[BioC] Potential bug in package("rtracklayer") undefined symbol regcompA

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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> 
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> Search the archives: 
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