[BioC] The installation of XVector

[Hervé Pagès]

On 04/21/2014 12:34 AM, 管锐 wrote:
> Hi,

Hi,

Please use the "Reply All" button so the discussion stays on the mailing
list. Thanks!

> The IRanges I installed is version 1.22.2, the XVector depends IRanges
>  >1.21.25.
> Because the cluster computer is unable to connect to Internet, I used
> the command "R CMD INSTALL XVctor" to install the packges.

If you must absolutely use 'R CMD INSTALL' to install packages, you
should do it on the package source tarballs, not on the source tree.
The source tree can contain stalled .o or .so files that will only
cause problems. So:

   R CMD INSTALL IRanges_1.22.3.tar.gz
   R CMD INSTALL XVector_0.4.0.tar.gz

in *that* order.

Cheers,
H.


> And I have checked the LD_LIBRARY_PATH.
> Thanks!
>
> Sincerely,
> GUAN
>
>
>
> 2014-04-21 13:33 GMT+08:00 Hervé Pagès <hpages at fhcrc.org
> <mailto:hpages at fhcrc.org>>:
>
>     Hi,
>
>
>     On 04/20/2014 08:29 PM, GUAN Rui [guest] wrote:
>
>         Error in dyn.load(file, DLLpath = DLLpath, ...) :
>         unable to load shared object
>         '/guanrui/soft/R-3.1.0/__library/XVector/libs/XVector.__so':
>         /guanrui/soft/R-3.1.0/library/__XVector/libs/XVector.so:
>         undefined symbol: hold_IRanges
>               Error: loading failed
>               Execution halted
>               ERROR: loading failed"
>
>
>     How are you trying to install this? Are you sure your version of IRanges
>     is current?
>
>     Always use biocLite() to install Bioconductor packages.
>     See http://bioconductor.org/__install/
>     <http://bioconductor.org/install/>
>
>     Cheers,
>     H.
>
>
>
>            -- output of sessionInfo():
>
>         R version 3.1.0 (2014-04-10)
>         Platform: x86_64-unknown-linux-gnu (64-bit)
>
>         locale:
>         [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
>         [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
>         [5] LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915
>         [7] LC_PAPER=en_US.iso885915       LC_NAME=C
>         [9] LC_ADDRESS=C                   LC_TELEPHONE=C
>         [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C
>
>         attached base packages:
>         [1] stats     graphics  grDevices utils     datasets  methods   base
>
>
>         --
>         Sent via the guest posting facility at bioconductor.org
>         <http://bioconductor.org>.
>
>
>     --
>     Hervé Pagès
>
>     Program in Computational Biology
>     Division of Public Health Sciences
>     Fred Hutchinson Cancer Research Center
>     1100 Fairview Ave. N, M1-B514
>     P.O. Box 19024
>     Seattle, WA 98109-1024
>
>     E-mail: hpages at fhcrc.org <mailto:hpages at fhcrc.org>
>     Phone:  (206) 667-5791
>     Fax:    (206) 667-1319
>
>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319