[Gmod-help] Re: [Gmod-gbrowse] Help Installing Gmod-UCSC Plugin
Angie Hinrichs
angie at soe.ucsc.edu
Wed Nov 26 13:34:23 EST 2008
Hi Ramiro,
Thanks for giving that a try, and sorry it's not compiling yet. I see
a couple problems in the commands shown now:
1. It seems like the CCFLAGS are not propagating down all the way.
The compile command that fails seems to have somewhat mangled flags:
"-pipe -Wde-I/usr/include/gdbm" instead of
"-pipe -I/usr/local/include".
2. It is not finding your MySQL client include file mysql.h:
hdb.c:8:19: error: mysql.h: No such file or directory
For #1, perhaps you could try setting CCFLAGS inside
libucsc/libucsc/Makefile.PL instead of on the command line?
For #2, locate the system directory that contains mysql.h and add that
directory to @INC in libucsc/libucsc/Makefile.PL.
Also, can you send the output of gcc -v? Here is what I get:
Reading specs from /usr/lib/gcc/x86_64-redhat-linux/3.4.6/specs
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
--infodir=/usr/share/info --enable-shared --enable-threads=posix
--disable-checking --with-system-zlib --enable-__cxa_atexit
--disable-libunwind-exceptions --enable-java-awt=gtk
--host=x86_64-redhat-linux
Thread model: posix
gcc version 3.4.6 20060404 (Red Hat 3.4.6-9)
Thanks,
Angie
On Wed, 26 Nov 2008, Ramiro Costa wrote:
> 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
> > > > >
> > > > >
> > > > >
> > > >
> -------------------------------------------------------------------------
> > > > > 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>
> > > >
> > > >
> > > >
> -------------------------------------------------------------------------
> > > > 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
> > >
> >
> >
> >
> Software Developer, UCSC CBSE / Genome Bioinformatics Group
>
--
angie at soe.ucsc.edu
Software Developer, UCSC CBSE / Genome Bioinformatics Group
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