We run a mirror of the UCSC site. After our latest rsync we are getting errors during the "make" step. They appear to be related to SAMtools sam.h and bam.h. Are these a new prerequisite for mirroring the UCSC site? Or, are they supposed to be included in the mirroring step?
>> Making source version=[227] [/home/ucsc/bin/mirror_scripts/make_jksrc.sh >> /ucsc/db2/ucsc_mirror_src/kent/src /home/ucsc/logs/build.log] | Tue Apr 13 >> 09:52:14 2010 In file included from validateFiles.c:9: ../../inc/bamFile.h:10:17: error: bam.h: No such file or directory ../../inc/bamFile.h:11:17: error: sam.h: No such file or directory In file included from validateFiles.c:9: ../../inc/bamFile.h:21: error: expected declaration specifiers or â...â before âbam_fetch_fâ cc1: warnings being treated as errors ../../inc/bamFile.h:26: warning: type defaults to âintâ in declaration of âbam1_tâ ../../inc/bamFile.h:26: error: expected â;â, â,â or â)â before â*â token ../../inc/bamFile.h: In function âbamUnpackCigarElementâ: ../../inc/bamFile.h:36: error: âBAM_CIGAR_SHIFTâ undeclared (first use in this function) ../../inc/bamFile.h:36: error: (Each undeclared identifier is reported only once ../../inc/bamFile.h:36: error: for each function it appears in.) ../../inc/bamFile.h:37: error: âBAM_CIGAR_MASKâ undeclared (first use in this function) ../../inc/bamFile.h: At top level: ../../inc/bamFile.h:47: warning: type defaults to âintâ in declaration of âbam1_tâ ../../inc/bamFile.h:47: error: expected â;â, â,â or â)â before â*â token ../../inc/bamFile.h:53: warning: type defaults to âintâ in declaration of âbam1_tâ ../../inc/bamFile.h:53: error: expected â;â, â,â or â)â before â*â token ../../inc/bamFile.h:59: warning: type defaults to âintâ in declaration of âbam1_tâ ../../inc/bamFile.h:59: error: expected â;â, â,â or â)â before â*â token ../../inc/bamFile.h:62: warning: type defaults to âintâ in declaration of âbam1_tâ ../../inc/bamFile.h:62: error: expected â;â, â,â or â)â before â*â token ../../inc/bamFile.h:65: warning: type defaults to âintâ in declaration of âbam1_tâ ../../inc/bamFile.h:65: error: expected â;â, â,â or â)â before â*â token ../../inc/bamFile.h:68: warning: type defaults to âintâ in declaration of âbam1_tâ ../../inc/bamFile.h:68: error: expected â;â, â,â or â)â before â*â token ../../inc/bamFile.h:71: warning: type defaults to âintâ in declaration of âbam1_tâ ../../inc/bamFile.h:71: error: expected â;â, â,â or â)â before â*â token ../../inc/bamFile.h:75: warning: type defaults to âintâ in declaration of âbam1_tâ ../../inc/bamFile.h:75: error: expected â;â, â,â or â)â before â*â token ../../inc/bamFile.h:80: error: expected â=â, â,â, â;â, âasmâ or â__attribute__â before â*â token ../../inc/bamFile.h:83: warning: type defaults to âintâ in declaration of âbam1_tâ ../../inc/bamFile.h:83: error: expected â;â, â,â or â)â before â*â token ../../inc/bamFile.h:86: warning: type defaults to âintâ in declaration of âbam1_tâ ../../inc/bamFile.h:86: error: expected â;â, â,â or â)â before â*â token validateFiles.c:1061: warning: type defaults to âintâ in declaration of âbam1_tâ validateFiles.c:1061: error: expected â;â, â,â or â)â before â*â token validateFiles.c: In function âvalidateBAMâ: validateFiles.c:1122: error: âsamfile_tâ undeclared (first use in this function) validateFiles.c:1122: error: âfhâ undeclared (first use in this function) validateFiles.c:1122: warning: implicit declaration of function âsamopenâ validateFiles.c:1127: error: âbam_header_tâ undeclared (first use in this function) validateFiles.c:1127: error: âheadâ undeclared (first use in this function) make[2]: *** [validateFiles.o] Error 1 make[1]: *** [encode/validateFiles.utils] Error 2 make: *** [utils] Error 2 -- Wes Barris _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
