[Transdecoder-users] transdecoder ffindex error

[ERIC W. <ek...@ps...>]

Hi Brian,

I tried for days now install transdecoder without success. I keep getting
ffindex error to do with some kind of incompatabilty.

sudo make

if [[ ! -s pfam/Pfam-AB.hmm.bin ]]; then echo "Downloading PFAM database"
&& wget '
http://sourceforge.net/projects/transdecoder/files/Pfam-AB.hmm.bin/download'
-O pfam/Pfam-AB.hmm.bin; fi

if [[ ! -e pfam/Pfam-AB.hmm.bin.h3i ]]; then echo "Preparing PFAM database"
&& hmmpress pfam/Pfam-AB.hmm.bin; fi

cd 3rd_party/ffindex && make HAVE_MPI=1 && make install
INSTALL_DIR=../../../util HAVE_MPI=1

make[1]: Entering directory
`/scratch/biotools/software/quality_control/transdecoder_rel16JAN2014/3rd_party/ffindex-0.9.9.3'

make -C src -f Makefile all

make[2]: Entering directory
`/scratch/biotools/software/quality_control/transdecoder_rel16JAN2014/3rd_party/ffindex-0.9.9.3/src'

gcc -fopenmp -std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1   -c -o
ffindex_apply.o ffindex_apply.c

gcc -fopenmp -std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1   -c -o
ffindex.o ffindex.c

ffindex.c: In function 'ffindex_tree_write':

ffindex.c:518: warning: ISO C forbids nested functions

gcc -fopenmp -std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1   -c -o
ffutil.o ffutil.c

gcc -fopenmp -Wl,-z,defs -shared -Wl,-soname,libffindex.so.0.1 -o
libffindex.so.0.1 ffindex.o ffutil.o -lc

ln -sf libffindex.so.0.1 libffindex.so

gcc -fopenmp -lffindex -L.  ffindex_apply.o libffindex.so libffindex.so.0.1
ffindex.h   -o ffindex_apply

gcc -fopenmp -std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1   -c -o
ffindex_from_fasta.o ffindex_from_fasta.c

gcc -fopenmp -o ffindex_from_fasta ffindex_from_fasta.o -lffindex -L. -L.
-lffindex

gcc -fopenmp -std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1   -c -o
ffindex_get.o ffindex_get.c

gcc -fopenmp -o ffindex_get ffindex_get.o -lffindex -L. -L. -lffindex

gcc -fopenmp -std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1   -c -o
ffindex_build.o ffindex_build.c

gcc -fopenmp -o ffindex_build ffindex_build.o -lffindex -L. -L. -lffindex

gcc -fopenmp -std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1   -c -o
ffindex_modify.o ffindex_modify.c

gcc -fopenmp -o ffindex_modify ffindex_modify.o -lffindex -L. -L. -lffindex

ar rcs libffindex.a ffutil.o ffindex.o

gcc -fopenmp -o ffindex_unpack ffindex_unpack.o -lffindex -L. -L. -lffindex

mpicc -std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1 -c
ffindex_apply_mpi.c -o ffindex_apply_mpi.o

ffindex_apply_mpi.c: In function 'ffindex_apply_by_entry':

ffindex_apply_mpi.c:151: warning: format '%ld' expects type 'long int', but
argument 4 has type 'size_t'

ffindex_apply_mpi.c:151: warning: format '%ld' expects type 'long int', but
argument 5 has type 'size_t'

mpicc -std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1 -o
ffindex_apply_mpi  ffindex_apply_mpi.o -lffindex -L.

*/usr/bin/ld: skipping incompatible ./libffindex.so when searching for
-lffindex*

*/usr/bin/ld: skipping incompatible ./libffindex.a when searching for
-lffindex*

*/usr/bin/ld: cannot find -lffindex*

*collect2: ld returned 1 exit status*

*make[2]: *** [ffindex_apply_mpi] Error 1*

*make[2]: Leaving directory
`/scratch/biotools/software/quality_control/transdecoder_rel16JAN2014/3rd_party/ffindex-0.9.9.3/src'*

*make[1]: *** [all] Error 2*

*make[1]: Leaving directory
`/scratch/biotools/software/quality_control/transdecoder_rel16JAN2014/3rd_party/ffindex-0.9.9.3'*

*make: *** [ffindex] Error 2*

Thanks for your help.

Eric


-- 
Eric Kenneth Wafula
Bioinformatics Programmer
Claude dePamphilis Lab
Department of Biology
Penn State University
814-865-2449
ek...@ps...