[BioC] installing biocLite('edgeR') issues

[Dan Tenenbaum]

Hi Markus,



On Mon, Jun 10, 2013 at 10:24 AM, Marinus Pennings <pennings at sc.tamu.edu> wrote:
> Hi,
>
>    I'm installing some bioconductor packages for one of our users. Here are
> the steps:
>
> - dource(http://bioconductor.org/biocLite.R")
> - biocLite()
> - biocLite('edgeR')
>
> The first steps can be executed without any problem but the
> biocLite('edgeR') command causes a lot of errors (below are the first few
> error lines):
>
> =====
> icpc -L/usr/local/lib64 -o edgeR.so R_exact_test_by_deviance.o
> R_loess_by_col.o R_cr_adjust.o R_levenberg.o R_maximize_interpolant.o
> R_one_group.o R_simple_good_turing.o core/adj_coxreid.o core/glm_levenberg.o
> core/glm_one_group.o core/interpolator.o core/fmm_spline.o
> -L/g/software/intelXE/composer_xe_2013/mkl/lib/intel64 -lmkl_intel_lp64
> -lmkl_intel_thread -lmkl_core -lpthread -lm -lifport -lifcoremt -limf -lsvml
> -lm -lipgo -liomp5 -lirc -lpthread -lirc_s -ldl
> /g/software/intelXE/composer_xe_2013.4.183/compiler/lib/intel64/libimf.so:
> warning: warning: feupdateenv is not implemented and will always fail
> /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64/crt1.o: In function
> `_start':
> (.text+0x20): undefined reference to `main'
> R_exact_test_by_deviance.o: In function `R_exact_test_by_deviance':
> /scratch/pennings/tmp/Rtmp5LmotH/R.INSTALL22017e509b8c/edgeR/src/R_exact_test_by_deviance.cpp:19:
> undefined reference to `Rf_isInteger'
> /scratch/pennings/tmp/Rtmp5LmotH/R.INSTALL22017e509b8c/edgeR/src/R_exact_test_by_deviance.cpp:19:
> undefined reference to `Rf_isInteger'
> =====
>
> Seems the problem starts when trying to create lib edgeR.so
>
> Here are the sytem specs  I use:
> R version 3.0.1
> intel compilers v13.1.2
> mkl v11.0.4
>
> When I build R using gcc and without mkl I can install "biocLite('edgeR')"
> without any problems. Anybody had similar problems with intel compilers?
>

These may be just warnings; it's hard to tell with this little bit of output.
Are you able to

library(edgeR)

After this?

Can you please send the complete output of the
biocLite("edgeR")
command as well as the output of sessionInfo()?
Thanks,
Dan


> Thanks,
>   Marinus
>
> --
> ------------------------
> Marinus Pennings
> pennings at sc.tamu.edu
> Supercomputing Facility
> Texas A&M University
>
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