[Gmod-help] gbrowse on ubuntu 64 bit
Dave Clements, GMOD Help Desk
gmodhelp at googlemail.com
Mon Apr 28 16:21:58 EDT 2008
Olaf,
I just reread my e-mail to you, and even I was confused by it.
Install the libc6-dev package and see if that works.
With apologies,
Dave C.
On Mon, Apr 28, 2008 at 1:09 PM, Dave Clements, GMOD Help Desk
<gmodhelp at googlemail.com> wrote:
> Dear Olaf,
>
> I think th emissing header files are causing the "unary *" errors.
> Most, possibly all of the missing header files are in the libc6-dev
> package. There is also a libc6-dev-amd64 package, that may actually
> be the one you want for your machine. I would try installing
> libc6-dev package using APT or Synaptic.
>
> Please let us know if that works.
>
> Thanks,
>
> Dave C
>
>
>
>
>
> On Mon, Apr 28, 2008 at 12:47 PM, Olaf Mueller <olaf-mueller at uiowa.edu> wrote:
> > Dear gmod team,
> >
> > I have installed gbrowse on a ubuntu 7.10 64 bit system (2 quadcore intel
> > Xeon E5410 CPUs). However, the installation didn't work, when I tried to
> > compile the gbrowse package with the DO_XS flag set to true (please find
> > included the attached error_msg file). Are there any additional
> > prerequisites needed for the C alignment subroutines on 64 bit systems?
> >
> > Many thanks and best regards
> >
> >
> > Olaf
> >
> > --
> > Olaf Mueller, Ph.D.
> > Roy J. Carver Center for Comparative Genomics
> > University of Iowa
> > Department of Biological Sciences
> > 303 Biology Building
> > Iowa City, IA 52242
> > Phone: (319) 335 1083
> > Email: olaf-mueller at uiowa.edu
> >
> >
> > root at saccharomyces:~/install/gbrowse# perl gbrowse_netinstall.pl
> > Prototype mismatch: sub main::get: none vs ($) at gbrowse_netinstall.pl
> > line 58
> >
> > About to install GBrowse and all its prerequisites.
> >
> > You will be asked various questions during this process. You can almost
> > always
> > accept the default answer (with a notable exception of libgd on MacOSX;
> > see the documentation on the GMOD website for more information.)
> > The whole process will take several minutes and will generate lots of
> > messages.
> >
> > Press return when you are ready to start!
> >
> > *** Installing Perl files needed for a net-based install ***
> > Dispatching deprecated method 'CPAN::Config::load' to CPAN::HandleConfig
> > Dispatching deprecated method 'CPAN::Config::commit' to CPAN::HandleConfig
> > commit: wrote '/etc/perl/CPAN/Config.pm'
> > CPAN: Storable loaded ok (v2.15)
> > Going to read /root/.cpan/Metadata
> > Database was generated on Mon, 28 Apr 2008 10:29:45 GMT
> > YAML is up to date (0.66).
> > Archive::Zip is up to date (1.23).
> > HTML::Tagset is up to date (3.20).
> > LWP::Simple is up to date (5.810).
> > Archive::Tar is up to date (1.38).
> >
> > *** Installing prerequisites for BioPerl ***
> > GD::SVG is up to date (0.28).
> > IO::String is up to date (1.08).
> > Text::Shellwords is up to date (1.08).
> > CGI::Session is up to date (4.30).
> > File::Temp is up to date (0.20).
> > Class::Base is up to date (0.03).
> > Digest::MD5 is up to date (2.36).
> > Statistics::Descriptive is up to date (2.6).
> > BioPerl is up to date.
> >
> > *** Installing Generic-Genome-Browser ***
> > Downloading
> > http://superb-west.dl.sourceforge.net/sourceforge/gmod/Generic-Genome-Browser--1.68.tar.gz...
> > Unpacking gbrowse.tgz...
> > Apache conf directory? [/etc/apache2]
> > Apache htdocs directory? [/var/www] /www/htdocs
> > Apache cgibin directory? [/usr/lib/cgi-bin] /www/cgi-bin
> > ----------------------------------------------
> > File Paths
> >
> > CONF /etc/apache2
> > HTDOCS /www/htdocs
> > CGIBIN /www/cgi-bin
> > LIB
> > BIN
> > DO_XS 1
> > NONROOT
> > SELINUX
> >
> > (Run perl Makefile.PL -h for help on changing)
> > ----------------------------------------------
> > Checking if your kit is complete...
> > Looks good
> > Checking if your kit is complete...
