I tried to run this command in the terminal from my Mac OS, which I copied from a protocol:
FEELnc_codpot.pl –i <unannotated_transcript.fa> -a <mRNA_sequence.fa> -g <reference_genome.fa> -m ’shuffle’ –o <unannotated_transcript>
However, I get an error that the command cannot be found, probably because I am not using perl, so I entered:
perl FEELnc_codpot.pl
which gives me the following error:
Can't locate Bio/SeqIO.pm in #INC (you may need to install the Bio::SeqIO module) (#INC contains: /opt/anaconda3/lib/site_perl/5.26.2/darwin-thread-multi-2level /opt/anaconda3/lib/site_perl/5.26.2 /opt/anaconda3/lib/5.26.2/darwin-thread-multi-2level /opt/anaconda3/lib/5.26.2 .) at FEELnc_codpot.pl line 14.
So I copied seqio.pm from the bioperl directory which I had downloaded and placed it in /opt/anaconda3/lib/site_perl/5.26.2/darwin-thread-multi-2level directory. However, this does not resolve the error. When I tried to run this command:
perl seqio.pm
I get this message:
Can't locate Bio/Factory/FTLocationFactory.pm in #INC (you may need to install the Bio::Factory::FTLocationFactory module) (#INC contains: /opt/anaconda3/lib/site_perl/5.26.2/darwin-thread-multi-2level /opt/anaconda3/lib/site_perl/5.26.2 /opt/anaconda3/lib/5.26.2/darwin-thread-multi-2level /opt/anaconda3/lib/5.26.2 .) at seqio.pm line 339. BEGIN failed--compilation aborted at seqio.pm line 339.
So I copied FTLocationFactory.pm into /opt/anaconda3/lib/site_perl/5.26.2/darwin-thread-multi-2level.
Again this did not resolve the error. But gives the message that I also need Simple.pm in #INC. Which I copied into the correct directory (darwin-thread-multi-2level)
However, again this is not sufficient.
Does anyone know how to get this perl script working and resolve this error?
Edit:
Test Summary Report
-------------------
t/00-compile.t (Wstat: 7168 Tests: 511 Failed: 28)
Failed tests: 51, 64, 69, 81, 158, 170, 179-184, 331
337-342, 358, 365, 375, 430, 467, 470, 482
494, 507
Non-zero exit status: 28
t/Root/RootIO.t (Wstat: 512 Tests: 1 Failed: 0)
Non-zero exit status: 2
Parse errors: Bad plan. You planned 3 tests but ran 1.
Files=211, Tests=13892, 138 wallclock secs ( 2.50 usr 0.72 sys + 100.25 cusr 18.37 csys = 121.84 CPU)
Result: FAIL
Failed 2/211 test programs. 28/13892 subtests failed.
make: *** [test_dynamic] Error 255
CJFIELDS/BioPerl-1.7.8.tar.gz
9 dependencies missing (Graph::Directed,LWP::UserAgent,List::MoreUtils,Test::Memory::Cycle,XML::DOM,XML::LibXML,XML::LibXML::Reader,XML::Parser::PerlSAX,XML::Twig); additionally test harness failed
/usr/bin/make test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
reports CJFIELDS/BioPerl-1.7.8.tar.gz**
The full output is several pages long so for now I just inserted the summary output.
It is not a good idea to try to resolve these errors by simply copying modules around your filesystem. You need to install them into your Perl module library correctly.
Both of the modules you mention are part of the BioPerl distribution, so it's likely that you can solve your problems by installing that.
$ sudo cpan BioPerl
See cpan for more details.
