[BioC] Rsamtools installation

Bruce Hayward medbha at leeds.ac.uk
Fri Mar 30 11:50:31 CEST 2012

Hi Martin,

On 03/29/12 17:21, Martin Morgan wrote:
> On 03/29/2012 04:22 AM, Bruce Hayward wrote:
>> Hi,
>> I'm trying to install Rsamtools (Rsamtools_1.6.3) on a FreeBSD8.2 amd64
>> system with R (R-2.14.2) and quite a few other Bioconductor packages
>> successfully running.
>> I'm running the installation as root btw.
>> The error line is (the full installation output is at the end of this
>> post):
>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>> unable to load shared object
>> '/usr/local/lib/R/library/Rsamtools/libs/Rsamtools.so':
>> /usr/local/lib/R/library/Rsamtools/libs/Rsamtools.so: Undefined symbol
>> "ti_conf_sam"
>> If it isn't a zlib.h problem .... help!
> Hi Bruce -- I don't think it's zlib.h, so revert all those changes 
> (FWIW, the 'devel' version of Rsamtools addresses the problem in the 
> post you cite).

I have deleted everything and started again from Rsamtools_1.6.3.tar.gz
> ti_conf_sam should be defined in libtabix.a
> R CMD nm Rsamtools/src/libtabix.a |grep ti_conf_sam
> 0000000000000060 D ti_conf_sam
While Rsamtools/src/libtabix.a exists it does not contain a reference to 
ti_conf_sam (using the above command) or, apparently, a reference to 
anything else:
 >more Rsamtools/src/libtabix.a

> and Rsamtools.so should be built to find it in the final line of the 
> compilation output below
> gcc46 -std=gnu99 -fpic -shared -L/usr/local/lib 
> -Wl,-rpath=/usr/local/lib/gcc46 -o Rsamtools.so Biostrings_stubs.o 
> IRanges_stubs.o R_init_Rsamtools.o as_bam.o bamfile.o bcffile.o 
> encode.o fafile.o io_sam.o pileupbam.o samtools_patch.o tabixfile.o 
> utilities.o vcffile.o zip_compression.o -fopenmp 
> /usr/local/lib/R/library/Rsamtools/usrlib/libbam.a 
> /usr/local/lib/R/library/Rsamtools/usrlib/libbcf.a 
> /usr/local/lib/R/library/Rsamtools/usrlib/libtabix.a -lz 
> -L/usr/local/lib/R/lib -lR
> I wonder if there is a libtabix.a already under /usr/local/lib
> find /usr/local/lib -name libtabix.a
There is no other libtabix anywhere in /usr.

> Also, I do not have immediate access to gcc 4.6, which appears to be 
> the version you're using?
The FreeBSD ports have gcc47 and gcc48 available (as well as older 

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