> > Looks good
> > Writing Makefile for Bio::Graphics::Browser::CAlign
> > Writing Makefile for Generic-Genome-Browser
> > cp lib/Bio/Graphics/Glyph/trace.pm blib/lib/Bio/Graphics/Glyph/trace.pm
> > cp lib/Bio/Graphics/Browser/I18n.pm blib/lib/Bio/Graphics/Browser/I18n.pm
> > cp lib/Bio/Graphics/Browser/Plugin.pm
> > blib/lib/Bio/Graphics/Browser/Plugin.pm
> > cp lib/Bio/Graphics/Browser/Realign.pm
> > blib/lib/Bio/Graphics/Browser/Realign.pm
> > cp lib/Bio/Graphics/Glyph/genscan_transcript.pm
> > blib/lib/Bio/Graphics/Glyph/genscan_transcript.pm
> > cp lib/Bio/Graphics/FeatureFile.pm blib/lib/Bio/Graphics/FeatureFile.pm
> > cp lib/Bio/Graphics/Glyph/wormbase_transcript.pm
> > blib/lib/Bio/Graphics/Glyph/wormbase_transcript.pm
> > cp lib/Bio/DB/GFF/Aggregator/reftranscript.pm
> > blib/lib/Bio/DB/GFF/Aggregator/reftranscript.pm
> > cp lib/Bio/DB/Das/BioSQL/PartialSeqAdaptor.pm
> > blib/lib/Bio/DB/Das/BioSQL/PartialSeqAdaptor.pm
> > cp lib/Bio/DB/Das/BioSQL/BioDatabaseAdaptor.pm
> > blib/lib/Bio/DB/Das/BioSQL/BioDatabaseAdaptor.pm
> > cp lib/Bio/DB/Das/Chado/Segment/Feature.pm
> > blib/lib/Bio/DB/Das/Chado/Segment/Feature.pm
> > cp lib/Bio/Graphics/Glyph/ld_plot.pm blib/lib/Bio/Graphics/Glyph/ld_plot.pm
> > cp lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
> > blib/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
> > cp lib/Bio/DB/GFF/Aggregator/orf.pm blib/lib/Bio/DB/GFF/Aggregator/orf.pm
> > cp lib/Bio/Graphics/Glyph/drosophila_arrow.pm
> > blib/lib/Bio/Graphics/Glyph/drosophila_arrow.pm
> > cp lib/Bio/Graphics/Glyph/spectrogram.pm
> > blib/lib/Bio/Graphics/Glyph/spectrogram.pm
> > cp lib/Bio/Graphics/Browser/PadAlignment.pm
> > blib/lib/Bio/Graphics/Browser/PadAlignment.pm
> > cp lib/Bio/DB/Das/BioSQL/Iterator.pm blib/lib/Bio/DB/Das/BioSQL/Iterator.pm
> > cp lib/Bio/DB/Das/BioSQL/DBAdaptor.pm
> > blib/lib/Bio/DB/Das/BioSQL/DBAdaptor.pm
> > cp lib/Bio/Graphics/Browser.pm blib/lib/Bio/Graphics/Browser.pm
> > cp lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
> > blib/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
> > cp lib/Bio/Graphics/Glyph/ideogram.pm
> > blib/lib/Bio/Graphics/Glyph/ideogram.pm
> > cp lib/Bio/Graphics/Glyph/phased_exons.pm
> > blib/lib/Bio/Graphics/Glyph/phased_exons.pm
> > cp lib/Bio/DB/Das/BioSQL/Segment.pm blib/lib/Bio/DB/Das/BioSQL/Segment.pm
> > cp lib/Bio/Graphics/Browser/PageSettings.pm
> > blib/lib/Bio/Graphics/Browser/PageSettings.pm
> > cp lib/Bio/Graphics/Browser/PluginSet.pm
> > blib/lib/Bio/Graphics/Browser/PluginSet.pm
> > cp lib/CGI/Session/ID/salted_md5.pm blib/lib/CGI/Session/ID/salted_md5.pm
> > cp lib/Bio/DB/GFF/Aggregator/match_gap.pm
> > blib/lib/Bio/DB/GFF/Aggregator/match_gap.pm
> > cp lib/Bio/Graphics/Glyph/heat_map.pm
> > blib/lib/Bio/Graphics/Glyph/heat_map.pm
> > cp lib/CGI/Toggle.pm blib/lib/CGI/Toggle.pm
> > cp lib/Bio/Graphics/Browser/GFFhelper.pm
> > blib/lib/Bio/Graphics/Browser/GFFhelper.pm
> > cp lib/Bio/Graphics/Browser/RemoteSet.pm
> > blib/lib/Bio/Graphics/Browser/RemoteSet.pm
> > cp lib/Bio/Graphics/Glyph/insertion_chromosome.pm
> > blib/lib/Bio/Graphics/Glyph/insertion_chromosome.pm
> > cp lib/Bio/Graphics/Glyph/allele_tower.pm
> > blib/lib/Bio/Graphics/Glyph/allele_tower.pm
> > cp lib/Bio/Graphics/Glyph/pairwise_plot.pm
> > blib/lib/Bio/Graphics/Glyph/pairwise_plot.pm
> > cp lib/Bio/Graphics/Browser/Util.pm blib/lib/Bio/Graphics/Browser/Util.pm
> > cp lib/Bio/DB/Das/Chado.pm blib/lib/Bio/DB/Das/Chado.pm
> > cp lib/Bio/Graphics/Browser/Markup.pm
> > blib/lib/Bio/Graphics/Browser/Markup.pm
> > cp lib/Bio/Graphics/Glyph/heat_map_ideogram.pm
> > blib/lib/Bio/Graphics/Glyph/heat_map_ideogram.pm