Related
I want to install DBD::AnyData which requires SQL::Statement which requires Math::Base::Convert. However, it's giving me this error
$ cpan install Math::Base::Convert
...
t/overload.t .............. couldn't find diagnostic data in /usr/lib/perl5/5.22/pods/perldiag.pod /home/Chloe/.cpan/build/Math-Base-Convert-0.11-EySfLp/blib/lib /home/Chloe/.cpan/build/Math-Base-Convert-0.11-EySfLp/blib/arch /usr/lib/perl5/site_perl/5.22/i686-cygwin-threads-64int /usr/lib/perl5/site_perl/5.22 /usr/lib/perl5/vendor_perl/5.22/i686-cygwin-threads-64int /usr/lib/perl5/vendor_perl/5.22 /usr/lib/perl5/5.22/i686-cygwin-threads-64int /usr/lib/perl5/5.22 . t/overload.t at /usr/lib/perl5/5.22/diagnostics.pm line 259, <POD_DIAG> line 704.
Compilation failed in require at t/overload.t line 1.
BEGIN failed--compilation aborted at t/overload.t line 1.
t/overload.t .............. Dubious, test returned 2 (wstat 512, 0x200)
Test Summary Report
-------------------
t/overload.t (Wstat: 512 Tests: 0 Failed: 0)
Non-zero exit status: 2
Parse errors: No plan found in TAP output
Files=20, Tests=5327, 2 wallclock secs ( 0.28 usr 0.01 sys + 0.76 cusr 0.42 csys = 1.48 CPU)
Result: FAIL
Failed 1/20 test programs. 0/5327 subtests failed.
Makefile:859: recipe for target 'test_dynamic' failed
make: *** [test_dynamic] Error 255
MIKER/Math-Base-Convert-0.11.tar.gz
/usr/bin/make test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
reports MIKER/Math-Base-Convert-0.11.tar.gz
I already ran cpan -u.
CPAN version 1.61, Perl 5.22.0
The diagnostics module gets its explanations for messages from the perldoc file perldiag.pod. Both of these are core parts of perl, but some packaging systems choose to distribute documentation in a separate package that might not be installed even when perl is. In the case of Cygwin this package is perl_pods. Installing that package should make the diagnostics module work properly.
When I try to install the Inline package with cpan via cpan> install Inline I get the following error at the end:
make: *** [test_dynamic] Error 255
SISYPHUS/Inline-0.53.tar.gz
/opt/bin/make test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
reports SISYPHUS/Inline-0.53.tar.gz
Running make install
make test had returned bad status, won't install without force
Failed during this command:
SISYPHUS/Inline-0.53.tar.gz : make_test NO
Here is the complete installation log:
cpan[1]> install Inline
CPAN: Storable loaded ok (v2.18)
Going to read /root/.cpan/sources/authors/01mailrc.txt.gz
CPAN: Compress::Zlib loaded ok (v2.008)
CPAN: YAML loaded ok (v0.88)
Going to read /root/.cpan/build/
............................................................................DONE
Found 1 old build, restored the state of 1
............................................................................DONE
Going to read /root/.cpan/sources/modules/02packages.details.txt.gz
Database was generated on Wed, 08 Jan 2014 07:41:07 GMT
HTTP::Date not available
..............
New CPAN.pm version (v2.00) available.
[Currently running version is v1.9205]
You might want to try
install CPAN
reload cpan
to both upgrade CPAN.pm and run the new version without leaving
the current session.
CPAN: Time::HiRes loaded ok (v1.9711)
..............................................................DONE
Going to read /root/.cpan/sources/modules/03modlist.data.gz
............................................................................DONE
Going to write /root/.cpan/Metadata
Running install for module 'Inline'
Running make for S/SI/SISYPHUS/Inline-0.53.tar.gz
Has already been unwrapped into directory /root/.cpan/build/Inline-0.53-gk9HIk
Has already been made
Running make test
make[1]: Entering directory `/root/.cpan/build/Inline-0.53-gk9HIk/C'
make[1]: Leaving directory `/root/.cpan/build/Inline-0.53-gk9HIk/C'
PERL_DL_NONLAZY=1 /share/MD0_DATA/.qpkg/Optware/bin/perl5.10.0 "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/00init...............ok
t/01usages.............couldn't find diagnostic data in /opt/lib/perl5/5.10.0/pods/perldiag.pod blib/lib . /root/.cpan/build/Inline-0.53-gk9HIk/blib/lib /root/.cpan/build/Inline-0.53-gk9HIk/blib/arch /opt/lib/perl5/5.10.0/arm-linux /opt/lib/perl5/5.10.0 /opt/lib/perl5/site_perl/5.10.0/arm-linux /opt/lib/perl5/site_perl/5.10.0/arm-none-linux-gnueabi /opt/lib/perl5/site_perl/5.10.0 t/01usages.t at /opt/lib/perl5/5.10.0/diagnostics.pm line 268, <POD_DIAG> line 647.
