I modified all the env variables as proposed but failed to build libs (below a copy of the errors returned) I am not able to fish the origin of this myself please help I would like to use a lot of Jim's executables on my laptop for genome annotations and more.
Your help would be very welcome Thanks Stephane ========== did all exactly as in http://bergman-lab.blogspot.com/2009_03_01_archive.html only diff I see is MySQL version: 5.1.34 / OS X 10.5.7 (MBP 2,4GHz intel core duo) ====== # added to .profile and sourced MACHTYPE=i386 # (was i386-apple-darwin9.0) OSTYPE=darwin # (was darwin9.0) # obtained from mysql_config --libs (-L'/sw/lib/mysql' -lmysqlclient - lz -lm -L/sw/lib) MYSQLLIBS='/sw/lib/mysql/libmysqlclient.a -lz -lm -L/sw/lib' # obtainede from mysql_config --include MYSQLINC=/sw/include/mysql export MACHTYPE OSTYPE MYSQLINC MYSQLLIBS ======= BUILDING STEPS 1) >~/bin/jksrc/kent/src/lib$ make ... gff3.c:8:20: error: values.h: No such file or directory gff3.c: In function ‘gff3FileOpen’: gff3.c:864: error: ‘MAXINT’ undeclared (first use in this function) gff3.c:864: error: (Each undeclared identifier is reported only once gff3.c:864: error: for each function it appears in.) make: *** [gff3.o] Error 1 2) >~/bin/jksrc/kent/src/lib$ cd ../jkOwnLib/ >~/bin/jksrc/kent/src/jkOwnLib$ make ... no error message here OK! 3) >~/bin/jksrc/kent/src/jkOwnLib$ cd .. >~/bin/jksrc/kent/src$ make gcc -O -Wall -Werror -Wformat -Wimplicit -Wreturn-type - Wuninitialized -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE - D_GNU_SOURCE -DMACHTYPE_i386 -Wall -Werror -Wformat -Wimplicit - Wreturn-type -Wuninitialized -I../inc -I../../inc -I../../../inc - I../../../../inc -I../../../../../inc -o gff3.o -c gff3.c gff3.c:8:20: error: values.h: No such file or directory gff3.c: In function ‘gff3FileOpen’: gff3.c:864: error: ‘MAXINT’ undeclared (first use in this function) gff3.c:864: error: (Each undeclared identifier is reported only once gff3.c:864: error: for each function it appears in.) make[1]: *** [gff3.o] Error 1 make: *** [topLibs] Error 2 nothing in /bin/i386 HELP! -- email: [email protected] BITS - VIB headquarters, Rijvisschestraat 120, BE-9052 Gent, Belgium website: http://www.bits.vib.be/index.php NEW! http://sites.google.com/site/dmbits/ phone: +32 9 244 66 11, fax: +32 9 244 66 10 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
