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 -DNO_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 -DNO_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 -DNO_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
[root@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: shrish.geo@yahoo.com

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