Somehow you have "-I/usr/local/include/boost" on your compiler line, even though rtracklayer never uses boost. Boost has a regex.h that is overriding the system one and is aliasing 'regcomp' to 'regcompA'. Since Boost is not linked (and it shouldn't be), there is a missing symbol. Michael On Thu, Apr 18, 2013 at 2:11 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > On Thu, Apr 18, 2013 at 2:01 PM, Thornton, Matthew > <matthew.thornton@med.usc.edu> wrote: > > Hello! > > > > I am trying to install the bioconductor package ("rtracklayer"); and I > am getting the following error > > > > Error in dyn.load(file, DLLpath = DLLpath, ...) : > > unable to load shared object > '/usr/local/R/library/rtracklayer/libs/rtracklayer.so': > > /usr/local/R/library/rtracklayer/libs/rtracklayer.so: undefined > symbol: regcompA > > Error: loading failed > > Execution halted > > ERROR: loading failed > > * removing ‘/usr/local/R/library/rtracklayer’ > > > > Is anyone else getting this error? > > > > Here is sessionInfo(); > > > >> sessionInfo(); > > R Under development (unstable) (2013-04-08 r62528) > > > I'm not sure if this is your problem or not, but BioC 2.13 packages > (like rtracklayer 1.21.*) are meant to run under R 3.0.0, not R-devel > (with useDevel() as discussed in > http://www.bioconductor.org/developers/how-to/useDevel/). > > Dan > > > > Platform: x86_64-unknown-linux-gnu (64-bit) > > > > locale: > > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > > [7] LC_PAPER=C LC_NAME=C > > [9] LC_ADDRESS=C LC_TELEPHONE=C > > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] BiocInstaller_1.11.0 > > > > loaded via a namespace (and not attached): > > [1] tools_3.1.0 > > > > Here is the entire output of biocLite("rtracklayer"); > > > > biocLite("rtracklayer"); > > BioC_mirror: http://bioconductor.org > > Using Bioconductor version 2.13 (BiocInstaller 1.11.0), R version 3.1.0. > > Installing package(s) 'rtracklayer' > > trying URL ' > http://bioconductor.org/packages/2.13/bioc/src/contrib/rtracklayer_1 .21.1.tar.gz > ' > > Content type 'application/x-gzip' length 1323428 bytes (1.3 Mb) > > opened URL > > ================================================== > > downloaded 1.3 Mb > > > > * installing *source* package ‘rtracklayer’ ... > > ** libs > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c IRanges_stubs.c -o > IRanges_stubs.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c R_init_rtracklayer.c -o > R_init_rtracklayer.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c bigWig.c -o bigWig.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c chain_io.c -o chain_io.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c twoBit.c -o twoBit.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c handlers.c -o handlers.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c utils.c -o utils.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/bPlusTree.c -o > ucsc/bPlusTree.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/bbiRead.c -o > ucsc/bbiRead.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/bbiWrite.c -o > ucsc/bbiWrite.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/bwgCreate.c -o > ucsc/bwgCreate.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/bwgQuery.c -o > ucsc/bwgQuery.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/cirTree.c -o > ucsc/cirTree.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/common.c -o > ucsc/common.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/dnaseq.c -o > ucsc/dnaseq.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/dnautil.c -o > ucsc/dnautil.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/errabort.c -o > ucsc/errabort.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/hash.c -o > ucsc/hash.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/linefile.c -o > ucsc/linefile.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/localmem.c -o > ucsc/localmem.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/sqlNum.c -o > ucsc/sqlNum.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/zlibFace.c -o > ucsc/zlibFace.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/dystring.c -o > ucsc/dystring.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/hmmstats.c -o > ucsc/hmmstats.