> > cp lib/Bio/DB/Das/BioSQL.pm blib/lib/Bio/DB/Das/BioSQL.pm
> > cp lib/Bio/Graphics/Glyph/connector.pm
> > blib/lib/Bio/Graphics/Glyph/connector.pm
> > cp lib/Bio/Graphics/Browser/UploadSet.pm
> > blib/lib/Bio/Graphics/Browser/UploadSet.pm
> > cp lib/Bio/DB/Das/Chado/Segment.pm blib/lib/Bio/DB/Das/Chado/Segment.pm
> > make[1]: Entering directory
> > `/tmp/8guscoqtKl/Generic-Genome-Browser-1.68/libalign'
> > cp CAlign.pm ../blib/lib/Bio/Graphics/Browser/CAlign.pm
> > /usr/bin/perl /usr/share/perl/5.8.8/ExtUtils/xsubpp -typemap
> > /usr/share/perl/5.8/ExtUtils/typemap CAlign.xs > CAlign.xsc && mv
> > CAlign.xsc CAlign.c
> > cc -c -D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS -DDEBIAN
> > -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE
> > -D_FILE_OFFSET_BITS=64 -O2 -DVERSION=\"1.00\" -DXS_VERSION=\"1.00\" -fPIC
> > "-I/usr/lib/perl/5.8/CORE" CAlign.c
> > In file included from CAlign.xs:2:
> > /usr/lib/perl/5.8/CORE/perl.h:420:24: error: sys/types.h: No such file or
> > directory
> > /usr/lib/perl/5.8/CORE/perl.h:451:19: error: ctype.h: No such file or
> > directory
> > /usr/lib/perl/5.8/CORE/perl.h:463:23: error: locale.h: No such file or
> > directory
> > /usr/lib/perl/5.8/CORE/perl.h:480:20: error: setjmp.h: No such file or
> > directory
> > /usr/lib/perl/5.8/CORE/perl.h:486:26: error: sys/param.h: No such file or
> > directory
> > /usr/lib/perl/5.8/CORE/perl.h:491:23: error: stdlib.h: No such file or
> > directory
> > /usr/lib/perl/5.8/CORE/perl.h:496:23: error: unistd.h: No such file or
> > directory
> > /usr/lib/perl/5.8/CORE/perl.h:776:23: error: string.h: No such file or
> > directory
> > /usr/lib/perl/5.8/CORE/perl.h:925:27: error: netinet/in.h: No such file or
> > directory
> > /usr/lib/perl/5.8/CORE/perl.h:929:26: error: arpa/inet.h: No such file or
> > directory
> > /usr/lib/perl/5.8/CORE/perl.h:939:25: error: sys/stat.h: No such file or
> > directory
> > /usr/lib/perl/5.8/CORE/perl.h:961:21: error: time.h: No such file or
> > directory
> > /usr/lib/perl/5.8/CORE/perl.h:968:25: error: sys/time.h: No such file or
> > directory
> > /usr/lib/perl/5.8/CORE/perl.h:975:27: error: sys/times.h: No such file or
> > directory
> > /usr/lib/perl/5.8/CORE/perl.h:982:19: error: errno.h: No such file or
> > directory
> > /usr/lib/perl/5.8/CORE/perl.h:997:25: error: sys/socket.h: No such file or
> > directory
> > /usr/lib/perl/5.8/CORE/perl.h:1024:21: error: netdb.h: No such file or
> > directory
> > /usr/lib/perl/5.8/CORE/perl.h:1127:24: error: sys/ioctl.h: No such file or
> > directory
> > /usr/lib/perl/5.8/CORE/perl.h:1156:23: error: dirent.h: No such file or
> > directory
> > In file included from
> > /usr/lib/gcc/x86_64-linux-gnu/4.1.3/include/syslimits.h:7,
> > from
> > /usr/lib/gcc/x86_64-linux-gnu/4.1.3/include/limits.h:11,
> > from /usr/lib/perl/5.8/CORE/perl.h:1510,
> > from CAlign.xs:2:
> > /usr/lib/gcc/x86_64-linux-gnu/4.1.3/include/limits.h:122:61: error:
> > limits.h: No such file or directory
> > In file included from /usr/lib/perl/5.8/CORE/perl.h:2120,
> > from CAlign.xs:2:
> > /usr/lib/perl/5.8/CORE/handy.h:136:25: error: inttypes.h: No such file or
> > directory
> > In file included from /usr/lib/perl/5.8/CORE/perl.h:2284,
> > from CAlign.xs:2:
> > /usr/lib/perl/5.8/CORE/unixish.h:106:21: error: signal.h: No such file or
> > directory
> > In file included from CAlign.xs:2:
> > /usr/lib/perl/5.8/CORE/perl.h:2421:33: error: pthread.h: No such file or
> > directory
> > In file included from CAlign.xs:2:
> > /usr/lib/perl/5.8/CORE/perl.h:2423: error: expected '=', ',', ';', 'asm' or
> > '__attribute__' before 'perl_os_thread'
