Many thanks Eric, your instructions are very useful, would help many others (cc'ing to mart-dev).
cheers syed On Thu, 2008-02-21 at 14:05 -0500, Wooten, Eric wrote: > Just to close the circle: got mart working on 10.5.2 on a MacPro (Intel). > What was necessary in my case, at least: > > a) get rid of any and all existing CPAN-, Fink-, or MacPorts-installed > libraries that biomart is dependent upon (see list in the user-docs). > > b) put: export ARCHFLAGS='-arch i386 -arch ppc -arch ppc64 -arch x86_64' > into ~/.profile > > c) Download, perl Makefile.PL, make or make test, and sudo make install > each and every required dependency, at least initially ensuring that all > four archflags are actually being recognized (even with ARCHFLAGS set in > .profile, CPAN still only wants to build i386 and ppc...the others and, most > critically, the x86_64 variant only seem to get built when you're manually > doing installations from the terminal). > > d) FORGET using the Apple's included Apache at usr/sbin. Mod_perl just will > not work with it. It will seem to test and install without error, but it > won't actually function. Somewhere, something is either not built for > threaded perl (which perl 5.8.8 as included in 10.5 is), or is not x86_64 > compatible, or has some other cryptic problem. Always, always fails to load > properly, at least in terms of martview. > Depending on the contents of your /Library/Perl/5.8.8 folder, you may also > have to get rid of some non-threaded versions of mart-dependencies that lurk > there and ultimately kick errors when you try to launch martview...these > should be pretty obvious when/if they come up but will be specific to your > existing setup. > > e) Now just follow the User-docs description for installing > Apache2/mod_perl (begins on page 9; httpd 2.2.8 and mod_perl 2.0.3 work fine > even though they're marginally newer than the versions specified in the > docs; same goes for all the required perl libraries: newest version works > fine. NB: Readonly is at 1.03, I think the listed 1.13 is a typo). Again, be > sure to point mod_perl at the httpd in your/special/apache/directory. I just > used the very common /usr/local/apache2 (this location won't overwrite any > of the Apple-provided files and is easy to remember). > > f) After running the configure.pl script as described, double check that > /biomart-perl/conf/httpd.conf ends up with the right settings, especially > the proper location of your "special" httpd (ie, in my case it would need to > be /usr/local/apache2/bin/httpd). > > g) Start martview just as described in the docs. A few benign warnings > about AllowOveride appeared, but it loads and works. > > Thanks for all the prompt help and advice along the way. Hopefully this > rather long-winded description is useful to you in some way as you continue > to develop BioMart. The process described probably contains a fair bit of > overkill, but (right or wrong) it's what got the thing working in the end. > > Eric > > > On 2/6/08 10:47 AM, "Syed Haider" <[EMAIL PROTECTED]> wrote: > > > Hi Eric, > > as mentioned by the previous user, mod_perl installation should be > > tested in this case. please reinstall it from source. > > cheers > > syed > > > > > > On Wed, 2008-02-06 at 10:27 -0500, Wooten, Eric wrote: > >> I seem to have gotten around most of the issues by adding some -arch extras > >> to Zlib and Digest::SHA, and ironing out some lingering issues from an > >> older > >> ActivePerl install that was (apparently) confusing matters, and was > >> definitely causing the previous dynaloader issue referenced in the earlier > >> emails...but now I'm getting this error: > >> > >>> Syntax error on line 44 of > >>> /Library/WebServer/Documents/biomart/conf/httpd.conf: > >>> Can't call method "settingsParams" on an undefined value at > >>> /Library/WebServer/Documents/biomart/lib/BioMart/Initializer.pm line > >>> 639.