[Gmod-help] Re: [Gmod-gbrowse] Help Installing Gmod-UCSC Plugin

Tue Nov 25 13:45:00 EST 2008

Hi Angie,

Ramiro Costa is having problems with the UCSC plugin, and is probably the
first outsider to attempt this. Here is the original correspondence and Dave
Clement's analysis of the problem. Do you have any suggestions for a fix?

Lincoln

On Tue, Nov 25, 2008 at 12:55 PM, Dave Clements, GMOD Help Desk <
gmodhelp at googlemail.com> wrote:

> Hi Ramiro,
>
> The problem appears to be that
>
> 1. The file axt.c contains a C variable declaration after a C
> statement (not a problem in itself)
> 2. The makefile specifically asks the C compiler for a warning when
> that happens. (-Wdeclaration-after-statement)
> 3. The makefile specifically asks for all warnings to be promoted to
> fatal compile errors. (-Werror)
>
> However, I can't find anywhere in the Makefile.PL file for either
> GBrowse or the UCSC plugin where they specifically ask for the
> -Wdeclaration-after-statement or -Werror options on C compilations.
>
> Is it possible these options are coming from the local environment?
> If you get rid of these 2 otpions it should compile (or at least get
> farther).
>
> Does anyone with a better understanding of Makefile.PL have a suggestion?
>
> Thanks,
>
> Dave C.
>
> Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback
>
>
> On Sat, Nov 22, 2008 at 4:55 AM, Ramiro Costa
> <costar at childpsych.columbia.edu> wrote:
> >
> > Hi Lincoln,
> >
> > Thanks for your installation instructions. Here is what I get when I try
> > the installation (note the Warning line bellow):
> >
> > =======================================================
> > perl Makefile.PL HTDOCS=/var/www/html CONF=/etc/httpd/conf
> > CGIBIN=/var/www/cgi-bin
> >
> > ----------------------------------------------
> >                File Paths
> >
> >  APACHE /usr/local/apache
> >   CONF /etc/httpd/conf
> >  HTDOCS /var/www/html
> >  CGIBIN /var/www/cgi-bin
> >    LIB
> >    BIN
> >  DO_XS 1
> > NONROOT
> > SELINUX
> >
> > (Run perl Makefile.PL -h for help on changing)
> > ----------------------------------------------
> > Writing Makefile for Bio::Graphics::Browser::CAlign
> > Warning: -L./libucsc changed to
> >
> -L/var/www/html/gmod_ucsc_plugin/Generic-Genome-Browser-1.69/libucsc/./libucsc
> > Note (probably harmless): No library found for -lucsc
> > Writing Makefile for Bio::Graphics::Browser::UcscTrackImage::libucsc
> > Writing Makefile for Bio::Graphics::Browser::UcscTrackImage
> > Writing Makefile for Generic-Genome-Browser
> > =======================================================
> >
> > Then, when I try to proceed with the installation, I get the following:
> >
> > =======================================================
> > -bash-3.1$ make
> > make[1]: Entering directory
> > `/var/www/html/gmod_ucsc_plugin/Generic-Genome-Browser-1.69/libalign'
> > gcc -c   -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
> > -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
> > -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2 -g -pipe -Wall
> > -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> > --param=ssp-buffer-size=4 -m64 -mtune=generic   -DVERSION=\"1.00\"
> > -DXS_VERSION=\"1.00\" -fPIC
> > "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE"   CAlign.c
> > Running Mkbootstrap for Bio::Graphics::Browser::CAlign ()
> > chmod 644 CAlign.bs
> > rm -f ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
> > gcc  -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
> > -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic CAlign.o
> >  -o ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so         \
> >                \
> >
> > chmod 755 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.so
> > cp CAlign.bs ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs
> > chmod 644 ../blib/arch/auto/Bio/Graphics/Browser/CAlign/CAlign.bs
> > Manifying ../blib/man3/Bio::Graphics::Browser::CAlign.3pm
> > make[1]: Leaving directory
> > `/var/www/html/gmod_ucsc_plugin/Generic-Genome-Browser-1.69/libalign'
> > make[1]: Entering directory
> > `/var/www/html/gmod_ucsc_plugin/Generic-Genome-Browser-1.69/libucsc'
> > cd libucsc && make
> > make[2]: Entering directory
> >
> `/var/www/html/gmod_ucsc_plugin/Generic-Genome-Browser-1.69/libucsc/libucsc'
> > gcc -c  -I/usr/local/include -I/usr/include -I../inc -D_REENTRANT