Compilation failed in require at t/01usages.t line 5, <POD_DIAG> line 647.
BEGIN failed--compilation aborted at t/01usages.t line 5, <POD_DIAG> line 647.
t/01usages.............dubious
Test returned status 9 (wstat 2304, 0x900)
t/02config.............couldn't find diagnostic data in /opt/lib/perl5/5.10.0/pods/perldiag.pod blib/lib . /root/.cpan/build/Inline-0.53-gk9HIk/blib/lib /root/.cpan/build/Inline-0.53-gk9HIk/blib/arch /opt/lib/perl5/5.10.0/arm-linux /opt/lib/perl5/5.10.0 /opt/lib/perl5/site_perl/5.10.0/arm-linux /opt/lib/perl5/site_perl/5.10.0/arm-none-linux-gnueabi /opt/lib/perl5/site_perl/5.10.0 t/02config.t at /opt/lib/perl5/5.10.0/diagnostics.pm line 268, <POD_DIAG> line 647.
Compilation failed in require at t/02config.t line 5, <POD_DIAG> line 647.
BEGIN failed--compilation aborted at t/02config.t line 5, <POD_DIAG> line 647.
t/02config.............dubious
Test returned status 9 (wstat 2304, 0x900)
t/03errors.............couldn't find diagnostic data in /opt/lib/perl5/5.10.0/pods/perldiag.pod blib/lib . /root/.cpan/build/Inline-0.53-gk9HIk/blib/lib /root/.cpan/build/Inline-0.53-gk9HIk/blib/arch /opt/lib/perl5/5.10.0/arm-linux /opt/lib/perl5/5.10.0 /opt/lib/perl5/site_perl/5.10.0/arm-linux /opt/lib/perl5/site_perl/5.10.0/arm-none-linux-gnueabi /opt/lib/perl5/site_perl/5.10.0 t/03errors.t at /opt/lib/perl5/5.10.0/diagnostics.pm line 268, <POD_DIAG> line 647.
Compilation failed in require at t/03errors.t line 5, <POD_DIAG> line 647.
BEGIN failed--compilation aborted at t/03errors.t line 5, <POD_DIAG> line 647.
t/03errors.............dubious
Test returned status 9 (wstat 2304, 0x900)
t/04create.............couldn't find diagnostic data in /opt/lib/perl5/5.10.0/pods/perldiag.pod blib/lib . /root/.cpan/build/Inline-0.53-gk9HIk/blib/lib /root/.cpan/build/Inline-0.53-gk9HIk/blib/arch /opt/lib/perl5/5.10.0/arm-linux /opt/lib/perl5/5.10.0 /opt/lib/perl5/site_perl/5.10.0/arm-linux /opt/lib/perl5/site_perl/5.10.0/arm-none-linux-gnueabi /opt/lib/perl5/site_perl/5.10.0 t/04create.t at /opt/lib/perl5/5.10.0/diagnostics.pm line 268, <POD_DIAG> line 647.
Compilation failed in require at t/04create.t line 5, <POD_DIAG> line 647.
