Re: gbrowse2 on Lion, Apache, error log...

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Re: gbrowse2 on Lion, Apache, error log...

Scott Cain
Hi Bert,

Your problems start with the line that has this in it:

  Can't locate Bio/Graphics.pm

The GBrowse cgi can't find Bio::Graphics.  Is it installed, and if it is, is it in one of the directories listed as part of the @INC in the error message?  I believe you said before that you were using macports for some installation (like libgd I imagine); where do things installed with macports go?  I'd guess that's the problem.

Scott



On Mon, May 5, 2014 at 1:40 PM, Bert Gold <[hidden email]> wrote:
Hi!  You are welcome to post to list.

When I now hit the yeast demo at http://theta2.ncifcrf.gov/theta/Documents.html
under the simple yeast (first one), I get apache error with following error_log in
/var/log/apache2

Mon May 05 13:32:37 2014] [error] [client <a href="tel:66.249.76.125" value="+16624976125" target="_blank">66.249.76.125] script not found or unable to stat: /Library/WebServer/CGI-Executables/gbrowse
[Mon May 05 13:32:38 2014] [error] [client 101.226.166.236] script not found or unable to stat: /Library/WebServer/CGI-Executables/gbrowse_img, referer: http://theta2.ncifcrf.gov/cgi-bin/gbrowse_img/yeast/?name=chrI:143000..180000;type=Centro%3Aoverview+Landmarks%3Aregion+Genes+CDS+tRNAs+Transp;width=800;id=c7905e1d18718c2b558211b179130612;format=GD::SVG;keystyle=between;grid=1
[Mon May 05 13:32:39 2014] [error] [client 101.226.166.241] script not found or unable to stat: /Library/WebServer/CGI-Executables/gbrowse_img, referer: http://theta2.ncifcrf.gov/cgi-bin/gbrowse_img/yeast/?name=chrI:143000..180000;type=Centro%3Aoverview+Landmarks%3Aregion+Genes+CDS+tRNAs+Transp;width=800;id=bff35982c3139b457781660c7b3aa42f;format=GD::SVG;keystyle=between;grid=1
[Mon May 05 13:32:40 2014] [error] [client 101.226.166.235] script not found or unable to stat: /Library/WebServer/CGI-Executables/gbrowse_img, referer: http://theta2.ncifcrf.gov/cgi-bin/gbrowse_img/yeast/?name=chrI:143000..180000;type=Centro%3Aoverview+Landmarks%3Aregion+Genes+CDS+tRNAs+Transp;width=800;id=db5402d95ad9d26898156eb269f51410;format=GD::SVG;keystyle=between;grid=1
[Mon May 05 13:32:43 2014] [error] [client 101.226.166.236] script not found or unable to stat: /Library/WebServer/CGI-Executables/gbrowse_img, referer: http://theta2.ncifcrf.gov/cgi-bin/gbrowse_img/yeast/?name=chrI:143000..180000;type=Centro%3Aoverview+Landmarks%3Aregion+Genes+CDS+tRNAs+Transp;width=800;id=e5d2d16515b00bf32232877fcb480391;format=GD::SVG;keystyle=between;grid=1
[Mon May 05 13:32:43 2014] [error] [client 101.226.166.242] script not found or unable to stat: /Library/WebServer/CGI-Executables/gbrowse_img, referer: http://theta2.ncifcrf.gov/cgi-bin/gbrowse_img/yeast/?name=chrI:143000..180000;type=Centro%3Aoverview+Landmarks%3Aregion+Genes+CDS+tRNAs+Transp;width=800;id=e89b3711087e93da9e6213a707ff0868;format=GD::SVG;keystyle=between;grid=1
[Mon May 05 13:32:48 2014] [error] [client 101.226.166.239] script not found or unable to stat: /Library/WebServer/CGI-Executables/gbrowse_img, referer: http://theta2.ncifcrf.gov/cgi-bin/gbrowse_img/yeast/?name=chrI:143000..180000;type=Centro%3Aoverview+Landmarks%3Aregion+Genes+CDS+tRNAs+Transp;width=800;id=eafabe5ea5c28827cf03454afafcbf17;format=GD::SVG;keystyle=between;grid=1
[Mon May 05 13:32:48 2014] [error] [client 101.226.166.235] script not found or unable to stat: /Library/WebServer/CGI-Executables/gbrowse_img, referer: http://theta2.ncifcrf.gov/cgi-bin/gbrowse_img/yeast/?name=chrI:143000..180000;type=Centro%3Aoverview+Landmarks%3Aregion+Genes+CDS+tRNAs+Transp;width=800;id=fa321515a2f241d6dec5dca8935f7dae;format=GD::SVG;keystyle=between;grid=1
[Mon May 05 13:33:32 2014] [error] [client 129.43.64.65] Can't locate Bio/Graphics.pm in @INC (@INC contains: /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.16.3 /opt/local/lib/perl5/vendor_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.16.3 /opt/local/lib/perl5/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/5.16.3 /opt/local/lib/perl5/site_perl /opt/local/lib/perl5/vendor_perl/5.16.1/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.16.1 /opt/local/lib/perl5/vendor_perl/5.16.0/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.16.0 /opt/local/lib/perl5/vendor_perl .) at /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm line 5., referer: http://theta2.ncifcrf.gov/gbrowse2/
[Mon May 05 13:33:32 2014] [error] [client 129.43.64.65] BEGIN failed--compilation aborted at /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm line 5., referer: http://theta2.ncifcrf.gov/gbrowse2/
[Mon May 05 13:33:32 2014] [error] [client 129.43.64.65] Compilation failed in require at (eval 3) line 2., referer: http://theta2.ncifcrf.gov/gbrowse2/
[Mon May 05 13:33:32 2014] [error] [client 129.43.64.65] \t...propagated at /opt/local/lib/perl5/5.16.3/base.pm line 84., referer: http://theta2.ncifcrf.gov/gbrowse2/
[Mon May 05 13:33:32 2014] [error] [client 129.43.64.65] BEGIN failed--compilation aborted at /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Bio/Graphics/Browser2.pm line 9., referer: http://theta2.ncifcrf.gov/gbrowse2/
[Mon May 05 13:33:32 2014] [error] [client 129.43.64.65] Compilation failed in require at /Library/WebServer/CGI-Executables/gb2/gbrowse line 8., referer: http://theta2.ncifcrf.gov/gbrowse2/
[Mon May 05 13:33:32 2014] [error] [client 129.43.64.65] BEGIN failed--compilation aborted at /Library/WebServer/CGI-Executables/gb2/gbrowse line 8., referer: http://theta2.ncifcrf.gov/gbrowse2/
[Mon May 05 13:33:32 2014] [error] [client 129.43.64.65] Premature end of script headers: gbrowse, referer: http://theta2.ncifcrf.gov/gbrowse2/

I am thinking this is an apache configuration or growse/apache configuration issue.

Any help graciously accepted.



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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