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
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> Search the archives:
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>

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