Entering edit mode
9.1 years ago
Avro
▴
160
Hi everyone,
I am trying to install RNAz-2.1 to predict secondary structure in non-coding RNA, but I get the following errors:
Avro@~/downloads/RNAz-2.1> make
/Applications/Xcode.app/Contents/Developer/usr/bin/make all-recursive
Making all in librna
gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT fold_vars.o -MD -MP -MF .deps/fold_vars.Tpo -c -o fold_vars.o fold_vars.c
mv -f .deps/fold_vars.Tpo .deps/fold_vars.Po
gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT read_epars.o -MD -MP -MF .deps/read_epars.Tpo -c -o read_epars.o read_epars.c
mv -f .deps/read_epars.Tpo .deps/read_epars.Po
gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT energy_par.o -MD -MP -MF .deps/energy_par.Tpo -c -o energy_par.o energy_par.c
mv -f .deps/energy_par.Tpo .deps/energy_par.Po
gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT utils.o -MD -MP -MF .deps/utils.Tpo -c -o utils.o utils.c
mv -f .deps/utils.Tpo .deps/utils.Po
gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT fold.o -MD -MP -MF .deps/fold.Tpo -c -o fold.o fold.c
mv -f .deps/fold.Tpo .deps/fold.Po
gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT params.o -MD -MP -MF .deps/params.Tpo -c -o params.o params.c
mv -f .deps/params.Tpo .deps/params.Po
gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT alifold.o -MD -MP -MF .deps/alifold.Tpo -c -o alifold.o alifold.c
mv -f .deps/alifold.Tpo .deps/alifold.Po
rm -f libRNA.a
ar cru libRNA.a fold_vars.o read_epars.o energy_par.o utils.o fold.o params.o alifold.o
ranlib libRNA.a
Making all in rnaz
gcc -DHAVE_CONFIG_H -I. -I.. -I../librna -I../libsvm-2.89 -I../models -g -O2 -MT RNAz.o -MD -MP -MF .deps/RNAz.Tpo -c -o RNAz.o RNAz.c
mv -f .deps/RNAz.Tpo .deps/RNAz.Po
gcc -DHAVE_CONFIG_H -I. -I.. -I../librna -I../libsvm-2.89 -I../models -g -O2 -MT rnaz_utils.o -MD -MP -MF .deps/rnaz_utils.Tpo -c -o rnaz_utils.o rnaz_utils.c
rnaz_utils.c:534:1: warning: control may reach end of non-void function [-Wreturn-type]
}
^
rnaz_utils.c:591:10: warning: using the result of an assignment as a condition without parentheses
[-Wparentheses]
while (c=currField[j]!='\0'){
~^~~~~~~~~~~~~~~~~~~
rnaz_utils.c:591:10: note: place parentheses around the assignment to silence this warning
while (c=currField[j]!='\0'){
^
( )
rnaz_utils.c:591:10: note: use '==' to turn this assignment into an equality comparison
while (c=currField[j]!='\0'){
^
==
2 warnings generated.
mv -f .deps/rnaz_utils.Tpo .deps/rnaz_utils.Po
gcc -DHAVE_CONFIG_H -I. -I.. -I../librna -I../libsvm-2.89 -I../models -g -O2 -MT svm_helper.o -MD -MP -MF .deps/svm_helper.Tpo -c -o svm_helper.o svm_helper.c
svm_helper.c:343:23: warning: format specifies type 'double *' but the argument has type 'int *' [-Wformat]
sscanf(value,"%lf",&model->param.degree);
~~~ ^~~~~~~~~~~~~~~~~~~~
%d
svm_helper.c:488:29: warning: format specifies type 'double' but the argument has type 'int' [-Wformat]
fprintf(fp,"degree %g\n", model->param.degree);
~~ ^~~~~~~~~~~~~~~~~~~
%d
2 warnings generated.
mv -f .deps/svm_helper.Tpo .deps/svm_helper.Po
gcc -DHAVE_CONFIG_H -I. -I.. -I../librna -I../libsvm-2.89 -I../models -g -O2 -MT zscore.o -MD -MP -MF .deps/zscore.Tpo -c -o zscore.o zscore.c
zscore.c:354:21: warning: implicit declaration of function 'time' is invalid in C99
[-Wimplicit-function-declaration]
srand((unsigned)time(NULL));
^
1 warning generated.
mv -f .deps/zscore.Tpo .deps/zscore.Po
gcc -DHAVE_CONFIG_H -I. -I.. -I../librna -I../libsvm-2.89 -I../models -g -O2 -MT cmdline.o -MD -MP -MF .deps/cmdline.Tpo -c -o cmdline.o cmdline.c
mv -f .deps/cmdline.Tpo .deps/cmdline.Po
gcc -DHAVE_CONFIG_H -I. -I.. -I../librna -I../libsvm-2.89 -I../models -g -O2 -MT strand.o -MD -MP -MF .deps/strand.Tpo -c -o strand.o strand.c
strand.c:126:41: warning: incompatible integer to pointer conversion passing 'int' to parameter of type
'int *'; take the address with & [-Wint-conversion]
singleZ=mfe_zscore(woGapsSeq,singleMFE,z_score_type,0,warningString_strand);
^~~~~~~~~~~~
&
./zscore.h:17:53: note: passing argument to parameter 'type' here
double mfe_zscore(const char *seq, double mfe, int *type, int avoid_shuffle, char* warning_string);
^
strand.c:128:65: warning: incompatible integer to pointer conversion passing 'int' to parameter of type
'int *'; take the address with & [-Wint-conversion]
singleZ_reverse=mfe_zscore(woGapsSeq_reverse,singleMFE_reverse,z_score_type,0,warningString...
^~~~~~~~~~~~
&
./zscore.h:17:53: note: passing argument to parameter 'type' here
double mfe_zscore(const char *seq, double mfe, int *type, int avoid_shuffle, char* warning_string);
^
2 warnings generated.
mv -f .deps/strand.Tpo .deps/strand.Po
g++ -DHAVE_CONFIG_H -I. -I.. -I../librna -I../libsvm-2.89 -I../models -g -O2 -MT svm.o -MD -MP -MF .deps/svm.Tpo -c -o svm.o `test -f '../libsvm-2.89/svm.cpp' || echo './'`../libsvm-2.89/svm.cpp
mv -f .deps/svm.Tpo .deps/svm.Po
g++ -o RNAz RNAz.o rnaz_utils.o svm_helper.o zscore.o cmdline.o strand.o svm.o -L../librna -lRNA -lm
Undefined symbols for architecture x86_64:
"_HairpinE", referenced from:
_alifold in libRNA.a(alifold.o)
"_LoopEnergy", referenced from:
_alifold in libRNA.a(alifold.o)
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [RNAz] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
Avro@~/downloads/RNAz-2.1> make install
Making install in librna
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
Making install in rnaz
g++ -o RNAz RNAz.o rnaz_utils.o svm_helper.o zscore.o cmdline.o strand.o svm.o -L../librna -lRNA -lm
Undefined symbols for architecture x86_64:
"_HairpinE", referenced from:
_alifold in libRNA.a(alifold.o)
"_LoopEnergy", referenced from:
_alifold in libRNA.a(alifold.o)
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[1]: *** [RNAz] Error 1
make: *** [install-recursive] Error 1
I would greatly appreciate the community's help. I can't get to contact the original authors. Thank you!