\n > >> > >> An issue that seems very similar was reported here: > >> http://www.mail-archive.com/[email protected]/msg00788.html > >> > >> But the "solution" there is pretty nebulous...sorry to keep bugging you, > >> but > >> do you have any extra insight into this? Otherwise I'll keep tinkering with > >> mod-perl and my apache install, as the poster suggests ultimately worked > >> for > >> him. > >> > >> Eric > >> > >> > >> > >> On 2/4/08 5:33 PM, "Syed Haider" <[EMAIL PROTECTED]> wrote: > >> > >>> Hi Eric, > >>> > >>> On Mon, 2008-02-04 at 17:25 -0500, Wooten, Eric wrote: > >>>> Does this error mean anything to you (in response to sudo /usr/sbin/httpd > >>>> -d > >>>> $PWD -f $PWD/conf/httpd.conf): > >>>> > >>>>> > >>>>> dyld: lazy symbol binding failed: Symbol not found: _Perl_newXS_flags > >>>>> Referenced from: > >>>>> /usr/local/ActivePerl-5.8/site/lib/auto/Digest/SHA/SHA.bundle > >>>>> Expected in: dynamic lookup > >>>>> > >>>>> dyld: Symbol not found: _Perl_newXS_flags > >>>>> Referenced from: > >>>>> /usr/local/ActivePerl-5.8/site/lib/auto/Digest/SHA/SHA.bundle > >>>>> Expected in: dynamic lookup > >>>>> > >>>>> Trace/BPT trap > >>>>> > >>> > >>> pardon my knowledge on this. > >>> > >>>> I think the issue may be that 10.5 includes a 64-bit version of > >>>> apache2...I > >>>> tried making Digest::SHA for x86_64 (and succeeded in quashing a previous > >>>> complaint about incompatible architecture), but now this error turns up > >>>> and > >>>> is particularly uninformative, at least to me. > >>>> > >>>> Should I just compile a separate, 32-bit targeted apache2 and use that? > >>>> Or > >>>> have you heard of successful work-arounds using the version included with > >>>> 10.5? > >>> > >>> Again, I cant suggest anything concrete, I would compile a 32-bit > >>> version and see if it fixes the problem. If this turns out to be the > >>> case, I would appreciate your feedback. > >>> > >>> syed > >>> > >>> > >>> > >>>> Thanks so much for your help to get this far, > >>>> Eric > >>>> > >>>> > >>>> On 2/4/08 12:10 PM, "Syed Haider" <[EMAIL PROTECTED]> wrote: > >>>> > >>>>> yes, i would recommend to have a clean installation. its most certainly > >>>>> because of problematic installation. > >>>>> > >>>>> thanks > >>>>> syed > >>>>> > >>>>> On Mon, 2008-02-04 at 12:05 -0500, Wooten, Eric wrote: > >>>>>> That's the weird part...cpan reports that Exception::Class is up to > >>>>>> date > >>>>>> (1.23). This was actually the first thing I checked. I've verified that > >>>>>> it's > >>>>>> where it thinks it is. Perhaps I should just try reinstalling it? > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> On 2/4/08 12:01 PM, "Syed Haider" <[EMAIL PROTECTED]> wrote: > >>>>>> > >>>>>>> Eric, > >>>>>>> install the following module, it seems missing. > >>>>>>> > >>>>>>> > >> http://search.cpan.org/~drolsky/Exception-Class-1.23/lib/Exception/Class.p>>> > >> >> > >> m > >>>>>>> > >>>>>>> and then redo the configure and restart the server (sudo). > >>>>>>> > >>>>>>> cheers > >>>>>>> syed > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> On Mon, 2008-02-04 at 11:55 -0500, Wooten, Eric wrote: > >>>>>>>> Seems the same (though there's no new entry in the error_log): > >>>>>>>> > >>>>>>>> ecwooten$ sudo /usr/sbin/httpd -d $PWD -f $PWD/conf/httpd.conf > >>>>>>>> Syntax error on line 44 of > >>>>>>>> /Library/WebServer/Documents/biomart/conf/httpd.conf: > >>>>>>>> Can't