> > /usr/lib/perl/5.8/CORE/perl.h:2424: error: expected '=', ',', ';', 'asm' or
> > '__attribute__' before 'perl_mutex'
> > /usr/lib/perl/5.8/CORE/perl.h:2425: error: expected '=', ',', ';', 'asm' or
> > '__attribute__' before 'perl_cond'
> > /usr/lib/perl/5.8/CORE/perl.h:2426: error: expected '=', ',', ';', 'asm' or
> > '__attribute__' before 'perl_key'
> > In file included from /usr/lib/perl/5.8/CORE/iperlsys.h:51,
> > from /usr/lib/perl/5.8/CORE/perl.h:2733,
> > from CAlign.xs:2:
> > /usr/lib/perl/5.8/CORE/perlio.h:65:19: error: stdio.h: No such file or
> > directory
> > In file included from /usr/lib/perl/5.8/CORE/iperlsys.h:51,
> > from /usr/lib/perl/5.8/CORE/perl.h:2733,
> > from CAlign.xs:2:
> > /usr/lib/perl/5.8/CORE/perlio.h:259: error: expected ')' before '*' token
> > /usr/lib/perl/5.8/CORE/perlio.h:262: error: expected '=', ',', ';', 'asm'
> > or '__attribute__' before '*' token
> > /usr/lib/perl/5.8/CORE/perlio.h:265: error: expected '=', ',', ';', 'asm'
> > or '__attribute__' before '*' token
> > /usr/lib/perl/5.8/CORE/perlio.h:268: error: expected declaration specifiers
> > or '...' before 'FILE'
> > In file included from /usr/lib/perl/5.8/CORE/perl.h:2747,
> > from CAlign.xs:2:
> > /usr/lib/perl/5.8/CORE/sv.h:389: error: expected specifier-qualifier-list
> > before 'DIR'
> > In file included from /usr/lib/perl/5.8/CORE/op.h:497,
> > from /usr/lib/perl/5.8/CORE/perl.h:2754,
> > from CAlign.xs:2:
> > /usr/lib/perl/5.8/CORE/reentr.h:72:20: error: pwd.h: No such file or
> > directory
> > /usr/lib/perl/5.8/CORE/reentr.h:75:20: error: grp.h: No such file or
> > directory
> > /usr/lib/perl/5.8/CORE/reentr.h:85:26: error: crypt.h: No such file or
> > directory
> > /usr/lib/perl/5.8/CORE/reentr.h:90:27: error: shadow.h: No such file or
> > directory
> > In file included from /usr/lib/perl/5.8/CORE/op.h:497,
> > from /usr/lib/perl/5.8/CORE/perl.h:2754,
> > from CAlign.xs:2:
> > /usr/lib/perl/5.8/CORE/reentr.h:612: error: field '_crypt_struct' has
> > incomplete type
> > /usr/lib/perl/5.8/CORE/reentr.h:620: error: field '_drand48_struct' has
> > incomplete type
> > /usr/lib/perl/5.8/CORE/reentr.h:624: error: field '_grent_struct' has
> > incomplete type
> > /usr/lib/perl/5.8/CORE/reentr.h:635: error: field '_hostent_struct' has
> > incomplete type
> > /usr/lib/perl/5.8/CORE/reentr.h:654: error: field '_netent_struct' has
> > incomplete type
> > /usr/lib/perl/5.8/CORE/reentr.h:669: error: field '_protoent_struct' has
> > incomplete type
> > /usr/lib/perl/5.8/CORE/reentr.h:684: error: field '_pwent_struct' has
> > incomplete type
> > /usr/lib/perl/5.8/CORE/reentr.h:695: error: field '_servent_struct' has
> > incomplete type
> > /usr/lib/perl/5.8/CORE/reentr.h:710: error: field '_spent_struct' has
> > incomplete type
> > /usr/lib/perl/5.8/CORE/reentr.h:721: error: field '_gmtime_struct' has
> > incomplete type
> > /usr/lib/perl/5.8/CORE/reentr.h:724: error: field '_localtime_struct' has
> > incomplete type
> > /usr/lib/perl/5.8/CORE/reentr.h:771: error: field '_random_struct' has
> > incomplete type
> > /usr/lib/perl/5.8/CORE/reentr.h:772: error: expected
> > specifier-qualifier-list before 'int32_t'
> > In file included from /usr/lib/perl/5.8/CORE/perl.h:2756,
> > from CAlign.xs:2:
> > /usr/lib/perl/5.8/CORE/av.h:13: error: expected specifier-qualifier-list
> > before 'ssize_t'
> > In file included from /usr/lib/perl/5.8/CORE/perl.h:2759,
> > from CAlign.xs:2:
> > /usr/lib/perl/5.8/CORE/scope.h:232: error: expected
> > specifier-qualifier-list before 'sigjmp_buf'
> > In file included from CAlign.xs:2:
> > /usr/lib/perl/5.8/CORE/perl.h:2931: error: expected '=', ',', ';', 'asm' or
> > '__attribute__' before 'getuid'
