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
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
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’
:-)
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
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.
Hi! Thanks for your effort.
Here are my trials for the installation of the Rsamtools onto our cluster.
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 0ERROR 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?)
:-(
Thanks.
Sorry, I (think) I should ahve grabbed the https link
git clone https://github.com/Bioconductor-mirror/Rsamtools.gitor 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...
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.
:-)