[Gmod-help] Re: [Gmod-gbrowse] Help Installing Gmod-UCSC Plugin
Ramiro Costa
costar at childpsych.columbia.edu
Wed Nov 26 08:47:12 EST 2008
Hi All,
First of all thanks a lot for your valuable help.
Regarding the installation, I tried both passing the CCFLAGS parameter
in the Makefile.PL execution and also removing the -Werror from
libucsc/libucsc/Makefile.PL, but still no luck.
I still get the same error (see bellow), perhaps I'm making some mistake
in the installation process so I'm detailing the steps I'm following
bellow just to make sure these are correct:
1) I downloaded the latest Gbrowse version (1.69) and untarred it in a
temp dir
2) I downloaded the Gmod UCSC plug files and untarred in a separate temp
dir
3) I copied all non-CVS files from gmod-ucsc/Generic-Genome-Browser into
the corresponding locations in the GBrowse installation's
Generic-Genome-Browser tree
4) I installed Gbrowse and got the errors bellow.
Please let me know if I'm missing something in the above steps.
Thanks again for the help!
Regards,
Ramiro Costa
====================================================================================
-bash-3.1$ pwd
/var/www/html/gmod_ucsc_plugin/Generic-Genome-Browser-1.69
-bash-3.1$
-bash-3.1$ ls
bin cgi-bin conf DISCLAIMER GGB.def INSTALL lib
libucsc Makefile MANIFEST pm_to_blib README.berkeleydb
README.gff3 README.sessions t
blib Changes contrib docs htdocs install_util libalign
LICENSE Makefile.PL META.yml README README.fedora
README.MacOSX README.Ubuntu TODO
-bash-3.1$
-bash-3.1$ perl Makefile.PL HTDOCS=/var/www/html CONF=/etc/httpd/conf
CGIBIN=/var/www/cgi-bin 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'
----------------------------------------------
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
-bash-3.1$
-bash-3.1$
-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 -Wde-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 hdb.c
hdb.c:8:19: error: mysql.h: No such file or directory
In file included from ../inc/hgColors.h:7,
from ../inc/hCommon.h:7,
from hdb.c:18:
../inc/hvGfx.h: In function âhvGfxAdjXXâ:
../inc/hvGfx.h:47: warning: ISO C90 forbids mixed declarations and code
hdb.c: In function âhTableOrSplitExistsDbâ:
hdb.c:988: warning: ISO C90 forbids mixed declarations and code
hdb.c: In function âfetchTwoBitSeqâ:
hdb.c:1086: warning: ISO C90 forbids mixed declarations and code
hdb.c: In function âseqGetâ:
hdb.c:1462: warning: ISO C90 forbids mixed declarations and code
hdb.c:1466: warning: ISO C90 forbids mixed declarations and code
hdb.c:1476: warning: ISO C90 forbids mixed declarations and code
hdb.c:1481: warning: ISO C90 forbids mixed declarations and code
hdb.c: In function âgetSeqAndIdâ:
hdb.c:1584: warning: ISO C90 forbids mixed declarations and code
hdb.c: In function âloadTrackDbâ:
hdb.c:3553: warning: ISO C90 forbids mixed declarations and code
hdb.c: In function âhTrackDbLoadSuperâ:
hdb.c:3833: warning: ISO C90 forbids mixed declarations and code
make[2]: *** [hdb.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
-bash-3.1$
====================================================================================
>>> Angie Hinrichs <angie at soe.ucsc.edu> 11/25/08 4:38 PM >>>
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 sh> > 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 declara> >
`/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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Developer's
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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>
> > >
> > >
> > >
-------------------------------------------------------------------------
> > > 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
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> > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> >
>
>
>
Software Developer, UCSC CBSE / Genome Bioinformatics Group
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