Question: I am trying to install RNAz-2.1
0
gravatar for Avro
3.9 years ago by
Avro130
Canada
Avro130 wrote:

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!

install rnaz • 1.3k views
ADD COMMENTlink written 3.9 years ago by Avro130
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 701 users visited in the last hour