> > /usr/lib/perl/5.8/CORE/perl.h:2932: error: expected '=', ',', ';', 'asm' or
> > '__attribute__' before 'geteuid'
> > /usr/lib/perl/5.8/CORE/perl.h:2933: error: expected '=', ',', ';', 'asm' or
> > '__attribute__' before 'getgid'
> > /usr/lib/perl/5.8/CORE/perl.h:2934: error: expected '=', ',', ';', 'asm' or
> > '__attribute__' before 'getegid'
> > In file included from CAlign.xs:2:
> > /usr/lib/perl/5.8/CORE/perl.h:3238:22: error: math.h: No such file or
> > directory
> > In file included from /usr/lib/perl/5.8/CORE/perl.h:3881,
> > from CAlign.xs:2:
> > /usr/lib/perl/5.8/CORE/thrdvar.h:85: error: field 'Tstatbuf' has incomplete
> > type
> > /usr/lib/perl/5.8/CORE/thrdvar.h:86: error: field 'Tstatcache' has
> > incomplete type
> > /usr/lib/perl/5.8/CORE/thrdvar.h:91: error: field 'Ttimesbuf' has
> > incomplete type
> > In file included from /usr/lib/perl/5.8/CORE/perl.h:3883,
> > from CAlign.xs:2:
> > /usr/lib/perl/5.8/CORE/intrpvar.h:66: error: expected
> > specifier-qualifier-list before 'time_t'
> > In file included from /usr/lib/perl/5.8/CORE/perl.h:3950,
> > from CAlign.xs:2:
> > /usr/lib/perl/5.8/CORE/proto.h:128: error: expected declaration specifiers
> > or '...' before 'mode_t'
> > /usr/lib/perl/5.8/CORE/proto.h:128: error: expected declaration specifiers
> > or '...' before 'uid_t'
> > /usr/lib/perl/5.8/CORE/proto.h:297: error: expected declaration specifiers
> > or '...' before 'off64_t'
> > /usr/lib/perl/5.8/CORE/proto.h:299: error: expected '=', ',', ';', 'asm' or
> > '__attribute__' before 'Perl_do_sysseek'
> > /usr/lib/perl/5.8/CORE/proto.h:300: error: expected '=', ',', ';', 'asm' or
> > '__attribute__' before 'Perl_do_tell'
> > /usr/lib/perl/5.8/CORE/proto.h:411: error: expected declaration specifiers
> > or '...' before 'gid_t'
> > /usr/lib/perl/5.8/CORE/proto.h:411: error: expected declaration specifiers
> > or '...' before 'uid_t'
> > /usr/lib/perl/5.8/CORE/proto.h:736: error: expected '=', ',', ';', 'asm' or
> > '__attribute__' before 'Perl_my_fork'
> > /usr/lib/perl/5.8/CORE/proto.h:1020: error: expected declaration specifiers
> > or '...' before 'pid_t'
> > /usr/lib/perl/5.8/CORE/proto.h:1300: error: expected declaration specifiers
> > or '...' before 'pid_t'
> > /usr/lib/perl/5.8/CORE/proto.h:1456: error: expected '=', ',', ';', 'asm'
> > or '__attribute__' before '*' token
> > /usr/lib/perl/5.8/CORE/proto.h:2001: error: expected '=', ',', ';', 'asm'
> > or '__attribute__' before 'Perl_PerlIO_read'
> > /usr/lib/perl/5.8/CORE/proto.h:2002: error: expected '=', ',', ';', 'asm'
> > or '__attribute__' before 'Perl_PerlIO_write'
> > /usr/lib/perl/5.8/CORE/proto.h:2003: error: expected '=', ',', ';', 'asm'
> > or '__attribute__' before 'Perl_PerlIO_unread'
> > /usr/lib/perl/5.8/CORE/proto.h:2004: error: expected '=', ',', ';', 'asm'
> > or '__attribute__' before 'Perl_PerlIO_tell'
> > /usr/lib/perl/5.8/CORE/proto.h:2005: error: expected declaration specifiers
> > or '...' before 'off64_t'
> > In file included from /usr/lib/perl/5.8/CORE/perl.h:3988,
> > from CAlign.xs:2:
> > /usr/lib/perl/5.8/CORE/perlvars.h:31: error: expected '=', ',', ';', 'asm'
> > or '__attribute__' before 'PL_thr_key'
> > /usr/lib/perl/5.8/CORE/perlvars.h:48: error: expected '=', ',', ';', 'asm'
> > or '__attribute__' before 'PL_op_mutex'
> > /usr/lib/perl/5.8/CORE/perlvars.h:52: error: expected '=', ',', ';', 'asm'
> > or '__attribute__' before 'PL_dollarzero_mutex'
> > /usr/lib/perl/5.8/CORE/perl.h:4485:24: error: sys/ipc.h: No such file or
> > directory
> > /usr/lib/perl/5.8/CORE/perl.h:4486:24: error: sys/sem.h: No such file or
> > directory
> > /usr/lib/perl/5.8/CORE/perl.h:4611:24: error: sys/file.h: No such file or