BEGIN failed--compilation aborted at t/04create.t line 5, <POD_DIAG> line 647.
t/04create.............dubious
Test returned status 9 (wstat 2304, 0x900)
t/05files..............couldn't find diagnostic data in /opt/lib/perl5/5.10.0/pods/perldiag.pod blib/lib . /root/.cpan/build/Inline-0.53-gk9HIk/blib/lib /root/.cpan/build/Inline-0.53-gk9HIk/blib/arch /opt/lib/perl5/5.10.0/arm-linux /opt/lib/perl5/5.10.0 /opt/lib/perl5/site_perl/5.10.0/arm-linux /opt/lib/perl5/site_perl/5.10.0/arm-none-linux-gnueabi /opt/lib/perl5/site_perl/5.10.0 t/05files.t at /opt/lib/perl5/5.10.0/diagnostics.pm line 268, <POD_DIAG> line 647.
Compilation failed in require at t/05files.t line 5, <POD_DIAG> line 647.
BEGIN failed--compilation aborted at t/05files.t line 5, <POD_DIAG> line 647.
t/05files..............dubious
Test returned status 9 (wstat 2304, 0x900)
t/06rewrite_config.....ok
t/07rewrite2_config....ok
Failed Test Stat Wstat Total Fail List of Failed
-------------------------------------------------------------------------------
t/01usages.t 9 2304 ?? ?? ??
t/02config.t 9 2304 ?? ?? ??
t/03errors.t 9 2304 ?? ?? ??
t/04create.t 9 2304 ?? ?? ??
t/05files.t 9 2304 ?? ?? ??
Failed 5/8 test scripts. 0/5 subtests failed.
Files=8, Tests=5, 3 wallclock secs ( 2.30 cusr + 0.14 csys = 2.44 CPU)
Failed 5/8 test programs. 0/5 subtests failed.
make: *** [test_dynamic] Error 255
SISYPHUS/Inline-0.53.tar.gz
/opt/bin/make test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
reports SISYPHUS/Inline-0.53.tar.gz
Running make install
make test had returned bad status, won't install without force
Failed during this command:
SISYPHUS/Inline-0.53.tar.gz : make_test NO
Unfortunately I'm a newbie to cpan and perl, so I don't know how to resolve this issue. I already tried to reinstall perl but with no success.
If it is important for you I'm running this on my QNAP NAS TS-419P+:
[~] # uname -a
Linux QNAP 2.6.33.2 #1 Fri Jul 26 04:41:05 CST 2013 armv5tel unknown
Here is the perl version I'm using:
[~] # perl --version
This is perl, v5.10.0 built for arm-none-linux-gnueabi
As DavidO wrote, the test fails at use diagnostics; You can check this by executing this line by itself (perl -e 'use diagnostics;').
diagnostics.pm tries to read diagnostic messages from perldiag.pod (which is mentioned in the error message).
Looks like it's missing on your system.
So, you need to install the package with that file (or otherwise get it to the specified path) of the version corresponding to your Perl's. E.g. in Cygwin, it's in the perl_pods package which, you guessed it, is not installed by default.
Investigating the first error first is always a good course of action. In this case, that's the following:
couldn't find diagnostic data in
(long list of paths excluded from copy/paste)
Compilation failed in require at t/01usages.t line 5,
Looking at the distribution's source code we find that line 5 of t/01usages.t is:
use diagnostics;
The diagnostics pragma is part of the core Perl distribution. For diagnostics to be missing necessary files indicates that the problem is that your installation of Perl is either broken or incomplete (which is the subset of "broken" most likely to be at cause here). Resolve that issue first.
brian's Guide to Solving Any Perl Problem: "Solve the first problem first." In this case, in doing so, we discover the problem is unrelated to the module, and instead, related to the quality of your Perl installation.
I am tiring to run multiple jobs in parallel by using perl script which use Parallel:ForkManager.
#!/usr/bin/perl -w
use Parallel::ForkManager;
my #make_obj = qw(
mode1_testlist
mode1_testlist1
mode1_testlist2
);
my $fm = $pm = Parallel::ForkManager-> new(3);
foreach my $obj (#make_obj) {
$fm->start and next;
print("make regression MODE=1 MODELIST=$make_obj");
$fm->finish();
}
but it throws me below error.
