mirdeep2 installation (make_html.pl error)

[lran2008]

Hi,

I am installing mirdeep2 now. At the last step, when I tested make_html.pl, error appeared as following:

[liran@ip14-mp2 tools]$ make_html.pl
Can't locate PDF/API2.pm in @INC (@INC contains: /home/liran/tools/mirdeep2/lib64/perl5 /home/liran/tools/ViennaRNA-2.1.2/install_dir/lib64/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /home/liran/tools/mirdeep2/make_html.pl line 9.
BEGIN failed--compilation aborted at /home/liran/tools/mirdeep2/make_html.pl line 9.

Could anybody tell me what should I do now? I really don't know how to interpret the error.

Thanks.

[rhinoceros]

Quite simply, API2pm from a directory called PDF can't be found from any of the listed locations. Is this folder in the same directory as make_html.pl? Are you running it from this directory?

[GenoMax]

It is possible that mirdeep2 does not include the perl module to create PDF's (which is what is being referenced in the error).

You may need to install it: http://search.cpan.org/~areibens/PDF...ib/PDF/API2.pm

[lran2008]

Quite simply, API2pm from a directory called PDF can't be found from any of the listed locations. Is this folder in the same directory as make_html.pl? Are you running it from this directory?

Thanks. I have specified the location of API2.pm. It works now.

[lran2008]

It is possible that mirdeep2 does not include the perl module to create PDF's (which is what is being referenced in the error).

You may need to install it: http://search.cpan.org/~areibens/PDF...ib/PDF/API2.pm

Thank you. I have solved it. I have installed the module. I followed the instructions of mirDeep2 manual, but there was something that in the manual didn't fit my operating system. I changed the directory to specify the location of API2.pm

[hemant]

same problem

I also have same problem can anyone please tell me where I have to provide the location of API2.pm

I am also having problem with installing randfold

[hgu223@dlxlogin2-1 randfold-2.0]$ make
gcc -O3 -I. -I/home/hgu223/squid-1.9g/ -L/home/hgu223/squid-1.9g/ -o randfold params.o energy_par.o fold.o fold_vars.o utils.o randfold.c -lm -lsquid
randfold.c:24:18: error: squid.h: No such file or directory
randfold.c: In function ‘main’:
randfold.c:30: error: ‘SQFILE’ undeclared (first use in this function)
randfold.c:30: error: (Each undeclared identifier is reported only once
randfold.c:30: error: for each function it appears in.)
randfold.c:30: error: ‘sqfp’ undeclared (first use in this function)
randfold.c:38: error: ‘SQINFO’ undeclared (first use in this function)
randfold.c:38: error: expected ‘;’ before ‘sqinfo’
randfold.c:89: warning: incompatible implicit declaration of built-in function ‘strcpy’
randfold.c:96: error: ‘SQFILE_FASTA’ undeclared (first use in this function)
randfold.c:100: error: ‘sqinfo’ undeclared (first use in this function)
randfold.c:103: warning: incompatible implicit declaration of built-in function ‘malloc’
randfold.c:103: warning: incompatible implicit declaration of built-in function ‘strlen’
randfold.c:136: warning: incompatible implicit declaration of built-in function ‘fabs’
randfold.c:158: warning: incompatible implicit declaration of built-in function ‘free’
make: *** [randfold] Error 1
[hgu223@dlxlogin2-1 randfold-2.0]$

what should i do

Thanks for the reply
Hemant

[GenoMax]

As indicated in the "README" file from mirdeep2 install tarball, you need to install Dr. Sean Eddy's SQUID library and a few other per-requisites listed in part 2.1.