> > directory
> > In file included from /usr/lib/perl/5.8/CORE/perlapi.h:38,
> > from /usr/lib/perl/5.8/CORE/XSUB.h:349,
> > from CAlign.xs:3:
> > /usr/lib/perl/5.8/CORE/intrpvar.h:66: error: expected '=', ',', ';', 'asm'
> > or '__attribute__' before '*' token
> > /usr/lib/perl/5.8/CORE/intrpvar.h:237: error: expected '=', ',', ';', 'asm'
> > or '__attribute__' before '*' token
> > /usr/lib/perl/5.8/CORE/intrpvar.h:238: error: expected '=', ',', ';', 'asm'
> > or '__attribute__' before '*' token
> > /usr/lib/perl/5.8/CORE/intrpvar.h:239: error: expected '=', ',', ';', 'asm'
> > or '__attribute__' before '*' token
> > /usr/lib/perl/5.8/CORE/intrpvar.h:240: error: expected '=', ',', ';', 'asm'
> > or '__attribute__' before '*' token
> > In file included from /usr/lib/perl/5.8/CORE/perlapi.h:39,
> > from /usr/lib/perl/5.8/CORE/XSUB.h:349,
> > from CAlign.xs:3:
> > /usr/lib/perl/5.8/CORE/perlvars.h:31: error: expected '=', ',', ';', 'asm'
> > or '__attribute__' before '*' token
> > /usr/lib/perl/5.8/CORE/perlvars.h:48: error: expected '=', ',', ';', 'asm'
> > or '__attribute__' before '*' token
> > /usr/lib/perl/5.8/CORE/perlvars.h:52: error: expected '=', ',', ';', 'asm'
> > or '__attribute__' before '*' token
> > CAlign.xs: In function 'new_row':
> > CAlign.xs:13: warning: incompatible implicit declaration of built-in
> > function 'calloc'
> > CAlign.xs: In function 'realign':
> > CAlign.xs:46: warning: incompatible implicit declaration of built-in
> > function 'strlen'
> > CAlign.xs:49: warning: incompatible implicit declaration of built-in
> > function 'calloc'
> > CAlign.c: In function 'XS_Bio__Graphics__Browser__CAlign__do_alignment':
> > CAlign.c:196: error: invalid type argument of 'unary *'
> > CAlign.c:196: warning: cast to pointer from integer of different size
> > CAlign.c:196: error: invalid type argument of 'unary *'
> > CAlign.c:196: warning: cast to pointer from integer of different size
> > CAlign.c:196: error: invalid type argument of 'unary *'
> > CAlign.c:196: warning: cast to pointer from integer of different size
> > CAlign.c:198: error: invalid type argument of 'unary *'
> > CAlign.c:198: warning: cast to pointer from integer of different size
> > CAlign.c:202: error: invalid type argument of 'unary *'
> > CAlign.c:202: warning: cast to pointer from integer of different size
> > CAlign.c:202: error: invalid type argument of 'unary *'
> > CAlign.c:202: warning: cast to pointer from integer of different size
> > CAlign.c:202: error: invalid type argument of 'unary *'
> > CAlign.c:202: warning: cast to pointer from integer of different size
> > CAlign.c:202: error: invalid type argument of 'unary *'
> > CAlign.c:202: warning: cast to pointer from integer of different size
> > CAlign.c:203: error: invalid type argument of 'unary *'
> > CAlign.c:203: warning: cast to pointer from integer of different size
> > CAlign.c:203: error: invalid type argument of 'unary *'
> > CAlign.c:203: warning: cast to pointer from integer of different size
> > CAlign.c:203: error: invalid type argument of 'unary *'
> > CAlign.c:203: warning: cast to pointer from integer of different size
> > CAlign.c:203: error: invalid type argument of 'unary *'
> > CAlign.c:203: warning: cast to pointer from integer of different size
> > CAlign.c:217: error: invalid type argument of 'unary *'
> > CAlign.c:217: warning: cast to pointer from integer of different size
> > CAlign.c:217: error: invalid type argument of 'unary *'
> > CAlign.c:217: warning: cast to pointer from integer of different size
> > CAlign.c:217: error: invalid type argument of 'unary *'
