[Gmod-help] Re: [Gmod-gbrowse] Help Installing Gmod-UCSC Plugin
Angie Hinrichs
angie at soe.ucsc.edu
Tue Nov 25 14:38:30 EST 2008
Hi Lincoln and Ramiro,
I agree with Dave that it is necessary to remove the
-Wdeclaration-after-statement from the compile command. The UCSC code
has many instances of variable declarations following statements. And
in case of other gotchas, it wouldn't hurt to also remove -Werror.
I believe Makefile.PL gets some of its settings from the local perl
installation, i.e. if perl was compiled with those CCFLAGS, they
automatically are picked up by ExtUtils::MakeMaker. (Correct me if
I'm wrong, those with more MakeMaker experience.)
Ramiro, here is something to try next: invoke Makefile.PL with a
trimmed-down CCFLAGS on the command line, like this (no linebreaks):
perl Makefile.PL CCFLAGS='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm'
And you can modify libucsc/libucsc/Makefile.PL to remove the -Werror
if you like.
If that doesn't work, please send the failing make output like you did
below.
Thanks,
Angie
On Tue, 25 Nov 2008, Lincoln Stein wrote:
> 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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> > > >
> > >
> > >
> > >
> > > --
> > > 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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> > prizes
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> > world
> > > http://moblin-contest.org/redirect.php?banner_id=100&url=/
> > > _______________________________________________
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> >
>
>
>
>
--
angie at soe.ucsc.edu
Software Developer, UCSC CBSE / Genome Bioinformatics Group
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