[Bioperl-l] Installing BioPerl1.5/DBD/Gbrowse 1.6.2 on MacOSX
10.3.9
Sam Kalat
sam.kalat at gmail.com
Mon Apr 25 08:43:52 EDT 2005
I recently started to move some of my bioinformatics work from a Linux
machine to a Mac. I can't help you with gbrowse yet, but I might be
able to help with some of its prerequisites like GD.
I compiled GD from source, and found that in its initial state my
machine did not have the JPEG and PNG libraries. I installed these
through fink, although in hindsight I would have probably done them by
hand.
My config.log reminds me that this is what I used for my configure
step with GD (libgd):
$ ./configure --with-jpeg=/sw --disable-gif
The --with-jpeg directing to /sw is because that is the root folder
for fink, so YMMV. I recall being very confused about some errors
relating to GIF. I was never sure if the GIF libraries were missing
due to its patent nonsense or what, and I had not encountered that
error before on Linux or Solaris. But the --disable-gif was enough
for me. I can't say if I have the same errors as you, your compile
messages are encoded in some non-ascii format and I'm too lazy to
figure out how to convert it.
Subsequently when I installed the GD perl module under CPAN, I had to
use 'look GD' and run the make steps by hand, to tell it that libgd
had installed in /usr/local/lib rather than /usr/lib. At least I
think that's what I did, all I actually wrote down was that I was
having problems with paths.
I also installed perl from source so that I could compile additional
modules that we need, that in turn require perl headers that don't
come by default with the mac. YMMV there too, but it is something to
watch out for, and then you'll have two perls on your hands.
Good luck,
Sam Kalat
On 4/22/05, David Adelson <david.adelson at tamu.edu> wrote:
> 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/darwin-thread-multi-2level
> /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/darwin-thread-multi-2level
> /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)
> /Library/Perl/5.8.1/darwin-thread-multi-2level/Bio/Graphics/Browser/Util.pm:
> 158
> STACK Bio::Graphics::Browser::Util::open_database
> /Library/Perl/5.8.1/darwin-thread-multi-2level/Bio/Graphics/Browser/Util.pm:
> 158
> 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
> sql_common.h
>
> So, my DBD problem is probably still a problem, but much less clear to me
> now.
>
> 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.
>
> Dave
>
> Versions of stuff being used:
> Bundle Bundle::BioPerl (C/CR/CRAFFI/Bundle-BioPerl-2.1.5.tar.gz)
> bioperl-1.5.0 from source
> gd-2.0.33
> zlib-1.2.2
> libpng-1.2.8-config
> jpeg-6b
> GD-2.23
> DBD-mysql-2.9006
> 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
> powerpc
> 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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