locate Exception/Class.pm in @INC (@INC contains: > >>>>>>>> /Library/WebServer/Documents/biomart/lib > >>>>>>>> /System/Library/Perl/5.8.8/darwin-thread-multi-2level > >>>>>>>> /System/Library/Perl/5.8.8 > >>>>>>>> /Library/Perl/5.8.8/darwin-thread-multi-2level > >>>>>>>> /Library/Perl/5.8.8 /Library/Perl > >>>>>>>> /Network/Library/Perl/5.8.8/darwin-thread-multi-2level > >>>>>>>> /Network/Library/Perl/5.8.8 /Network/Library/Perl > >>>>>>>> /System/Library/Perl/Extras/5.8.8/darwin-thread-multi-2level > >>>>>>>> /System/Library/Perl/Extras/5.8.8 > >>>>>>>> /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 > >>>>>>>> /Library/Perl/5.8.1 . /Library/WebServer/Documents/biomart) at > >>>>>>>> /Library/WebServer/Documents/biomart/lib/BioMart/Exception.pm line > >>>>>>>> 86.\nBEGIN failed--compilation aborted at > >>>>>>>> /Library/WebServer/Documents/biomart/lib/BioMart/Exception.pm line > >>>>>>>> 86.\nCompilation failed in require at > >>>>>>>> > >>>> /Library/WebServer/Documents/biomart/lib/BioMart/Configuration/DBLocation.p > >>>> >> > >>>>>> > >>>> m > >>>>>>>> line 40.\nBEGIN failed--compilation aborted at > >>>>>>>> > >>>> /Library/WebServer/Documents/biomart/lib/BioMart/Configuration/DBLocation.p > >>>> >> > >>>>>> > >>>> m > >>>>>>>> line 40.\n\t(in cleanup) Can't locate Exception/Class.pm in @INC > >>>>>>>> (@INC > >>>>>>>> contains: /Library/WebServer/Documents/biomart/lib > >>>>>>>> /System/Library/Perl/5.8.8/darwin-thread-multi-2level > >>>>>>>> /System/Library/Perl/5.8.8 > >>>>>>>> /Library/Perl/5.8.8/darwin-thread-multi-2level > >>>>>>>> /Library/Perl/5.8.8 /Library/Perl > >>>>>>>> /Network/Library/Perl/5.8.8/darwin-thread-multi-2level > >>>>>>>> /Network/Library/Perl/5.8.8 /Network/Library/Perl > >>>>>>>> /System/Library/Perl/Extras/5.8.8/darwin-thread-multi-2level > >>>>>>>> /System/Library/Perl/Extras/5.8.8 > >>>>>>>> /Library/Perl/5.8.6/darwin-thread-multi-2level /Library/Perl/5.8.6 > >>>>>>>> /Library/Perl/5.8.1 . /Library/WebServer/Documents/biomart) at > >>>>>>>> /Library/WebServer/Documents/biomart/lib/BioMart/Exception.pm line > >>>>>>>> 86.\nBEGIN failed--compilation aborted at > >>>>>>>> /Library/WebServer/Documents/biomart/lib/BioMart/Exception.pm line > >>>>>>>> 86.\nCompilation failed in require at > >>>>>>>> > >>>> /Library/WebServer/Documents/biomart/lib/BioMart/Configuration/DBLocation.p > >>>> >> > >>>>>> > >>>> m > >>>>>>>> line 40.\nBEGIN failed--compilation aborted at > >>>>>>>> > >>>> /Library/WebServer/Documents/biomart/lib/BioMart/Configuration/DBLocation.p > >>>> >> > >>>>>> > >>>> m > >>>>>>>> line 40.\nCompilation failed in require at > >>>>>>>> /Library/WebServer/Documents/biomart/conf/httpd.conf line 55.\n > >>>>>>>> > >>>>>>>> > >>>>>>>> On 2/4/08 11:53 AM, "Syed Haider" <[EMAIL PROTECTED]> wrote: > >>>>>>>> > >>>>>>>>> Hi Eric > >>>>>>>>> Just for testing sake, try to start the server as sudo. If this > >>>>>>>>> works, > >>>>>>>>> then its definitely write permissions problem. You can fix this by > >>>>>>>>> modifying the httpd.conf manually by adding the user directive. > >>>>>>>>> cheers > >>>>>>>>> syed > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> On Mon, 2008-02-04 at 11:37 -0500, Wooten, Eric wrote: > >>>>>>>>>> Full outputs in the attached file; also attached httpd.conf. > >>>>>>>>>> > >>>>>>>>>> Trying to simplify matters, I used the unmodified > >>>>>>>>>> /registryURLPointer.xml > >>>>>>>>>> file for the --clean configuration that you suggested. I get > >>>>>>>>>> permissions > >>>>>>>>>> errors if I don't use sudo (though it would appear that I have full > >>>>>>>>>> privileges in the folders at issue; maybe this is where the problem > >>>>>>>>>> starts?). > >>>>>>>>>> > >>>>>>>>>> At any rate, got the same end result. > >>>>>>>>>> > >>>>>>>>>> Thanks for taking a look at all this. > >>>>>>>>>> Eric > >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> On 2/2/08 6:36 AM, "Syed Haider" <[EMAIL PROTECTED]> wrote: > >>>>>>>>>> > >>>>>>>>>>> Hi Eric, > >>>>>>>>>>> > >>>>>>>>>>> - send me the onscreen response when you run > >>>>>>>>>>> perl bin/configure.pl -r conf/your_registry.xml --clean > >>>>>>>>>>> > >>>>>>>>>>> - once you run this, it regenerates conf/httpd.conf, send it to > >>>>>>>>>>> me. > >>>>>>>>>>> > >>>>>>>>>>> - kill and restart your sever, and let me know what you get in > >>>>>>>>>>> terminal > >>>>>>>>>>> and send me logs/error_log as well. > >>>>>>>>>>> > >>>>>>>>>>> thanks > >>>>>>>>>>> syed > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> On Fri, 2008-02-01 at 17:04 -0500, Wooten, Eric wrote: > >>>>>>>>>>>> Hi...I'm having problems getting martview running. Upon issuing > >>>>>>>>>>>> this > >>>>>>>>>>>> command: > >>>>>>>>>>>> /usr/sbin/httpd -d $PWD -f $PWD/conf/httpd.conf > >>>>>>>>>>>> > >>>>>>>>>>>> I get this: > >>>>>>>>>>>> Syntax error on line 44 of > >>>>>>>>>>>> /usr/local/biomart-perl/conf/httpd.conf: > >>>>>>>>>>>> Can't locate Exception/Class.pm in @INC (@INC contains: > >>>>>>>>>>>> /usr/local/biomart-perl/lib [...many other paths...] at > >>>>>>>>>>>> /usr/local/biomart-perl/lib/BioMart/Exception.pm line 86.\nBEGIN > >>>>>>>>>>>> failed--compilation aborted at > >>>>>>>>>>>> /usr/local/biomart-perl/lib/BioMart/Exception.pm line > >>>>>>>>>>>> 86.\nCompilation > >>>>>>>>>>>> failed in require at > >>>>>>>>>>>> /usr/local/biomart-perl/lib/BioMart/Configuration/DBLocation.pm > >>>>>>>>>>>> line > >>>>>>>>>>>> 40.\nBEGIN failed--compilation aborted at > >>>>>>>>>>>> /usr/local/biomart-perl/lib/BioMart/Configuration/DBLocation.pm > >>>>>>>>>>>> line > >>>>>>>>>>>> 40.\n\t(in cleanup) > >>>>>>>>>>>> > >>>>>>>>>>>> Needless to say, Exception.pm is indeed at its > >>>>>>>>>>>> httpd.conf-anticipated > >>>>>>>>>>>> location. > >>>>>>>>>>>> Any thoughts on this? I've found some cryptic descriptions of a > >>>>>>>>>>>> problem > >>>>>>>>>>>> not > >>>>>>>>>>>> unlike this in the archive, but no solutions (other than ~"it > >>>>>>>>>>>> started > >>>>>>>>>>>> working"). I'm using Apache 2.2.6 and mod_perl 2.0.2; OSX10.5.1; > >>>>>>>>>>>> martj > >>>>>>>>>>>> 0.6. > >>>>>>>>>>>> > >>>>>>>>>>>> Thanks in advance, > >>>>>>>>>>>> Eric > >>>>>>>>>>>> > >>>>>>>>>>>> > >>>>>>>>>>>> ----------------------- > >>>>>>>>>>>> Eric C. Wooten Ph.D. > >>>>>>>>>>>> Tufts-New England Medical Center > >>>>>>>>>>>> ----------------------- > >>>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> ----------------------- > >>>>>>>>>> Eric C. Wooten Ph.D. > >>>>>>>>>> [EMAIL PROTECTED] > >>>>>>>>>> (617) 636-7433 > >>>>>>>>>> ----------------------- > >>>>>>>>>> > >>>>>>>>>> > >>>>>>>> > >>>>>>>> ----------------------- > >>>>>>>> Eric C. Wooten Ph.D. > >>>>>>>> [EMAIL PROTECTED] > >>>>>>>> (617) 636-7433 > >>>>>>>> ----------------------- > >>>>>>>> > >>>>>> > >>>>>> ----------------------- > >>>>>> Eric C. Wooten Ph.D. > >>>>>> [EMAIL PROTECTED] > >>>>>> (617) 636-7433 > >>>>>> ----------------------- > >>>>>> > >>>> > >>>> ----------------------- > >>>> Eric C. Wooten Ph.D. > >>>> [EMAIL PROTECTED] > >>>> (617) 636-7433 > >>>> ----------------------- > >>>> > >>> > >> > >> ----------------------- > >> Eric C. Wooten Ph.D. > >> [EMAIL PROTECTED] > >> (617) 636-7433 > >> ----------------------- > >> > > > > ----------------------- > Eric C. Wooten Ph.D. > [EMAIL PROTECTED] > (617) 636-7433 > ----------------------- >
