Angie, I have realized that after I stumbled for a long while and tried a few other tricks. I have successfully compiled the uscs genome browser last Friday, but I just forgot to write back to the list.
I am also glad that I am able to use the new "defaultGenome: option in my configuration file to configure a minimum ucsc genome browser without referencing to an empty hg18 genome. Thank you very much for your help. On 02/11/2011 02:52 PM, Angie Hinrichs wrote: > Hi Zhi-Wei, > > Thank you for reporting this bug. I just pushed a fix to our main git > repository (commit id 625a9fdc), but it may take some time to appear on the > public server. > > The bug affects only compiles without the environment variable USE_BAM=1, > which is set in our default compile for development. If you would like > support for BAM data in your browser mirror (and fewer compile bugs :), see > http://genomewiki.ucsc.edu/index.php/Build_Environment_Variables . > > Hope that helps and please write back to the list if you encounter any more > trouble or have questions. > > Angie > > > ----- "Zhi-Wei Lu" <[email protected]> wrote: > >> From: "Zhi-Wei Lu" <[email protected]> >> To: [email protected] >> Sent: Friday, February 11, 2011 9:03:51 AM GMT -08:00 US/Canada Pacific >> Subject: [Genome] error compiling uscs genome browser >> >> Hi, >> >> I am trying to update our uscs genome browser to the latest in git. When >> I tried to make lib, I am getting this error: >> >> bamFile.c:816: error: conflicting types for ‘bamOpen’ >> ../inc/bamFile.h:66: error: previous declaration of ‘bamOpen’ was here >> cc1: warnings being treated as errors >> bamFile.c:847: warning: ‘struct samfile_t’ declared inside parameter list >> bamFile.c:847: warning: its scope is only this definition or >> declaration, which is probably not what you want >> bamFile.c:850: error: conflicting types for ‘bamReadNextSamAlignments’ >> ../inc/bamFile.h:62: error: previous declaration of >> ‘bamReadNextSamAlignments’ was here >> make[1]: *** [bamFile.o] Error 1 >> make[1]: Leaving directory >> `/gbdb2/src/ucsc_genome_browser/kent/src/hg/lib' >> make: *** [hgLib] Error 2 >> >> Does anyone know what the problem is, am I missing something? >> >> I am working on a CentOS 5.5 x86_64 system. >> >> Thank you. >> >> -- >> Zhi-Wei Lu >> Bioinformatics Core >> Genome Center >> University of California, Davis >> (530) 752-2698 >> >> >> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome -- Zhi-Wei Lu Bioinformatics Core Genome Center University of California, Davis (530) 752-2698 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
