[Bioperl-l] Installing BioPerl1.5/DBD/Gbrowse 1.6.2 on MacOSX 10.3.9

David Adelson david.adelson at tamu.edu
Fri Apr 22 10:48:27 EDT 2005

Dear all,

Thanks for your replies.

Gbrowse from memory adaptor is still not working fully.  I get no graphics
(problems with GD, libgd; see below).

Gbrowse from mysql is not working.  Originally I got this message:
Could not open database.

------------- EXCEPTION  -------------
MSG: Unable to load mysql adaptor: Can't locate Bio/DB/GFF/Adaptor/mysql.pm
in @INC (@INC contains:
/System/Library/Perl/5.8.1 /Library/Perl/5.8.1/darwin-thread-multi-2level
/Library/Perl/5.8.1 /Library/Perl
/Network/Library/Perl/5.8.1 /Network/Library/Perl .) at (eval 19) line 1.

STACK Bio::DB::GFF::new /Library/Perl/5.8.1/Bio/DB/GFF.pm:643
STACK (eval) 
STACK Bio::Graphics::Browser::Util::open_database
STACK main::get_settings /usr/local/apache2/cgi-bin/gbrowse:516
STACK toplevel /usr/local/apache2/cgi-bin/gbrowse:135

I was able to copy mysql.pm up one level in the directory hierarchy and as a
result no longer get this error.  Now I get:
An internal error has occurred

Could not open database.

Can't locate object method "new" via package "Bio::DB::GFF::Adaptor::mysql"
at /Library/Perl/5.8.1/Bio/DB/GFF.pm line 649.

Please contact this site's maintainer (you at example.com) for assistance.

This message, while deliciously ironic (last line) seems much less tractable
to me.  Suggestions made include the possibility that the mysql header files
are not present.  They are in fact present at:

fisher.tamu.edu [/usr/local/mysql/include] % ls
config-os2.h      m_string.h        my_dir.h          my_sys.h
mysql_time.h      sql_state.h
config.h          md5.h             my_getopt.h       my_time.h
mysql_version.h   sslopt-case.h
errmsg.h          merge.h           my_global.h       my_tree.h
mysqld_error.h    sslopt-longopts.h
ft_global.h       my_aes.h          my_handler.h      my_xml.h
mysys_err.h       sslopt-vars.h
hash.h            my_alarm.h        my_list.h         myisam.h
nisam.h           t_ctype.h
heap.h            my_alloc.h        my_net.h          myisammrg.h
queues.h          thr_alarm.h
help_end.h        my_base.h         my_no_pthread.h   myisampack.h
raid.h            thr_lock.h
help_start.h      my_bitmap.h       my_nosys.h        mysql.h
rijndael.h        typelib.h
keycache.h        my_config.h       my_pthread.h      mysql_com.h
sha1.h            violite.h
m_ctype.h         my_dbug.h         my_semaphore.h    mysql_embed.h

So, my DBD problem is probably still a problem, but much less clear to me

As far as the graphics issue is concerned, I thought I had identified the
problem(s).  The problem with GD is that it could not find gd.h which was
not surprising since I could not get libgd to compile.  It seemed that the
header file for fontconfig library was not part of my X11 installation
(Apple X11) which means libgd would not compile (I got this feedback from
correspondence with the author of gd at Boutell.com). After installing the
X11 SDK I can now compile lidgd AND GD!!! However, there were some warnings
during the compile of libgd and the upshot is I still can't get any
graphics:-( .  Jason Stavich (I think) made the comment in an e-mail to me
that I had to be careful about the library versions for gd.  When I compiled
gd I did get some warnings about library versions, but nothing fatal
happened. (see attachment for output from gd and GD compiles)

In the mean time, sorry to keep beating this horse, but it is not quite dead
yet.  Any additional suggestions will be gratefully accepted.


Versions of stuff being used:
Bundle          Bundle::BioPerl (C/CR/CRAFFI/Bundle-BioPerl-2.1.5.tar.gz)
bioperl-1.5.0 from source
MySQL 4.1.8-standard

fisher.tamu.edu% uname -a
Darwin fisher.tamu.edu 7.9.0 Darwin Kernel Version 7.9.0: Wed Mar 30
20:11:17 PST 2005; root:xnu/xnu-517.12.7.obj~1/RELEASE_PPC  Power Macintosh
fisher.tamu.edu % sw_vers
ProductName:    Mac OS X
ProductVersion: 10.3.9
BuildVersion:   7W98

On 04/22/2005 05:02 AM, "Sean Davis" <sdavis2 at mail.nih.gov> wrote:

> Ditto from me.
> Sean
> On Apr 21, 2005, at 8:56 PM, Todd Harris wrote:
>> Hi David -
>> I've been running GBrowse day in and day out on Mac OS X.  If you are
>> having
>> problem installing DBD, I suspect that you need to install the header
>> files
>> for MySQL.
>> Todd
>>> On 4/20/05 1:06 PM, David Adelson wrote:
>>> Has anyone had any luck getting gbrowse 1.6.2 to work on Mac OSX
>>> (10.3.9)?
>>> I am having trouble installing DBD and BioPerl1.5 from source.  I have
>>> wasted way too much time on this today, but if anyone has any tips on
>>> getting these things to install/compile properly I would appreciate
>>> hearing
>>> from you.
>>> Dave Adelson, Texas A&M University
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at portal.open-bio.org
>> http://portal.open-bio.org/mailman/listinfo/bioperl-l

There's no trick to being a humorist when you have the whole government
working for you.
    Will Rogers (1879 - 1935)

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