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.
Related
I have installed ActivePerl in order to run a bioinformatic tool.
after running the tool on Windows PowerShell I got this message:
Perl module Archive::Extract (in core since 2007-07-07) is not installed on this machine!
Perl modules are available for download at http://www.cpan.org/
If you have CPAN installed try the following: cpan install
Archive::Extract exit
If you are on Mac or Unix you should run cpan with sudo: sudo cpan
install Archive::Extract exit
So I tried to install it:
cpan
install Archive::Extract
and got this:
"C:\Perl64\bin\perl.exe" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef Test::Harness::Switches; test_harness(0, 'blib\lib', 'blib\arch')" t/.t
t/01_Archive-Extract.t .. # Older versions of Archive::Zip may cause File::Spec warnings
See bug #19713 in rt.cpan.org. It is safe to ignore them
t/01_Archive-Extract.t .. 87/?
As I'm not adept at this I thought that I should try to install again the Archive::Zip
install Archive::Zip
but I got :
t/25_traversal.t .............. 1/41
Failed test 'Tree extraction aborted'
at t/25_traversal.t line 97.
got: '0'
expected: '2'
Looks like you failed 1 test of 41.
t/25_traversal.t .............. Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/41 subtests
(less 32 skipped subtests: 8 okay)
Test Summary Report
t/25_traversal.t (Wstat: 256 Tests: 41 Failed: 1)
Failed test: 16
Non-zero exit status: 1
Files=25, Tests=346, 18 wallclock secs ( 0.19 usr + 0.13 sys = 0.31 CPU)
Result: FAIL
Failed 1/25 test programs. 1/346 subtests failed.
dmake.exe: Error code 129, while making 'test_dynamic'
Could you please explain what's the particular problem in order to understand it and how can I solve it?
I don't know if it's a naive question as I have just started learning about command line tools, Linux, Perl etc.
Active Perl uses the ppm script to install modules, mixing this with cpan can cause the problems you have seen above. You may find that using Strawberry Perl works better for you as this comes with a c compiler that will allow you to install non pure Perl modules from cpan
I have installed ActivePerl PPM and Strawberry Perl(Padre). Tried installing WWW::Selenium CPAN from command prompt through
perl -MCPAN -e shell
install WWW::Selenium
It throws the following error
Test Summary Report
-------------------
t/test_default_server.t (Wstat: 65280 Tests: 1 Failed: 1)
Failed test: 1
Non-zero exit status: 255
Parse errors: Bad plan. You planned 7 tests but ran 1.
Files=12, Tests=344, 31 wallclock secs ( 0.14 usr + 0.06 sys = 0.20 CPU)
Result: FAIL
Failed 1/12 test programs. 1/344 subtests failed.
dmake.exe: Error code 255, while making 'test_dynamic'
MATTP/Test-WWW-Selenium-1.36.tar.gz
C:\STRAWB~1\c\bin\dmake.exe test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
reports MATTP/Test-WWW-Selenium-1.36.tar.gz
Running make install
make test had returned bad status, won't install without force
Failed during this command:
MATTP/Test-WWW-Selenium-1.36.tar.gz : make_test NO
Also I have installed Selenium stand alone server (a jar file). But the following code doesn't work in command prompt.
java -jar <path of the selenium server>
P.S: I don't know Perl. I'm a beginner.
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 get the following results when doing cpan install CGI on Ubuntu 10.4.
Test Summary Report
-------------------
t/tmpdir.t (Wstat: 0 Tests: 9 Failed: 0)
TODO passed: 3, 6, 8
t/url.t (Wstat: 65280 Tests: 0 Failed: 0)
Non-zero exit status: 255
Parse errors: No plan found in TAP output
Files=39, Tests=695, 2 wallclock secs ( 0.45 usr 0.11 sys + 1.19 cusr 0.21 csys = 1.96 CPU)
Result: FAIL
Failed 1/39 test programs. 0/695 subtests failed.
make: *** [test_dynamic] Error 255
MARKSTOS/CGI.pm-3.55.tar.gz
/usr/bin/make test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
reports MARKSTOS/CGI.pm-3.55.tar.gz
Running make install
make test had returned bad status, won't install without force
Failed during this command:
MARKSTOS/CGI.pm-3.55.tar.gz : make_test NO
And cpan force install also create same results. Has anyone had this error, does anyone know how to fix it?
Don't install modules from CPAN if you have a packet manager. This may cause problems with update or with other modules.
