Good Morning Jeremy: Please verify the -m64 flag was used during the build of the libraries. Go to src/lib and run the 'file' command on an object file there, for example:
$ cd src/lib $ file wormdna.o wormdna.o: Mach-O 64-bit object x86_64 And, verify your wigToBigWig is compiled correctly: $ cd ../utils/wigToBigWig $ file *.o wigToBigWig.o: Mach-O 64-bit object x86_64 They should both indicate this 64 bit type. --Hiram Jeremy Simon wrote: > Hi, > I would like to run the wigToBigWig conversion on my Mac Pro for > fixedStep formatted wiggle files (>3B lines) generated for human data. > I tried installed the pre-compiled i386 binary (available at > http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/) > but this clearly did not run in 64-bit, as I received an "out of > memory" error. I also usually see 64-bit jobs marked as "Intel (64- > bit)" under Activity Monitor and this job prior to its failure was > listed only as "Intel". > > I next tried to compile it myself from source using the following steps: > > Set the following environment variables: > export MACHTYPE=x86_64 > export MYSQLLIBS="/sw/lib/mysqlclient.a -lz -lm" > export MYSQLINC="/sw/include/mysql" > Compile the kent libraries using "make libs" in the /path/to/kent/src > directory. > > Run 'make' within the /path/to/kent/src/utils/wigToBigWig directory. > Run wigToBigWig from the newly-created $HOME/$MACHTYPE directory. > > This also failed to run in 64-bit and failed with the same "out of > memory" error. Note that I also tried running the pre-compiled 64-bit > binary for linux, but this gives a "cannot execute binary file" error. > > Lastly, I saw a suggestion on the web somewhere to modify the > "common.mk" file to include "-m64" in the CCFLAGS. After making this > change, I ran a "make clean" then "make libs" in the /kent/src > directory. I then ran "make" in the utils/wigToBigWig directory and > got the following error: > > > ######## > gcc -O -g -Wall -Wno-unused-variable -D_FILE_OFFSET_BITS=64 - > D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -m64 -DUSE_SSL - > DCOLOR32 -Wall -Wno-unused-variable -I../inc -I../../inc -I../../../ > inc -I../../../../inc -I../../../../../inc -o wigToBigWig.o -c > wigToBigWig.c > gcc -O -g -Wall -Wno-unused-variable -o /Users/Jeremy/bin/x86_64/ > wigToBigWig wigToBigWig.o ../../lib/x86_64/jkweb.a -lssl -lcrypto - > lpng -lm -lz > ld warning: in wigToBigWig.o, file is not of required architecture > ld warning: in ../../lib/x86_64/jkweb.a, file is not of required > architecture > Undefined symbols: > "_main", referenced from: > start in crt1.10.5.o > ld: symbol(s) not found > collect2: ld returned 1 exit status > make: *** [wigToBigWig] Error 1 > ######## > > Right now I'm at a loss as to what to try next. Do you have any > suggestions? > > Thanks, > > > ========================================== > Jeremy Simon > Graduate Student > Davis and Lieb labs > University of North Carolina at Chapel Hill > 21-241 Lineberger Comprehensive Cancer Center > Chapel Hill, NC 27599 > (919) 966-4340 > ========================================== > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
