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 > ----------------------- >