> > CAlign.c:217: warning: cast to pointer from integer of different size
> > CAlign.c:217: error: invalid type argument of 'unary *'
> > CAlign.c:217: warning: cast to pointer from integer of different size
> > CAlign.c:223: error: invalid type argument of 'unary *'
> > CAlign.c:223: warning: cast to pointer from integer of different size
> > CAlign.xs:207: error: invalid type argument of 'unary *'
> > CAlign.xs:207: warning: cast to pointer from integer of different size
> > CAlign.xs:207: warning: incompatible implicit declaration of built-in
> > function 'strlen'
> > CAlign.xs:208: error: invalid type argument of 'unary *'
> > CAlign.xs:208: warning: cast to pointer from integer of different size
> > CAlign.xs:209: error: invalid type argument of 'unary *'
> > CAlign.xs:209: warning: cast to pointer from integer of different size
> > CAlign.xs:210: error: invalid type argument of 'unary *'
> > CAlign.xs:210: warning: cast to pointer from integer of different size
> > CAlign.xs:211: error: invalid type argument of 'unary *'
> > CAlign.xs:211: warning: cast to pointer from integer of different size
> > CAlign.xs:212: error: invalid type argument of 'unary *'
> > CAlign.xs:212: warning: cast to pointer from integer of different size
> > CAlign.xs:213: error: invalid type argument of 'unary *'
> > CAlign.xs:213: warning: cast to pointer from integer of different size
> > CAlign.xs:214: error: invalid type argument of 'unary *'
> > CAlign.xs:214: warning: cast to pointer from integer of different size
> > CAlign.xs:215: error: invalid type argument of 'unary *'
> > CAlign.xs:215: warning: cast to pointer from integer of different size
> > CAlign.xs:216: error: invalid type argument of 'unary *'
> > CAlign.xs:216: warning: cast to pointer from integer of different size
> > CAlign.xs:217: error: invalid type argument of 'unary *'
> > CAlign.xs:217: warning: cast to pointer from integer of different size
> > CAlign.xs:218: error: invalid type argument of 'unary *'
> > CAlign.xs:218: warning: cast to pointer from integer of different size
> > CAlign.xs:223: error: invalid type argument of 'unary *'
> > CAlign.xs:223: warning: cast to pointer from integer of different size
> > CAlign.xs:223: error: invalid type argument of 'unary *'
> > CAlign.xs:223: warning: cast to pointer from integer of different size
> > CAlign.xs:224: error: invalid type argument of 'unary *'
> > CAlign.xs:224: warning: cast to pointer from integer of different size
> > CAlign.xs:224: warning: incompatible implicit declaration of built-in
> > function 'strlen'
> > CAlign.xs:227: error: invalid type argument of 'unary *'
> > CAlign.xs:227: warning: cast to pointer from integer of different size
> > CAlign.xs:227: error: invalid type argument of 'unary *'
> > CAlign.xs:227: warning: cast to pointer from integer of different size
> > CAlign.xs:229: error: invalid type argument of 'unary *'
> > CAlign.xs:229: warning: cast to pointer from integer of different size
> > CAlign.xs:229: error: invalid type argument of 'unary *'
> > CAlign.xs:229: warning: cast to pointer from integer of different size
> > CAlign.xs:231: error: invalid type argument of 'unary *'
> > CAlign.xs:231: warning: cast to pointer from integer of different size
> > CAlign.xs:231: error: invalid type argument of 'unary *'
> > CAlign.xs:231: warning: cast to pointer from integer of different size
> > CAlign.xs:231: error: invalid type argument of 'unary *'
> > CAlign.xs:231: warning: cast to pointer from integer of different size
> > CAlign.xs:231: error: invalid type argument of 'unary *'
> > CAlign.xs:231: warning: cast to pointer from integer of different size