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/obscure.c -o > ucsc/obscure.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/pipeline.c -o > ucsc/pipeline.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/rangeTree.c -o > ucsc/rangeTree.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/rbTree.c -o > ucsc/rbTree.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/memalloc.c -o > ucsc/memalloc.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/dlist.c -o > ucsc/dlist.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/udc.c -o ucsc/udc.o > > ucsc/udc.c: In function ‘udcInfoViaHttp’: > > ucsc/udc.c:405:1: warning: implicit declaration of function ‘strptime’ > [-Wimplicit-function-declaration] > > ucsc/udc.c:405:62: warning: comparison between pointer and integer > [enabled by default] > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/net.c -o ucsc/net.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/bits.c -o > ucsc/bits.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/twoBit.c -o > ucsc/twoBit.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/_cheapcgi.c -o > ucsc/_cheapcgi.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/internet.c -o > ucsc/internet.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/https.c -o > ucsc/https.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/base64.c -o > ucsc/base64.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/verbose.c -o > ucsc/verbose.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/os.c -o ucsc/os.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/wildcmp.c -o > ucsc/wildcmp.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -I/usr/local/R/include -DNDEBUG > -D_FILE_OFFSET_BITS=64 -I/usr/lib64 -I/usr/local/include/boost > -I/usr/local/OpenMPI/include -I"/usr/local/R/library/IRanges/include" -O2 > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -g -fPIC > -mavx -march=athlon-fx -mtune=athlon-fx -shared -fopenmp -m64 -O2 -mavx > -march=athlon-fx -mtune=athlon-fx -fopenmp -m64 -c ucsc/_portimpl.c -o > ucsc/_portimpl.o > > /usr/bin/gcc-4.7 -std=gnu99 -m64 -shared -L/usr/lib64 > -L/usr/lib64/OpenBLAS/lib -L/usr/local/OpenMPI/include/ -o rtracklayer.so > IRanges_stubs.o R_init_rtracklayer.o bigWig.o chain_io.o twoBit.o > handlers.o utils.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o > ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.o ucsc/dnaseq.o > ucsc/dnautil.o ucsc/errabort.o ucsc/hash.o ucsc/linefile.o ucsc/localmem.o > ucsc/sqlNum.o ucsc/zlibFace.o ucsc/dystring.o ucsc/hmmstats.o > ucsc/obscure.o ucsc/pipeline.o ucsc/rangeTree.o ucsc/rbTree.o > ucsc/memalloc.o ucsc/dlist.o ucsc/udc.o ucsc/net.o ucsc/bits.o > ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o > ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -lz -pthread > -L/usr/local/R/lib -lR > > installing to /usr/local/R/library/rtracklayer/libs > > ** R > > ** data > > ** demo > > ** inst > > ** preparing package for lazy loading > > Creating a generic function for ‘offset’ from package ‘stats’ in package > ‘rtracklayer’ > > Creating a generic function from function ‘uri’ in package ‘rtracklayer’ > > ** help > > *** installing help indices > > ** building package indices > > ** installing vignettes > > ** testing if installed package can be loaded > > Error in dyn.load(file, DLLpath = DLLpath, ...) : > > unable to load shared object > '/usr/local/R/library/rtracklayer/libs/rtracklayer.so': > > /usr/local/R/library/rtracklayer/libs/rtracklayer.so: undefined > symbol: regcompA > > Error: loading failed > > Execution halted > > ERROR: loading failed > > * removing ‘/usr/local/R/library/rtracklayer’ > > > > The downloaded source packages are in > > ‘/tmp/RtmpkqJXrX/downloaded_packages’ > > Updating HTML index of packages in '.Library' > > Making 'packages.html' ... done > > 1: rtracklayer > > Warning message: > > In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > > installation of package ‘rtracklayer’ had non-zero exit status > > > > Matthew E. Thornton > > > > Research Lab Specialist > > Saban Research Institute > > > > USC/Children’s Hospital Los Angeles > > 513X, Mail Stop 35 > > 4661 W. Sunset Blvd. > > Los Angeles, CA 90027-6020 > > > > matthew.thornton@med.usc.edu > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]