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Question: Error installing cummeRbund/Rsamtools
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gravatar for rainer.rutka
20 months ago by
rainer.rutka10
Germany/Konstanz/University of Konstanz
rainer.rutka10 wrote:

Hi!
I try to install the R plugin cummeRbund at our cluster-system in the university of Konatanz. Unfortunately, I get an error while installing the Rsamtools-plugin.

These are the environments i use:

UC:[kn@uc1n997 2.13.1]$ module list
Currently Loaded Modulefiles:
  1) compiler/intel/15.0(default)   3) math/R/3.2.1
  2) numlib/mkl/11.2.3(default)
UC:[kn@uc1n997 2.13.1]$

In R i did this:

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.2 (BiocInstaller 1.20.1), ?biocLite for help

> biocLite("Rsamtools")

[...]

This is the output i get some minutes later:

"/pfs/data2/home/kn/kn_kn/kn/R/x86_64-unknown-linux-gnu-library/3.2/IRanges/include" -I"/pfs/data2/home/kn/kn_kn/kn/R/x86_64-unknown-linux-gnu-library/3.2/XVector/include" -I"/pfs/data2/home/kn/kn_kn/kn/R/x86_64-unknown-linux-gnu-library/3.2/Biostrings/include"   -fpic  -O3 -std=c++11 -fp-model strict -openmp -xHost  -c bam_mate_iter.cpp -o bam_mate_iter.o

/usr/include/c++/4.4.7/bits/stl_pair.h(90): error: a value of type "long" cannot be used to initialize an entity of type "const bam1_t *"
        second(std::forward<_U2>(__y)) { }
               ^
          detected during instantiation of "std::pair<_T1, _T2>::pair(_U1 &&, _U2 &&) [with _T1=int, _T2=const bam1_t *, _U1=const int &, _U2=long]" at line 173 of "Template.h"

compilation aborted for bam_mate_iter.cpp (code 2)
make: *** [bam_mate_iter.o] Fehler 2
ERROR: compilation failed for package ‘Rsamtools’
* removing ‘/pfs/data2/home/kn/kn_kn/kn/R/x86_64-unknown-linux-gnu-library/3.2/

Same with

> biocLite("cummeRbund")

Any help is much appreciated.

Thanks in advance.

rainer.rutka@uni-konstanz.de

ADD COMMENTlink modified 20 months ago • written 20 months ago by rainer.rutka10

Can you provide just a little more of the output, to capture the compiler (which I guess is intel) and possibly other flags? I have 

clang-3.5 -std=c++11 -O3 -I/home/mtmorgan/bin/R-devel/include -DNDEBUG  -I/usr/local/include -I"/home/mtmorgan/R/x86_64-pc-linux-gnu-library/3.3/S4Vectors/include" -I"/home/mtmorgan/R/x86_64-pc-linux-gnu-library/3.3/IRanges/include" -I"/home/mtmorgan/R/x86_64-pc-linux-gnu-library/3.3/XVector/include" -I"/home/mtmorgan/R/x86_64-pc-linux-gnu-library/3.3/Biostrings/include"   -fpic  -c bam_mate_iter.cpp -o bam_mate_iter.o

 

ADD REPLYlink written 20 months ago by Martin Morgan ♦♦ 20k

HI!

The compiler is Intel.

UC:[kn@uc1n997 ~]$ module whatis compiler/intel/15.0
compiler/intel/15.0  : Intel(R) compiler suite (icc, icpc, ifort), debugger (gdb-ia), IPP and TBB ver 15.0.3

[...]
setenv         CC icc
setenv         CXX icpc
setenv         F77 ifort
setenv         FC ifort
setenv         F90 ifort
setenv         TEST_MODULE_SCRIPT /opt/bwhpc/common/compiler/intel/compxe.2015.3.187/install-doc/test-compiler-intel.sh
setenv         TEST_MODULE_NAME compiler/intel/15.0
[...]

Here's the compilation output:

icc -std=gnu99 -I/opt/bwhpc/common/math/R/3.2.1-mkl-11.2.3-intel-15.0/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/pfs/data2/home/kn/kn_kn/kn_pop235844/R/x86_64-unknown-linux-gnu-library/3.2/S4Vectors/include" -I"/pfs/data2/home/kn/kn_kn/kn_pop235844/R/x86_64-unknown-linux-gnu-library/3.2/IRanges/include" -I"/pfs/data2/home/kn/kn_kn/kn_pop235844/R/x86_64-unknown-linux-gnu-library/3.2/XVector/include" -I"/pfs/data2/home/kn/kn_kn/kn_pop235844/R/x86_64-unknown-linux-gnu-library/3.2/Biostrings/include"   -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic  -O3 -fp-model strict -openmp -xHost  -c bam_data.c -o bam_data.o
icpc -I/opt/bwhpc/common/math/R/3.2.1-mkl-11.2.3-intel-15.0/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/pfs/data2/home/kn/kn_kn/kn_pop235844/R/x86_64-unknown-linux-gnu-library/3.2/S4Vectors/include" -I"/pfs/data2/home/kn/kn_kn/kn_pop235844/R/x86_64-unknown-linux-gnu-library/3.2/IRanges/include" -I"/pfs/data2/home/kn/kn_kn/kn_pop235844/R/x86_64-unknown-linux-gnu-library/3.2/XVector/include" -I"/pfs/data2/home/kn/kn_kn/kn_pop235844/R/x86_64-unknown-linux-gnu-library/3.2/Biostrings/include"   -fpic  -O3 -std=c++11 -fp-model strict -openmp -xHost  -c bam_mate_iter.cpp -o bam_mate_iter.o
/usr/include/c++/4.4.7/bits/stl_pair.h(90): error: a value of type "long" cannot be used to initialize an entity of type "const bam1_t *"
        second(std::forward<_U2>(__y)) { }
               ^
          detected during instantiation of "std::pair<_T1, _T2>::pair(_U1 &&, _U2 &&) [with _T1=int, _T2=const bam1_t *, _U1=const int &, _U2=long]" at line 173 of "Template.h"

