[BioC] Potential bug in package("rtracklayer") undefined symbol regcompA
Thornton, Matthew
Matthew.Thornton at med.usc.edu
Thu Apr 18 23:01:08 CEST 2013
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)
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 at med.usc.edu
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