Can't locate Parallel/ForkManager.pm in #INC (#INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at parallel_run.pl line 3.
BEGIN failed--compilation aborted at parallel_run.pl line 3.
I have downloaded Parallel-ForkManager-1.03.tar.gz but I don't know where to keep it I mean how to install it.
I tried perl Makefile.PL && make test && make install:
WARNING: META_MERGE is not a known parameter.
WARNING: BUILD_REQUIRES is not a known parameter.
WARNING: LICENSE is not a known parameter.
Checking if your kit is complete...
Looks good
'BUILD_REQUIRES' is not a known MakeMaker parameter name.
'LICENSE' is not a known MakeMaker parameter name.
'META_MERGE' is not a known MakeMaker parameter name.
Writing Makefile for Parallel::ForkManager
cp lib/Parallel/ForkManager.pm blib/lib/Parallel/ForkManager.pm
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"test_harness(0,'blib/lib', 'blib/arch')" t/*.t
t/00-load.............ok 1/3 (in cleanup) Undefined subroutine
&File::Path::remove_tree called at /h/altera_dump2/vjain419/regression_flow_bck
/regression_flow/MSS1/hw/verif/top_/00e/tools/Parallel-ForkManager-1.03/blib
/lib/Parallel /ForkManager.pm line 662.
t/00-load.............ok
t/01-utf8-all.........skipped
all skipped: Need utf8::all for this test crashing on Windows
t/02-callback.........Array found where operator expected at t/02-callback.t line
21,at end of line
(Do you need to predeclare explain?)
syntax error at t/02-callback.t line 21, near "explain #out"
xecution of t/02-callback.t aborted due to compilation errors.
# Looks like your test died before it could output anything.
t/02-callback.........dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 1-2
Failed 2/2 tests, 0.00% okay
t/03-callback-data....Array found where operator expected at t/03-callback-data.t line 13, at end of line
(Do you need to predeclare explain?)
syntax error at t/03-callback-data.t line 13, near "explain #out"
Execution of t/03-callback-data.t aborted due to compilation errors.
# Looks like your test died before it could output anything.
t/03-callback-data....dubious
Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED test 1
Failed 1/1 tests, 0.00% okay
Failed Test Stat Wstat Total Fail Failed List of Failed
t/02-callback.t 255 65280 2 4 200.00% 1-2
t/03-callback-data.t 255 65280 1 2 200.00% 1
1 test skipped.
Failed 2/4 test scripts, 50.00% okay. 3/6 subtests failed, 50.00% okay.
make: *** [test_dynamic] Error 255
Just use
cpan Parallel::ForkManager
Alternatively, execute the following command after making sure you have its dependencies (POSIX, Storable, File::Spec, File::Temp, File::Path 2.00 and Test::More 0.81_01) installed:
tar xvzf Parallel-ForkManager-1.03.tar.gz
cd Parallel-ForkManager-1.03
perl Makefile.PL && make test && make install
Like some of the comments on the accepted answer suggest, there can be a dependency missing. The following worked for me:
% cpan Test::More
% cpan Parallel::ForkManager
I am trying to get a Perl script running which was simply copied from one Windows 2003 x64 to another Windows machine of the same type.
I installed ActivePerl and I receive following error:
F:\Supportsaves\Scripts\Supportsave_Script>Can't locate Net/SSH/Perl.pm in #INC (#INC contains: C:/Perl64/site/lib C:/Perl64/lib .) at F:\Supportsaves\Scripts\switches_supportsave.pl line 11.
BEGIN failed--compilation aborted at F:\Supportsaves\Scripts\switches_supportsave.pl line 11.