compilation aborted for bam_mate_iter.cpp (code 2)
make: *** [bam_mate_iter.o] Fehler 2
ERROR: compilation failed for package ‘Rsamtools’
* removing ‘/pfs/data2/home/kn/kn_kn/kn_pop235844/R/x86_64-unknown-linux-gnu-library/3.2/Rsamtools’

:-)

ADD REPLYlink written 20 months ago by rainer.rutka10

I think I can emulate the problem in g++ with the compiler flag -Wzero-as-null-pointer-constant. Can you try installing the version available at https://github.com/Bioconductor-mirror/Rsamtools ? Something like

git clone git@github.com:Bioconductor-mirror/Rsamtools.git
R CMD INSTALL Rsamtools

There might be additional problems (this is the 'devel' version, but you have the release version of other packages), or the solution might be incomplete. If you provide some positive feedback I'll port to release.

ADD REPLYlink modified 20 months ago • written 20 months ago by Martin Morgan ♦♦ 20k

Hi! Thanks for your effort.

Here are my trials for the installation of the Rsamtools onto our cluster.

PERMISSION DENIED
$ git clone git@github.com:Bioconductor-mirror/Rsamtools.gitInitialized empty Git repository in /pfs/data2/home/kn/kn_kn/kn_pop235844/Rsamtools/.git/
Warning: Permanently added the RSA host key for IP address '192.30.252.129' to the list of known hosts.
Permission denied (publickey).
fatal: The remote end hung up unexpectedly

So I download the ZIP and put it to my $HOME dir.

$ Rscript -e "install.packages('Rsamtools-master.zip', repos=NULL, dependencies=TRUE)"
Installing package into ‘/pfs/data2/home/kn/kn_kn/kn_pop235844/R’
(as ‘lib’ is unspecified)
Fehler in rawToChar(block[seq_len(ns)]) :
  Zeichenkette 'PK\003\004\n\0\0\0\0\0J\x88vH\0\0\0\0\0\0\0\0\0\0\0\0\021\0\t\0Rsamtools-master/UT\005\0\001\r\xdd\xf1VPK\003\004\n\0\0\0\b\0J\x88vH\xf8\xe6kc\x91\0\0\0\xf2\0\0\0\033\0\t\0Rsamtools-mast' enthält nul Zeichen
Warnmeldung:
In install.packages("Rsamtools-master.zip", repos = NULL, dependencies = TRUE) :
  Installation des Pakets ‘Rsamtools-master.zip’ hatte Exit-Status ungleich 0

ERROR in installation.
Possibly the above " -Wzero-as-null-pointer-" problem?!

Same if I try to install the package within R.

Contents of my $HOME/.R/Makevars (maybe wrong?)

PKG_CXXFLAGS = -Wzero-as-null-pointer-constant

:-(

Thanks.

ADD REPLYlink modified 20 months ago • written 20 months ago by rainer.rutka10

Sorry, I (think) I should ahve grabbed the https link

git clone https://github.com/Bioconductor-mirror/Rsamtools.git

or unzip the zip and R CMD INSTALL Rsamtools-master.

If you mean that you have PKG_CXXFLAGS =  -Wzero-as-null-pointer-constant then I would suggest removing it (I added something like that for my own debugging purposes). Thanks for trying...

ADD REPLYlink written 20 months ago by Martin Morgan ♦♦ 20k

Hello!

Thanks for your help. Finally we got it.
I was still not able to compile the Rsamtools. But a combination between
'git clone...' (see above e-mail) and a normal installation of cummeRbund
worked fine in the end.

I will test the installation and add a document/howto (a URL) here if
desired.

:-)
 

 

ADD REPLYlink written 20 months ago by rainer.rutka10
0
gravatar for rainer.rutka
20 months ago by
rainer.rutka10
Germany/Konstanz/University of Konstanz
rainer.rutka10 wrote:

Hi!

RESOLVED!

Here are the installation instructions I supplied for our bwUniCluster users (so far) :

http://www.bwhpc-c5.de/wiki/index.php/CummeRbund_(R-package)

... and thanks for your inquiries.

 

 

ADD COMMENTlink modified 20 months ago • written 20 months ago by rainer.rutka10
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