[BioC] Potential bug in package("rtracklayer") undefined symbol regcompA
Thornton, Matthew
Matthew.Thornton at med.usc.edu
Fri Apr 19 18:20:05 CEST 2013
Hi Michael and Dan!
Thank you! I should have thought about the include directions. I removed the boost include and it installed fine.
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
From: Michael Lawrence [lawrence.michael at gene.com]
Sent: Friday, April 19, 2013 4:27 AM
To: Dan Tenenbaum
Cc: Thornton, Matthew; bioconductor at r-project.org
Subject: Re: [BioC] Potential bug in package("rtracklayer") undefined symbol regcompA
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 at fhcrc.org> wrote:
On Thu, Apr 18, 2013 at 2:01 PM, Thornton, Matthew
<Matthew.Thornton at 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 at med.usc.edu
>
> _______________________________________________
> Bioconductor mailing list
>
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