I have searched and possibly the Net::SSH::Perl is missing, but I don't get it installed (after setting the proxy) I get
F:\Supportsaves\Scripts\Supportsave_Script>ppm install Net-SSH-Perl
ppm install failed: Can't find any package that provides Net-SSH-Perl
When using ppm I can't find this module in GUI.
CPAN creates other errors.
Any help is appreciated.
Result after installing Net::SSH::Perl in Strawberry, CPAN Test Summary Report
-------------------
t/03-packet.t (Wstat: 65280 Tests: 0 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 10 tests but ran 0.
Files=12, Tests=106, 2 wallclock secs ( 0.09 usr + 0.03 sys = 0.12 CPU)
Result: FAIL`
Failed 1/12 test programs. 0/106 subtests failed.
dmake.EXE: Error code 255, while making 'test_dynamic'
TURNSTEP/Net-SSH-Perl-1.34.tar.gz
2 dependencies missing (Math::Pari,Crypt::RSA); additionally test harness failed`
C:\Perl\strawberry\c\bin\dmake.EXE test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
reports TURNSTEP/Net-SSH-Perl-1.34.tar.gz
Running make install
make test had returned bad status, won't install without force`
`F:\Supportsaves\Scripts\Supportsave_Script>`
-----------------
Installing in Active Perl with CPAN Net::SSH::Perl does partly work well, there are
missing dependencies, which can't be installed either...
Result: PASS
TURNSTEP/Net-SSH-Perl-1.34.tar.gz
Tests succeeded but 7 dependencies missin
(Crypt::IDEA,Math::Pari,Crypt::DSA,Convert::PEM,String::CRC32,Math::GMP,Crypt
::RSA)
TURNSTEP/Net-SSH-Perl-1.34.tar.gz
[dependencies] -- NA
Running make install
make test had returned bad status, won't install without force`
`F:\Supportsaves\Scripts\Supportsave_Script>`
Crypt::IDEA fails ...
C:\Perl\site\lib\auto\MinGW\bin\..\lib\gcc\mingw32\3.4.5\..\..\..\..\mingw32
\bin\ld.exe: cannot find -lbufferoverflowU
collect2: ld returned 1 exit status
dmake.exe: Error code 129, while making 'blib\arch\auto\Crypt\IDEA\IDEA.dll'
DPARIS/Crypt-IDEA-1.08.tar.gz
C:\Perl\site\bin\dmake.exe -- NOT OK
CPAN: YAML::XS loaded ok (v0.35)
Running make test
Can't test without successful make
Running make install
Make had returned bad status, install seems impossible `
As far as I can tell, the Net::SSH::Perl module is only in the Bribes ppm repository at
http://www.bribes.org/perl/ppm/
If you add that to your ppm's list of repositories it should install it correctly.
Try this, this may works:
ppm install http://theoryx5.uwinnipeg.ca/ppms/Net-SSH2.ppd
ppm install http://theoryx5.uwinnipeg.ca/ppms/Net-SSH-Perl.ppd
regards,
I have been trying to install GD library for perl to no avail a long while now. I've tried every little thing I could find on the internets but nothing. I am trying to get Circos graphs which require the GD package.
When I try to install it through CPAN it gives me this error:
Running make test
PERL_DL_NONLAZY=1 /usr/bin/perl/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/GD.t ........ 1/12 Can't load './blib/arch/auto/GD/GD.bundle' for module GD: dlopen(./blib/arch/auto/GD/GD.bundle, 2): Symbol not found: _jpeg_resync_to_restart
Referenced from: /usr/lib/libgd.2.dylib
Expected in: flat namespace
in /usr/lib/libgd.2.dylib at /opt/local/lib/perl5/5.14.1/darwin-multi-2level/DynaLoader.pm line 194.
at t/GD.t line 14
Compilation failed in require at t/GD.t line 14.