> > CAlign.xs:232: error: invalid type argument of 'unary *'
> > CAlign.xs:232: warning: cast to pointer from integer of different size
> > CAlign.xs:232: error: invalid type argument of 'unary *'
> > CAlign.xs:232: warning: cast to pointer from integer of different size
> > CAlign.xs:232: error: invalid type argument of 'unary *'
> > CAlign.xs:232: warning: cast to pointer from integer of different size
> > CAlign.xs:232: error: invalid type argument of 'unary *'
> > CAlign.xs:232: warning: cast to pointer from integer of different size
> > CAlign.c:262: error: invalid type argument of 'unary *'
> > CAlign.c:262: warning: cast to pointer from integer of different size
> > CAlign.c: In function 'boot_Bio__Graphics__Browser__CAlign':
> > CAlign.c:273: error: invalid type argument of 'unary *'
> > CAlign.c:273: warning: cast to pointer from integer of different size
> > CAlign.c:273: error: invalid type argument of 'unary *'
> > CAlign.c:273: warning: cast to pointer from integer of different size
> > CAlign.c:273: error: invalid type argument of 'unary *'
> > CAlign.c:273: warning: cast to pointer from integer of different size
> > CAlign.c:276: error: invalid type argument of 'unary *'
> > CAlign.c:276: warning: cast to pointer from integer of different size
> > CAlign.c:276: error: invalid type argument of 'unary *'
> > CAlign.c:276: warning: cast to pointer from integer of different size
> > CAlign.c:276: error: invalid type argument of 'unary *'
> > CAlign.c:276: warning: cast to pointer from integer of different size
> > CAlign.c:276: error: invalid type argument of 'unary *'
> > CAlign.c:276: warning: cast to pointer from integer of different size
> > CAlign.c:276: error: invalid type argument of 'unary *'
> > CAlign.c:276: warning: cast to pointer from integer of different size
> > CAlign.c:276: error: invalid type argument of 'unary *'
> > CAlign.c:276: warning: cast to pointer from integer of different size
> > CAlign.c:276: error: invalid type argument of 'unary *'
> > CAlign.c:276: warning: cast to pointer from integer of different size
> > CAlign.c:276: error: invalid type argument of 'unary *'
> > CAlign.c:276: warning: cast to pointer from integer of different size
> > CAlign.c:276: error: invalid type argument of 'unary *'
> > CAlign.c:276: warning: cast to pointer from integer of different size
> > CAlign.c:276: error: invalid type argument of 'unary *'
> > CAlign.c:276: warning: cast to pointer from integer of different size
> > CAlign.c:276: error: invalid type argument of 'unary *'
> > CAlign.c:276: warning: cast to pointer from integer of different size
> > CAlign.c:278: error: invalid type argument of 'unary *'
> > CAlign.c:278: warning: cast to pointer from integer of different size
> > CAlign.c:278: error: invalid type argument of 'unary *'
> > CAlign.c:278: warning: cast to pointer from integer of different size
> > CAlign.c:279: error: invalid type argument of 'unary *'
> > CAlign.c:279: warning: cast to pointer from integer of different size
> > CAlign.c:279: error: invalid type argument of 'unary *'
> > CAlign.c:279: warning: cast to pointer from integer of different size
> > CAlign.c:279: error: invalid type argument of 'unary *'
> > CAlign.c:279: warning: cast to pointer from integer of different size
> > CAlign.c:279: error: invalid type argument of 'unary *'
> > CAlign.c:279: warning: cast to pointer from integer of different size
> > make[1]: *** [CAlign.o] Error 1
> > make[1]: Leaving directory
> > `/tmp/8guscoqtKl/Generic-Genome-Browser-1.68/libalign'
> > make: *** [subdirs] Error 2
> >
> >
> >
>
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