[hemant]

Thanks genomax. can you tell about how to solve this error

[hgu223@dlxlogin2-1 randfold-2.0]$ make
gcc -O3 -I. -I/home/hgu223/squid-1.9g/ -L/home/hgu223/squid-1.9g/ -o randfold params.o energy_par.o fold.o fold_vars.o utils.o randfold.c -lm -lsquid
randfold.c: In function ‘main’:
randfold.c:89: warning: incompatible implicit declaration of built-in function ‘strcpy’
randfold.c:103: warning: incompatible implicit declaration of built-in function ‘strlen’

Thanks
Hemant

[hemant]

i have completed all the pre requisites mentioned.

[GenoMax]

Thanks genomax. can you tell about how to solve this error

[hgu223@dlxlogin2-1 randfold-2.0]$ make
gcc -O3 -I. -I/home/hgu223/squid-1.9g/ -L/home/hgu223/squid-1.9g/ -o randfold params.o energy_par.o fold.o fold_vars.o utils.o randfold.c -lm -lsquid
randfold.c: In function ‘main’:
randfold.c:89: warning: incompatible implicit declaration of built-in function ‘strcpy’
randfold.c:103: warning: incompatible implicit declaration of built-in function ‘strlen’

Thanks
Hemant

Those are warnings and hopefully will not cause problems. Did the compilation complete otherwise?

[hemant]

ranfold is working

but i realized there was a error message while installing Vienna.

after typing make I got this error message:-

In file included from rnafuncs.cpp:22:
rnafuncs.h:42: warning: ‘typedef’ was ignored in this declaration
rnafuncs.cpp: In static member function ‘static void RNAFuncs::drawRNAStructure(const std::string&, const std::string&, const std::string&, const std::string&, const std::list<std:air<unsigned int, unsigned int>, std::allocator<std:air<unsigned int, unsigned int> > >&, const RNAFuncs::SquigglePlotOptions&)’:
rnafuncs.cpp:341: error: ‘sprintf’ was not declared in this scope
rnafuncs.cpp:361: error: ‘sprintf’ was not declared in this scope
rnafuncs.cpp: In static member function ‘static void RNAFuncs::drawRNAAlignment(const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, const RNAFuncs::SquigglePlotOptions&)’:
rnafuncs.cpp:582: error: ‘sprintf’ was not declared in this scope
rnafuncs.cpp:588: error: ‘sprintf’ was not declared in this scope
make[4]: *** [rnafuncs.o] Error 1
make[4]: Leaving directory `/home/hgu223/ViennaRNA-1.8.4/RNAforester/src'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/home/hgu223/ViennaRNA-1.8.4/RNAforester'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/home/hgu223/ViennaRNA-1.8.4/RNAforester'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/hgu223/ViennaRNA-1.8.4'
make: *** [all] Error 2
[hgu223@dlxlogin2-1 ViennaRNA-1.8.4]$


can you please help

Thanks

[GenoMax]

What version of make/gcc compiler are you using? What OS?

You could get the pre-compiled version of Vienna and try that. Newest seems to be v.2.1.2.

[hemant]

This is Linux OS (RHEL)
there is Intel compilers and gcc v 3.3.3 etc

http://www.uky.edu/ukit/hpc/docs/intel-compilers

Hey, I was able to install ViennaRNA-2.1.2.

But I am still having problem with PDF:API2

after I type make test

Test Summary Report
-------------------
t/00-all-usable.t (Wstat: 512 Tests: 102 Failed: 2)
Failed tests: 75-76
Non-zero exit status: 2
Files=21, Tests=252, 3 wallclock secs ( 0.08 usr 0.02 sys + 2.57 cusr 0.49 csys = 3.16 CPU)
Result: FAIL
Failed 1/21 test programs. 2/252 subtests failed.
make: *** [test_dynamic] Error 255
hgu223@dlxlogin2-2 PDF-API2-2.020]$

and make_html.pl is giving same error as in first comment

Thanks

[GenoMax]

Any chance you can get your systems administrators to install that perl module?

If that is not possible then you may want to install that module in your personal space. See the instructions for doing that this page: http://openwall.info/wiki/internal/perl/cpan (first section)

Hopefully the CPAN module is installed on your system.