BEGIN failed--compilation aborted at t/GD.t line 14.
t/GD.t ........ Dubious, test returned 2 (wstat 512, 0x200)
Failed 12/12 subtests
t/Polyline.t .. Can't load '/Users/zehira/.cpan/build/GD-2.46-mp3nuO/blib/arch/auto/GD/GD.bundle' for module GD: dlopen(/Users/zehira/.cpan/build/GD-2.46-mp3nuO/blib/arch/auto/GD/GD.bundle, 2): Symbol not found: _jpeg_resync_to_restart
Referenced from: /usr/lib/libgd.2.dylib
Expected in: flat namespace
in /usr/lib/libgd.2.dylib at /opt/local/lib/perl5/5.14.1/darwin-multi-2level/DynaLoader.pm line 194.
at /Users/zehira/.cpan/build/GD-2.46-mp3nuO/blib/lib/GD/Polyline.pm line 45
Compilation failed in require at /Users/zehira/.cpan/build/GD-2.46-mp3nuO/blib/lib/GD/Polyline.pm line 45.
BEGIN failed--compilation aborted at /Users/zehira/.cpan/build/GD-2.46-mp3nuO/blib/lib/GD/Polyline.pm line 45.
Compilation failed in require at t/Polyline.t line 10.
BEGIN failed--compilation aborted at t/Polyline.t line 10.
t/Polyline.t .. Dubious, test returned 2 (wstat 512, 0x200)
Failed 1/1 subtests
Test Summary Report
-------------------
t/GD.t (Wstat: 512 Tests: 1 Failed: 1)
Failed test: 1
Non-zero exit status: 2
Parse errors: Bad plan. You planned 12 tests but ran 1.
t/Polyline.t (Wstat: 512 Tests: 0 Failed: 0)
Non-zero exit status: 2
Parse errors: Bad plan. You planned 1 tests but ran 0.
Files=2, Tests=1, 0 wallclock secs ( 0.02 usr 0.01 sys + 0.04 cusr 0.01 csys = 0.08 CPU)
Result: FAIL
Failed 2/2 test programs. 1/1 subtests failed.
make: *** [test_dynamic] Error 2
LDS/GD-2.46.tar.gz
make test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
reports LDS/GD-2.46.tar.gz
Running make install
make test had returned bad status, won't install without force
Failed during this command:
LDS/GD-2.46.tar.gz : make_test NO
I tried to reinstall jpeg libraries with --enable-shared --enable-static options but didn't help either. I also installed a MacPorts version of perl thinking I might have messed up the perl installation that comes with my mac. Anyone have any idea why this might be happening?
(yes, I'm relatively new to the world of terminal and all this and am still trying to navigate my way around)
Thanks!
I have solved this issue using homebrew to install libgd first, and then cpan. It worked perfectly.
brew install libgd
cpan install GD
i installed it step by step without any problem by
http://zientzilaria.herokuapp.com/blog/2012/06/03/installing-circos-on-os-x/
maybe that helps...
Firstly I'm also a circos user :) It's really not simple to install circos on win/linux/mac for perl and the modules circos needs .
Above my practice you'd better do like this from very begin:
install perl (choose the very popular new version)
install circos (ref http://circos.ca/software/installation/)
install the modules circos needs but exclude GD : this is easy, just download and copy, or install by CPAN (ref http://www.rcbowen.com/imho/perl/modules.html)
install GD : GD is a special module (not platform independently ), and you should build it on your OS and then install : http://www.sharedproteomics.com/forum/showthread.php?325-Installing-GD-on-Mac-OSX-10.6
It looks like your problem is at step3 !!! If Google can not help you to make it, another way to request help is using circos's google group: http://groups.google.com/group/circos-data-visualization there Martin and other circos users will help you directly.
For prerequisite of Circos installation, the documentation from CircosAPI is very helpful. It was written for OSX 10.8, and still works for OS X Yosemite.
http://kylase.github.io/CircosAPI/os-x-installation-guide/
You need libgd. If you are using ubuntu & you can get it using
sudo apt-get install libgd-gd2-perl
Then you can follow the normal procedure as mentioned in circos installation instructions.