Hi Syed, Could you please let me know how to add mod_deflate.so? when I ran ./configure --enable-deflate --prefix=/home/software/biomart-perl/apache make install it gave the following errors. so I just try to run : make install , that is the reason I miss mod_deflate.so please let me know how to add mod_deflate.so Thanks, Ray
________________________________ From: Syed Haider [mailto:[email protected]] Sent: Fri 12/4/2009 1:54 PM To: Jing, Rui Cc: Junjun Zhang; [email protected] Subject: Re: [mart-dev] errors when starting martview Hi Ray, you apaache needs the following module: mod_deflate.so as stated in the exception. Cheers Syed Jing, Rui wrote: > Hi, > > When I ran, it giave the following errors > /usr/local/apache2/bin/httpd -d $PWD -f $PWD/conf/httpd.conf > httpd: Syntax error on line 36 of /home/software/biomart-perl/conf/httpd.conf: > Cannot load /usr/local/apache2/modules/mod_deflate.so into server: > /usr/local/apache2/modules/mod_deflate.so: cannot open shared object file: No > such file or directory > > Could you please let me know the reason? > > Thanks, > > Ray > > > > > > ________________________________ > > From: Junjun Zhang [mailto:[email protected]] > Sent: Thu 12/3/2009 12:35 AM > To: Jing, Rui; Syed Haider > Cc: Arek Kasprzyk; [email protected] > Subject: RE: [mart-dev] errors when starting martview > > > > >> -----Original Message----- >> From: Jing, Rui [mailto:[email protected]] >> Sent: Thursday, December 03, 2009 12:13 AM >> To: Syed Haider >> Cc: Junjun Zhang; Arek Kasprzyk; [email protected] >> Subject: RE: [mart-dev] errors when starting martview >> >> Hi Syed, >> >> when I ran, it gave the following info. >> >>> /common/home/software/biomart-perl/apache/bin/httpd -d $PWD -f >> $PWD/conf/httpd.conf >> Processing Cached Registry: >> /common/home/software/biomart-perl/conf/cachedRegistries/martD >> BLocation.xml.cach >> ed >> >> then I try to visit biomart >> http://node01.com:8011/biomart-perl/martview >> it does not work. > > It looks fine when you start apache. Please try this URL instead: > > http://node01.com:8011/biomart/martview or just try this one > http://node01.com:8011/ (there is a link on this page that takes you to > martview). > > That should work. > > Cheers, > Junjun > > > > >> Could you please let me know what the problem is? >> Thanks, >> >> Ray >> >> >> >> ________________________________ >> >> From: Syed Haider [mailto:[email protected]] >> Sent: Thu 11/26/2009 9:59 AM >> To: Jing, Rui >> Cc: Junjun Zhang; Arek Kasprzyk; [email protected] >> Subject: Re: [mart-dev] errors when starting martview >> >> >> >> >> >> Jing, Rui wrote: >>> Hi Syed, >>> >>> Here is screen copy after execute b. >>> by the way, I installed my local biomart into >> /common/home/software/biomart-perl >>> (it is biomart-perl, do I need change settings.conf, >> LOCATION= biomart >>> to LOCATION=biomart-perl ? >> no biomart is just fine, thats what becomes the part of your >> URL, its not the location of biomart-perl on disk. >> >> could you also add the path to apxs or apxs2 in >> setttings.conf and redo the configure with --clean. >> >> once done, please let us know if that works, also send us the >> screen copy of terminal . >> >> thanks >> Syed >> >> >>> [r...@node01 50]> perl bin/configure.pl -r conf/martDBLocation.xml >>> --clean Do you want to install in API only mode [y/n] [n]: >> n Checking >>> prerequisites ...[Looks good] >>> APACHE: /common/home/software/biomart-perl/apache/bin/httpd >>> HOST: localhost >>> PORT: 8011 >>> PROXY: >>> LOCATION: biomart >>> APXS/2: >>> You can change the above configuration by editing >>> "biomart-perl/conf/settings.conf" >>> >>> Got usable Apache in >>> /common/home/software/biomart-perl/apache/bin/httpd, >>> probing for version & ModPerl configuration Have Apache DSO-support >>> and ModPerl library file present, configuring ModPerl >> in >>> httpd.conf. >>> Libdir /common/home/software/biomart-perl/lib is not in >> @INC, adding >>> to @INC Connection parameters of [My BioMart Database] [ OK ] >>> >>> [NEW CONFIGURATION] .... WITH MEMORY [default] default ... >> My BioMart >>> Database ...... 001/001 ... msd >>> ....................................... (RDBMS) >> martdb.ebi.ac.uk:3306 >> ......... >>> -> upgrading to 0.6/0.7 ... OK >>> Setting possible links between datasets >>> ....(scanning) 100% >>> ....(linking) 100% >>> ....