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Re: [Gmod-gbrowse] GBrowse error message on 'make install'
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From: Anelda B. <an...@sa...> - 2004-01-13 15:03:01
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Hi Scott, I'll tell you exactly what happened... I had v 1.54 working perfectly (of course had to build perl and get all the other dependencies to work first, but I got that all right), but then I saw your 1.58 release and decided I want to see how that works ;-( And I installed it over everything I had before. It gave the same error message as the one I sent to the mailing list. So I got a terrible fright, removed everything that gets installed when GBrowse is installed, and tried to reinstall 1.54... Now this is what I have :-( Do you think I have to rebuild perl?? Could something that I have done have broken perl or something else?? Thanks for your help so far! Anelda > Hi Anelda, > > I hate to tell you this, but I suspect that the your perl is at fault. > Are you using the perl built by RedHat? If so, I suggest you rebuild > perl from source. It's not hard; you can get the perl source code from > cpan: > > http://www.cpan.org/src/README.html > > If you are using a custom built perl, then I don't know what the problem > is. > > Scott > > On Tue, 2004-01-13 at 02:38, Anelda Boardman wrote: >> Hi Everyone! >> >> I've been trying to install GBrowse 1.54 (with RH9), but got the >> following error message: >> >> [root@jive Generic-Genome-Browser-1.54]# make install >> Writing >> /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi/auto/Generic-Genome-Browser/.packlist >> Appending installation info to >> /usr/lib/perl5/5.8.0/i386-linux-thread-multi/perllocal.pod >> /usr/bin/perl install_util/conf_install.pl 'CGIBIN=/var/www/cgi-bin' >> 'CONF=/etc/httpd/conf' 'PREFIX=/usr/local/apache' >> 'HTDOCS=/var/www/html' Installing sample configuration files... >> /usr/bin/perl install_util/cgi_install.pl 'CGIBIN=/var/www/cgi-bin' >> 'CONF=/etc/httpd/conf' 'PREFIX=/usr/local/apache' >> 'HTDOCS=/var/www/html' Installing gbrowse CGI scripts... >> copying gbrowse to /var/www/cgi-bin/gbrowse at >> install_util/cgi_install.pl line 27. >> copying gbrowse_details to /var/www/cgi-bin/gbrowse_details at >> install_util/cgi_install.pl line 27. >> copying gbrowse_img to /var/www/cgi-bin/gbrowse_img at >> install_util/cgi_install.pl line 27. >> copying gbrowse_syn to /var/www/cgi-bin/gbrowse_syn at >> install_util/cgi_install.pl line 27. >> /usr/bin/perl install_util/htdocs_install.pl 'CGIBIN=/var/www/cgi-bin' >> 'CONF=/etc/httpd/conf' 'PREFIX=/usr/local/apache' >> 'HTDOCS=/var/www/html' Installing stylesheet and images... >> Malformed UTF-8 character (unexpected continuation byte 0xad, with no >> preceding start byte) in substitution iterator at >> install_util/htdocs_install.pl line 198, <IN> line 194. >> Malformed UTF-8 character (unexpected non-continuation byte 0x5b, >> immediately after start byte 0xc6) in substitution iterator at >> install_util/htdocs_install.pl line 198, <IN> line 194. >> Malformed UTF-8 character (unexpected continuation byte 0xb9, with no >> preceding start byte) in substitution iterator at >> install_util/htdocs_install.pl line 198, <IN> line 194. >> Malformed UTF-8 character (unexpected non-continuation byte 0x41, 1 >> byte after start byte 0xee, expected 3 bytes) in substitution iterator >> at install_util/htdocs_install.pl line 198, <IN> line 194. >> Malformed UTF-8 character (unexpected continuation byte 0xa6, with no >> preceding start byte) in substitution iterator at >> install_util/htdocs_install.pl line 198, <IN> line 194. >> >> >> >> => This message continues for about 3 pages and then it ends with: >> >> Malformed UTF-8 character (unexpected end of string) at >> install_util/htdocs_install.pl line 204. >> Making /var/www/html/gbrowse/images... >> Making /var/www/html/gbrowse/images/buttons... >> Making /var/www/html/gbrowse/images/help... >> Installing temporary directory... >> Making /var/www/html/gbrowse/tmp... >> Installing documentation... >> Installing tutorial... >> Installing sample_data... >> Installing contrib... >> Installing sample data files... >> >> >> ############################################################################ >> GBrowse is now installed. Read INSTALL for further setup >> instructions. Go to http://localhost/gbrowse/ for the online tutorial >> and reference manual. >> ############################################################################ >> >> When I open GBrowse it's fine.. displays most things correct BUT only >> for short regions. Its behaviour is very inconsistent. With some of >> the databases it allows me to display up to 10kb with only one or two >> tracks turned on but if I want to display all available tracks for a >> region spanning only 1kb, it would either get stuck on "Transferring >> data from localhost..." forever or declare "Done" with only the header >> of GBrowse being displayed on the screen.... >> >> I've had a look around to try and figure out what to do, but couldn't >> come up with a solution.. Does anybody have any idea what I could do >> to solve this problem?? >> >> Thanks for your help! >> >> Anelda > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. ca...@cs... > GMOD Coordinator (http://www.gmod.org/) 216-392-3087 > Cold Spring Harbor Laboratory |