Hello sir,
i was trying to install gbrowse again since i was not able to figure out
the problem as mentioned by you in the previous mail.
while installing GD i faced the following error. Have checked for the
dependencies all were installed. When i was viewing in the root cpan it
said GD is already installed and updated to the latest version but it is
not showing in the installed modules directory (/root/.cpan/Build) . Kindly
revert me back the suitable solution to this ASAP.
Thanks and Regards,
Iti Gupta
.............................................................................................
cpan install GD
Loading internal null logger. Install Log::Log4perl for logging messages
CPAN: Storable loaded ok (v2.49_01)
Reading '/root/.cpan/Metadata'
Database was generated on Thu, 30 Apr 2015 05:53:27 GMT
Running install for module 'GD'
CPAN: Digest::SHA loaded ok (v5.95)
CPAN: Compress::Zlib loaded ok (v2.068)
Checksum for /root/.cpan/sources/authors/id/L/LD/LDS/GD-2.56.tar.gz ok
CPAN: File::Temp loaded ok (v0.2304)
CPAN: YAML loaded ok (v1.15)
CPAN: CPAN::Meta::Requirements loaded ok (v2.127)
CPAN: Parse::CPAN::Meta loaded ok (v1.4414)
CPAN: CPAN::Meta loaded ok (v2.150001)
CPAN: Module::CoreList loaded ok (v5.20150214)
CPAN: Module::Build loaded ok (v0.4211)
Configuring L/LD/LDS/GD-2.56.tar.gz with Build.PL
Configuring for libgd version 2.0.34.
Checking for stray libgd header files...none found.
Included Features: GD_XPM GD_JPEG GD_FONTCONFIG GD_FREETYPE GD_PNG
GD_GIF GD_GIFANIM GD_OPENPOLYGON GD_UNCLOSEDPOLY GD_ANIMGIF GD_FTCIRCLE
VERSION_33
GD library used from: /usr
Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'GD' version '2.56'
LDS/GD-2.56.tar.gz
/usr/local/bin/perl Build.PL -- OK
Running Build for L/LD/LDS/GD-2.56.tar.gz
Building GD
Extracting Image.pm (with variable substitutions)
cc -I/usr/include -I/usr/local/lib/perl5/5.20.2/x86_64-linux/CORE
-DXS_VERSION="2.56" -DVERSION="2.56" -fPIC -DHAVE_JPEG -DHAVE_FT -DHAVE_XPM
-DHAVE_GIF -DHAVE_PNG -DHAVE_ANIMGIF -DVERSION_33 -DHAVE_UNCLOSEDPOLY
-DHAVE_FONTCONFIG -DHAVE_FTCIRCLE -c -fwrapv -fno-strict-aliasing -pipe
-fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE
-D_FILE_OFFSET_BITS=64 -O2 -o lib/GD.o lib/GD.c
ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/GD/GD.bs')
cc -shared -O2 -L/usr/local/lib -fstack-protector -o
blib/arch/auto/GD/GD.so lib/GD.o -L/usr/lib64 -L/usr/lib64 -L/usr/lib64
-L/usr/lib64 -lXpm -lX11 -ljpeg -lfontconfig -lfreetype -lpng12 -lz -lm -lgd
LDS/GD-2.56.tar.gz
./Build -- OK
Running Build test
t/GD.t ........ 1/11 # Testing using gd2 support.
# Failed test 'image comparison test 7'
# at t/GD.t line 249.
# Looks like you failed 1 test of 11.
t/GD.t ........ Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/11 subtests
t/Polyline.t .. ok
Test Summary Report
-------------------
t/GD.t (Wstat: 256 Tests: 11 Failed: 1)
Failed test: 9
Non-zero exit status: 1
Files=2, Tests=12, 1 wallclock secs ( 0.02 usr 0.04 sys + 0.13 cusr
0.04 csys = 0.23 CPU)
Result: FAIL
Failed 1/2 test programs. 1/12 subtests failed.
