It worked! Thanks.. But then it broke again: pbCalResStdGlobal.c: In function main: pbCalResStdGlobal.c:233: error: ignoring return value of "system", declared with attribute warn_unused_result pbCalResStdGlobal.c:237: error: ignoring return value of "system", declared with attribute warn_unused_result pbCalResStdGlobal.c:240: error: ignoring return value of "fgets", declared with attribute warn_unused_result pbCalResStdGlobal.c:247: error: ignoring return value of "system", declared with attribute warn_unused_result pbCalResStdGlobal.c:258: error: ignoring return value of "fgets", declared with attribute warn_unused_result pbCalResStdGlobal.c:262: error: ignoring return value of "fgets", declared with attribute warn_unused_result pbCalResStdGlobal.c:268: error: ignoring return value of "fgets", declared with attribute warn_unused_result pbCalResStdGlobal.c:272: error: ignoring return value of "fgets", declared with attribute warn_unused_result make[2]: *** [pbCalResStdGlobal.o] Error 1 make[2]: Leaving directory `/home/ivan/setupGB/kent/src/hg/protein/pbCalResStdGlobal' make[1]: *** [pbCalResStdGlobal.utils] Error 2 make[1]: Leaving directory `/home/ivan/setupGB/kent/src/hg/protein' make: *** [protein.utils] Error 2
Ivan ________________________________________ From: Ann Zweig [[email protected]] Sent: Wednesday, March 03, 2010 1:55 PM To: Smirnov, Ivan Cc: [email protected] Subject: Re: [Genome] hgTrackDb errors Hello Ivan, One of our developers suggests that you change that line to: safef(previous, sizeof(previous), "%s", row[0]); then recompile. Be sure to let us know if this does not fix the problem. In the future, please send emails specific to your mirror site to this mailing list: [email protected]. Regards, ---------- Ann Zweig UCSC Genome Bioinformatics Group http://genome.ucsc.edu Smirnov, Ivan wrote: > When I try to make new src (v225) it breaks with: > > hgSuggest.c: In function 'main': > hgSuggest.c:74: error: format not a string literal and no format arguments > make[1]: *** [hgSuggest.o] Error 1 > make[1]: Leaving directory `/home/ivan/setupGB/kent/src/hg/hgSuggest' > make: *** [hgSuggest.bins] Error 2 > > I am running Ubuntu server 9.04, gcc version 4.3.3 > > Any ideas? > > Thanks > Ivan > > ________________________________________ > From: Jennifer Jackson [[email protected]] > Sent: Tuesday, March 02, 2010 4:26 PM > To: Smirnov, Ivan > Cc: [email protected] > Subject: Re: [Genome] hgTrackDb errors > > Hello, > > There have been some changes that need to be put into place for your > mirror to function correctly. Specifically, hgTrackDb and tdbQuery need > to be updated. Both are called when you do a make in the trackDb directory. > > https://lists.soe.ucsc.edu/pipermail/genome-mirror/2010-February/001584.html > https://lists.soe.ucsc.edu/pipermail/genome-mirror/2010-February/001599.html > > --------------------------------- > Jennifer Jackson > UCSC Genome Bioinformatics Group > http://genome.ucsc.edu/ > > On 3/2/10 12:41 PM, Smirnov, Ivan wrote: >> Hi, >> >> after I installed the most current Kent's source jksrc.v225.zip on my GB >> mirror (hg18 only), I am getting a lot of errors while rebuilding >> hg18.trackDB from the corresponding trackDb.ra files: >> >> Error: 'wgEncodeUwDGF' missing shortLabels or sortOrder setting is >> inconsistent. >> Error: 'wgEncodeUwChIPSeq' missing shortLabels or sortOrder setting is >> inconsistent. >> Error: 'wgEncodeGisPet' missing shortLabels or sortOrder setting is >> inconsistent. >> Error: 'wgEncodeSunyalbanyRnaGeneChip' missing shortLabels or sortOrder >> setting is inconsistent. >> Error: 'wgEncodeCshlShortRnaSeq' missing shortLabels or sortOrder setting is >> inconsistent. >> Error: 'wgEncodeRikenCage' missing shortLabels or sortOrder setting is >> inconsistent. >> Error: 'wgEncodeHudsonalphaChipSeq' missing shortLabels or sortOrder setting >> is inconsistent. >> Error: 'barskiChIPseq' missing shortLabels or sortOrder setting is >> inconsistent. >> Error: 'wgEncodeHudsonalphaRnaSeq' missing shortLabels or sortOrder setting >> is inconsistent. >> Error: 'wgEncodeHudsonalphaCnv' missing shortLabels or sortOrder setting is >> inconsistent. >> Error: 'wgEncodeUmasshaTfbsValid' missing shortLabels or sortOrder setting >> is inconsistent. >> Error: 'wgEncodeChromatinMap' missing shortLabels or sortOrder setting is >> inconsistent. >> Error: 'zhaoLabNucleosome' missing shortLabels or sortOrder setting is >> inconsistent. >> Error: 'wgEncodeCshlLongRnaSeq' missing shortLabels or sortOrder setting is >> inconsistent. >> Error: 'wgEncodeCaltechRnaSeq' missing shortLabels or sortOrder setting is >> inconsistent. >> Error: 'wgEncodeMapability' missing shortLabels or sortOrder setting is >> inconsistent. >> Error: 'wgEncodeBroadChipSeq' missing shortLabels or sortOrder setting is >> inconsistent. >> Error: 'wgEncodeGisDnaPet' missing shortLabels or sortOrder setting is >> inconsistent. >> Error: 'wgEncodeAffyRnaChip' missing shortLabels or sortOrder setting is >> inconsistent. >> Error: 'wgEncodeGisRnaSeq' missing shortLabels or sortOrder setting is >> inconsistent. >> Error: 'wgEncodeUwDnaseSeq' missing shortLabels or sortOrder setting is >> inconsistent. >> Error: 'wgEncodeNhgriNre' missing shortLabels or sortOrder setting is >> inconsistent. >> Error: 'wgEncodeYaleChIPseq' missing shortLabels or sortOrder setting is >> inconsistent. >> >> followed by 2000+ "parent X missing for subtrack Y" messages. >> >> Is it because those the new .ra files are broken, or I am doing something >> wrong? >> >> Thanks >> Ivan >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
