMBOSS-6.3.0/emboss'
make: *** [all-recursive] Error 1
[r...@bioinformaticccmb EMBOSS-6.3.0]# pwd
/usr/local/EMBOSS-6.3.0
Thanks.
Shrish
Dr. Shrish Tiwari
E503, Centre for Cellular and Molecular Biology
Uppal Road, Hyderabad - 500 007, INDIA
Phone: 91-40-27192777
Alternate email: [email protected]
"The person addressed in the email is the sole authorized recipient.
Should you receive it in error, immediately notify the sender of the
error and delete the e-mail. Any unauthorized dissemination or copying
of this e-mail (or any attachment to this e-mail) or the wrongful
disclosure of the information herein contained is prohibited.
Also note that this form of communication is not secure, it can be
intercepted, and may not necessarily be free of errors and viruses
in spite of reasonable efforts to secure this medium."
_______________________________________________
EMBOSS mailing list
[email protected]
http://lists.open-bio.org/mailman/listinfo/emboss