LDS/GD-2.56.tar.gz
./Build test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
reports LDS/GD-2.56.tar.gz
Post by Scott CainHi Ita,
Please keep the GBrowse mailing list cc'ed so other people can see and help.
The message about permission denied on /var/lib/gbrowse2/sessions/cgisess.db.lck
is definitely a problem. Check the ownership on the /var/lib/gbrowse2
directory and subdirectories. It should be owned by the same owner that
runs apache, which varies from system to system. If you're using Ubuntu, I
believe the owner should be www-data. If you find that the sessions
directory (or the other directories in the gbrowse2 directory) are not
sudo chown -R www-data:www-data /var/lib/gbrowse2
If you're not using Ubuntu, please change the "www-data" parts to the
appropriate owner's name.
Scott
Hey scott,
i do checked my javascript it was enabled and regarding the error log the
[Tue Apr 21 22:44:21 2015] [error] [client ::1] which: no inkscape in
(/sbin:/usr/sbin:/bin:/usr/bin)
[Tue Apr 21 22:44:21 2015] [error] [client ::1] couldn't create lock file
'/var/lib/gbrowse2/sessions/cgisess.db.lck': Permission denied at
/usr/local/share/perl5/CGI/Session/Driver/db_file.pm line 98.
[Tue Apr 21 22:44:22 2015] [error] [client ::1] CGI::param called in list
context from package Bio::Graphics::Browser2::Render line 69, this can lead
to vulnerabilities. See the warning in "Fetching the value or values of a
single named parameter" at /usr/local/share/perl5/CGI.pm line 408.,
referer: http://localhost.localdomain/cgi-bin/gb2/gbrowse/volvox/
[Tue Apr 21 22:44:22 2015] [error] [client ::1] Reverting coordinates to
last known good region (user probably hit 'back' button). at
http://localhost.localdomain/cgi-bin/gb2/gbrowse/volvox/
[Tue Apr 21 22:44:22 2015] [error] [client ::1] Use of uninitialized
value $name in pattern match (m//) at
http://localhost.localdomain/cgi-bin/gb2/gbrowse/volvox/
[Tue Apr 21 22:44:22 2015] [error] [client ::1] Use of uninitialized
value $name in pattern match (m//) at
http://localhost.localdomain/cgi-bin/gb2/gbrowse/volvox/
[Tue Apr 21 22:44:22 2015] [error] [client ::1] Use of uninitialized
value $name in pattern match (m//) at
http://localhost.localdomain/cgi-bin/gb2/gbrowse/volvox/
[Tue Apr 21 22:44:22 2015] [error] [client ::1] Use of uninitialized
value in concatenation (.) or string at
http://localhost.localdomain/cgi-bin/gb2/gbrowse/volvox/
[Tue Apr 21 22:44:22 2015] [error] [client ::1] Can't call method
"seq_id" on an undefined value at
/usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 2058.,
referer: http://localhost.localdomain/cgi-bin/gb2/gbrowse/volvox/
[Tue Apr 21 22:44:22 2015] [error] [client ::1] Premature end of script
http://localhost.localdomain/cgi-bin/gb2/gbrowse/volvox/
regards,
Iti gupta
Hello Iti,
Please make sure that javascript is turned on, as that is what you'd see
if it's not. Also, can you please check the apache error log for
messages? If something is going wrong during the creation of that image,
you'd see the message there.
Scott
Post by Iti GuptaDear sir/mam,
I am having an error while following one of your tutorial: Generic
Genome Browser Version 2: A Tutorial for Administrators.
In this i am able to see the genomic browser but not able to see the
blue tracks of genes in my browser.
Have checked all the path and other related issues as mention in your
tutorial.
Kindly help me to fix the issue.
I have attached a ppt containing screen shot of my browser.
Please find the attachment.
Thanks and Regards,
Iti Gupta
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GMOD Coordinator (http://gmod.org/) 216-392-3087
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--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain
dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research