Please do not run the make of trackDb in the source tree. Move your private track .ra files out of the source tree and follow the instructions in src/product/README.trackDb
Plus, it appears your binary hgTrackDb is out of date. If you have a new source tree, build all of the utilities and track loaders. --Hiram ----- Original Message ----- From: "WANG Wuqi" <[email protected]> To: "Hiram Clawson" <[email protected]> Cc: [email protected], "WANG Wuqi" <[email protected]> Sent: Tuesday, March 15, 2011 11:03:01 PM Subject: RE: [Genome] Upgrade UCSC genome browser Hi Hiram, Thanks a lot. Previous problems already are fixed depending on your advice. I already upgraded Genome browser from v218 to v247 with MySQL 5.1.54. In my source tree, I still use old directory .../trackDb/*, this is because I have myself customer data, and I can upload data but to encounter when I compile, error message the following: ............................................................... $ cd /home/wangp/jksrc/kent/src/hg/makeDb/trackDb $ make alpha DBS=hg18 find . -type l -exec rm {} \; ./loadTracks -release=alpha trackDb hgFindSpec hg18 hgTrackDb -priority=human/priority.ra -release=alpha human hg18 trackDb ../../lib/trackDb.sql . -priority is not a valid option make: *** [alpha] Error 255 ............................................................... Please give me some advice Best & Regards Wuqi -----Original Message----- From: Hiram Clawson [mailto:[email protected]] Sent: Wednesday, March 16, 2011 7:27 AM To: WANG Wuqi Cc: [email protected] Subject: Re: [Genome] Upgrade UCSC genome browser Good Afternoon: Please edit the src/hg/hgTables/makefile and remove the --executability argument from the rsyncDataOpts list. If you encounter this again in a different makefile, perform the same edit. We will be removing this argument from the source tree. --Hiram ================================================================= To encounter the following errors when I upgrade this genome browser from version 218 to 247: $ cd jksrc/kent/src/hg $ make compile $ make install ..., chmod g+w hgTables chmod a+rx hgTables rm -f /var/www/var/www/hgTables mv hgTables /var/www/var/www/hgTables rm -f /var/www/var/www/all.joiner cp ../makeDb/schema/all.joiner /var/www/var/www rm -rf /var/www/var/www/greatData rsync --times --recursive --executability --omit-dir-times --cvs-exclude --delete greatData /var/www/var/www/ rsync: --executability: unknown option rsync error: syntax or usage error (code 1) at main.c(1084) make[1]: *** [install] Error 1 make[1]: Leaving directory `/home/wangp/jksrc/kent/src/hg/hgTables' make: *** [hgTables.install] Error 2 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