(sorting) 100% >>> ....(clustering) 1/1 - 0 remain >>> ....(resolving) 100% >>> Building templates for visible datasets .... 100% Compiling >> templates >>> for visible datasets [1/1] Attribute Panel of Dataset.. :msd [1/1] >>> Filter Panel of Dataset..... :msd >>> >>> Thanks, >>> >>> Ray >>> >>> ________________________________ >>> >>> From: Syed Haider [mailto:[email protected]] >>> Sent: Thu 11/26/2009 9:27 AM >>> To: Jing, Rui >>> Cc: Junjun Zhang; Arek Kasprzyk; [email protected] >>> Subject: Re: [mart-dev] errors when starting martview >>> >>> >>> >>> a- please set the location param in conf/settings.conf to >>> location=biomart >>> >>> b- reconfigure the perl bin/configure.pl.... with --clean switch >>> >>> c- kill and restart apache and then access the URL as: >>> http://node01.com:8011/biomart/martview >>> >>> >>> please send us what see in terminal after executing 'b' >>> >>> thanks >>> Syed >>> >>> >>> >>> >>> Jing, Rui wrote: >>>> Hi Syed, >>>> >>>> Great. It started. >>>> Processing Cached Registry: >>>> >> /common/home/software/biomart-perl/conf/cachedRegistries/martD >> BLocation.xml.cach >>>> ed >>>> >>>> cat logs/httpd.pid >>>> 19006 >>>> >>>> but when I visit hthttp://node01.com:8011/biomart-perl/martview >>>> <http://node01.com:8011/biomart-perl/martview> >>>> it gave error: Oops! This link appears to be broken from IE. >>>> >>>> I used martDBLocation.xml >>>> perl bin/configure.pl -r conf/martDBLocation.xml --clean >>>> >>>> settings.conf is: >>>> 5 >> apacheBinary=/common/home/software/biomart-perl/apache/bin/httpd >>>> 6 serverHost=localhost >>>> 7 port=8011 >>>> 8 # to use proxying set the proxy port below (even >> if its 80) >>>> and set serverHost as your proxy host >>>> 9 proxy= >>>> 10 # if apxs or apxs2 is not in default directory where httpd >>>> lives, you may set this param to point to apxs/2 >>>> 11 apxs= >>>> 12 location=/common/home/software/biomart-perl >>>> 13 >>>> >>>> please advise what the problem is. >>>> Thanks, >>>> >>>> Ray >>>> >>>> ________________________________ >>>> >>>> From: Syed Haider [mailto:[email protected]] >>>> Sent: Thu 11/26/2009 8:39 AM >>>> To: Jing, Rui >>>> Cc: Junjun Zhang; Arek Kasprzyk; [email protected] >>>> Subject: Re: [mart-dev] errors when starting martview >>>> >>>> >>>> >>>> Hi Rui, >>>> >>>> >>>> the only critical error is : >>>> >>>> Syntax error on line 79 of /software/biomart-perl/conf/httpd.conf: >>>> Invalid command 'PerlOptions', perhaps misspelled or defined by a >>>> module not included in the server configuration >>>> >>>> >>>> you would need to see the onscreen instrcutions when you run: >>>> >>>> perl bin/configure.pl..... >>>> >>>> you probably dont have mod_perl or somehting configured correctly. >>>> >>>> >>>> Best, >>>> Syed >>>> >>>> Jing, Rui wrote: >>>>> Hi, >>>>> >>>>> When I am starting martview, there are some error and >> warn, please >>>>> advise >> how >>>> to >>>>> solve the problem. >>>>> >>>>> [r...@]> /software/biomart-perl/apache/bin/httpd -d $PWD -f >>>> $PWD/conf/httpd.conf >>>>> [Thu Nov 26 08:06:56 2009] [warn] Useless use of AllowOverride in >>>>> line 37 of /common/home/hge/software/biomart-perl/conf/httpd.conf. >>>>> [Thu Nov 26 08:06:56 2009] [warn] Useless use of AllowOverride in >>>>> line 45 of /common/home/hge/software/biomart-perl/conf/httpd.conf. >>>>> [Thu Nov 26 08:06:56 2009] [warn] Useless use of AllowOverride in >>>>> line 63 of /common/home/hge/software/biomart-perl/conf/httpd.conf. >>>>> [Thu Nov 26 08:06:56 2009] [warn] Useless use of AllowOverride in >>>>> line 73 of /software/biomart-perl/conf/httpd.conf. >>>>> Syntax error on line 79 of /software/biomart-perl/conf/httpd.conf: >>>>> Invalid command 'PerlOptions', perhaps misspelled or defined by a >>>>> module not included in the server configuration >>>>> >>>>> >>>>> Thanks, >>>>> >>>>> Ray >>>>> >>>>> >>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to >>>>> whom it is addressed. If you believe this e-mail was sent >> to you in >>>>> error and the >> e-mail >>>>> contains patient information, please contact the Partners >> Compliance >> HelpLine >>>> at >>>>> http://www.partners.org/complianceline . If the e-mail >> was sent to >>>>> you in >>>> error >>>>> but does not contain patient information, please contact >> the sender >>>>> and >>>> properly >>>>> dispose of the e-mail. >>>>> >>> >> >> >