Just use:
apt-get install libcgi-pm-perl
OR, if you can't find the package with needed module, you must make a package first ( you need to install dh-make-perl package for that)
sample of creating debian/ubuntu package:
wget http://search.cpan.org/CPAN/authors/id/M/MA/MARKSTOS/CGI.pm-3.63.tar.gz
tar -xvpf CGI.pm-3.63.tar.gz
cd CGI.pm-3.63/
dh-make-perl
debian/rules binary
and install it with
sudo dpkg -i packagename.deb
I am trying to install HTML-Parser-3.64 and I get following report while running make test:
ERL_DL_NONLAZY=1 /home/Perl/bin/perl -Iblib/arch -Iblib/lib -I/home/Perl/5.6.1-nothread/lib/perl5/5.6.1/sun4.SVR4 -I/home/Perl/5.6.1-nothread/lib/perl5/5.6.1 -e 'use Test::Harness qw(&runtests $verbose); $verbose=0; runtests #ARGV;' t/*.t
t/api_version........ok
t/argspec-bad........ok
t/argspec............ok
t/argspec2...........ok
t/attr-encoded.......ok
t/callback...........ok
t/case-sensitive.....ok
t/cases..............ok
t/comment............ok
t/crashme............ok
t/declaration........ok
t/default............ok
t/document...........ok
t/dtext..............ok
t/entities...........ok 1/17
t/entities...........NOK 17# Failed test (t/entities.t at line 74)
# got: 'Attention Homeοωnөrs...1ѕt Tімe Eνөг'
# expected: 'Attention HomeοÏnÓ©rs...1Ñt TÑмe Eνөг'
# Looks like you failed 1 test of 17.
t/entities...........dubious
Test returned status 1 (wstat 256, 0x100)
DIED. FAILED test 17
Failed 1/17 tests, 94.12% okay
t/entities2..........ok
t/filter-methods.....ok
t/filter.............ok
t/handler-eof........ok
t/handler............ok
t/headparser-http....ok
t/headparser.........ok
4/15 skipped: Need Unicode support
t/ignore.............ok
t/largetags..........ok
t/linkextor-base.....ok
t/linkextor-rel......ok
t/magic..............ok
t/marked-sect........ok
t/msie-compat........ok
t/offset.............ok
t/options............ok
t/parsefile..........ok
t/parser.............ok
t/plaintext..........ok
t/pod................skipped
all skipped: Test::Pod 1.00 required for testing POD
t/process............ok
t/pullparser.........ok
t/script.............ok
t/skipped-text.......ok
t/stack-realloc......ok
t/textarea...........ok
t/threads............skipped
all skipped: Not configured for threads
t/tokeparser.........ok
t/uentities..........ok 1/26# Looks like you planned 26 tests but ran 1 extra.
t/uentities..........dubious
Test returned status 1 (wstat 256, 0x100)
DIED. FAILED test 27
Failed 1/26 tests, 96.15% okay (less 27 skipped tests: -2 okay, -7.69%)
t/unbroken-text......ok
t/unicode-bom........ok
2/2 skipped: This perl does not support Unicode
t/unicode............skipped
all skipped: This perl does not support Unicode
t/xml-mode...........ok
Failed Test Stat Wstat Total Fail Failed List of Failed
-------------------------------------------------------------------------------
t/entities.t 1 256 17 1 5.88% 17
t/uentities.t 1 256 26 1 3.85% 27
3 tests and 33 subtests skipped.
Failed 2/48 test scripts, 95.83% okay. 0/338 subtests failed, 100.00% okay.
*** Error code 11
make: Fatal error: Command failed for target `test_dynamic'
I have Perl version 5.6.1. and 3.64 version of Parser on Solaris 8.
I have seen following similar error reported by another person on internet at http://www.cpantesters.org/cpan/report/6653478. But could not see any reply or solution for that.
If you are comfortable with the other test results, and you don't expect to use HTML::Parser for pages which require extended character sets, then you can force an install.
From command-line:
$ perl -MCPAN -e 'force install HTML::Parser'
From CPAN command line:
cpan> force install HTML::Parser
From your build directory (if you'd rather not use CPAN):
mv t/entities.t t/entities.tt
mv t/uentities.t t/uentities.tt
make install
You need to report it to HTML::Parser bug tracker. Cpantesters results are only reports, in many cases automatic, so to gain attention of author you need to use bug tracker.
P.S. Upgrading is also a good idea (in case you have no problems of doing this) - Perl has changed much in 9 years from 5.6.1.