> > -D_GNU_SOURCE -fno-strict-aliasing -pipe -Wdeclaration-after-statement
> > -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
> > -I/usr/include/gdbm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
> > -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64
> > -mtune=generic   -DVERSION=\"\" -DXS_VERSION=\"\" -fPIC
> > "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE"  -DGBROWSE
> > -Wall -Werror axt.c
> > cc1: warnings being treated as errors
> > axt.c: In function âaxtGetSubsetOnTâ:
> > axt.c:358: warning: ISO C90 forbids mixed declarations and code
> > make[2]: *** [axt.o] Error 1
> > make[2]: Leaving directory
> >
> `/var/www/html/gmod_ucsc_plugin/Generic-Genome-Browser-1.69/libucsc/libucsc'
> > make[1]: *** [libucsc/libucsc.a] Error 2
> > make[1]: Leaving directory
> > `/var/www/html/gmod_ucsc_plugin/Generic-Genome-Browser-1.69/libucsc'
> > make: *** [subdirs] Error 2
> > =======================================================
> >
> >
> > Do you know why could this be.
> >
> > Thanks a lot!!
> >
> > Regards,
> > Ramiro
> >
> > >>> "Lincoln Stein" <lincoln.stein at gmail.com> 11/12/08 1:39 PM >>>
> > Hi Ramiro,
> > The instructions assume that you have downloaded and unpacked GBrowse
> > into
> > your home directory and have not yet installed it. Go to www.gmod.org,
> > download the tar file for the 1.69 release:
> >
> > http://sourceforge.net/project/showfiles.php?group_idUnpack it into your
> home directory, and then proceed from there. Not
> > many
> > people have tried the UCSC plugin install, so please let me know what
> > your
> > experience is!
> >
> > Lincoln
> >
> > On Wed, Nov 12, 2008 at 10:20 AM, Ramiro Costa <
> > costar at childpsych.columbia.edu> wrote:
> >
> > > Hi All,
> > >
> > > I'm trying to install the Gmod-UCSC plugin to be able to load UCSC
> > tracks
> > > into Gbrowse.
> > >
> > > I followed the instructions given in the tutorial (
> > > http://gmod.org/wiki/GBrowse_UCSC_Plugin_Install_HOWTO) but still not
> > > clear to me.
> > > I downloaded the plugin but got stuck at the installing step. The
> > tutorial
> > > says I should copy all non-CVS files from
> > gmod-ucsc/Generic-Genome-Browser/
> > > into the corresponding locations in my GBrowse installation's
> > > Generic-Genome-Browser tree. When I search for the
> > Generic-Genome-Browser
> > > tree, I only found an empty dir except for a hidden file named
> > ".packlist".
> > > The location of this dir is the following:
> > >
> > >
> > >
> >
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/Generic-Genome-Browser
> > >
> > > Is this the correct place to install the plugin? Would someone please
> > > elaborate on the plugin installation steps?
> > >
> > > Thanks in advance!
> > >
> > > Regards,
> > >
> > > Ramiro
> > >
> > >
> > >
> > -------------------------------------------------------------------------
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> > > _______________________________________________
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> > > Gmod-gbrowse at lists.sourceforge.net
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> > >
> >
> >
> >
> > --
> > Lincoln D. Stein
> >
> > Ontario Institute for Cancer Research
> > 101 College St., Suite 800
> > Toronto, ON, Canada M5G0A3
> > 416 673-8514
> > Assistant: Stacey Quinn <Stacey.Quinn at oicr.on.ca>
> >
> > Cold Spring Harbor Laboratory
> > 1 Bungtown Road
> > Cold Spring Harbor, NY 11724 USA
> > (516) 367-8380
> > Assistant: Sandra Michelsen <michelse at cshl.edu>
> >
> >
> > -------------------------------------------------------------------------
> > This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> > Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> > Grand prize is a trip for two to an Open Source event anywhere in the
> world
> > http://moblin-contest.org/redirect.php?banner_id=100&url=/
> > _______________________________________________
> > Gmod-gbrowse mailing list
> > Gmod-gbrowse at lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>

-- 
Lincoln D. Stein

Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Stacey Quinn <Stacey.Quinn at oicr.on.ca>

Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724 USA
(516) 367-8380
Assistant: Sandra Michelsen <michelse at cshl.edu>
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