rMAT

Package: rMAT
Type: Package
Title: R implementation from MAT program to normalize and analyze
tiling arrays and ChIP-chip data.
Version: 3.22.0
Author: Charles Cheung and Arnaud Droit and Raphael Gottardo
Maintainer: Arnaud Droit <arnaud.droit@crchuq.ulaval.ca> and Raphael Gottardo <rgottard@fhcrc.org>
Description: This package is an R version of the package MAT and contains functions to parse and merge Affymetrix BPMAP and CEL tiling array files (using C++ based Fusion SDK and Bioconductor package affxparser), normalize tiling arrays using sequence specific models, detect enriched regions from ChIP-chip experiments. Note: users should have GSL and GenomeGraphs installed. Windows users: 'consult the README file available in the inst directory of the source distribution for necessary configuration instructions'. Snow Leopard users can take advantage of increase speed with Grand Central Dispatch!
Year: 2009.
License: Artistic-2.0
Depends: R (>= 2.9.0), BiocGenerics (>= 0.1.3), IRanges (>= 1.13.10),
Biobase (>= 2.15.1), affxparser
Imports: stats, methods, BiocGenerics, IRanges, Biobase, affxparser,
stats4
Suggests: GenomeGraphs, rtracklayer
biocViews: Microarray, Preprocessing
URL: http://www.rglab.org
NeedsCompilation: yes
Packaged: 2016-05-04 03:13:03 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'rMAT' ...
R_HOME: /home/ddbj/local/lib64/R
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dispatch/dispatch.h usability... no
checking dispatch/dispatch.h presence... no
checking for dispatch/dispatch.h... no
checking omp.h usability... yes
checking omp.h presence... yes
checking for omp.h... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/config.h
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c BARFileData.cpp -o BARFileData.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c BARFileWriter.cpp -o BARFileWriter.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c BARReader.cpp -o BARReader.o
In file included from /usr/include/stdio.h:936:0,
                 from BARReader.cpp:27:
In function 'int snprintf(char*, size_t, const char*, ...)',
    inlined from 'SEXPREC* Parser(SEXP)' at BARReader.cpp:260:45:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:65:44: warning: call to int __builtin___snprintf_chk(char*, long unsigned int, int, long unsigned int, const char*, ...) will always overflow destination buffer
        __bos (__s), __fmt, __va_arg_pack ());
                                            ^
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c BARWriter.cpp -o BARWriter.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c BPMAPFileData.cpp -o BPMAPFileData.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c BPMAPfunctions.cpp -o BPMAPfunctions.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -c DeclareAll.c -o DeclareAll.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c FileIO.cpp -o FileIO.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c FileWriter.cpp -o FileWriter.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include   -fopenmp -fpic  -g -O2  -c NormalizeProbes.c -o NormalizeProbes.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o rMAT.so BARFileData.o BARFileWriter.o BARReader.o BARWriter.o BPMAPFileData.o BPMAPfunctions.o DeclareAll.o FileIO.o FileWriter.o NormalizeProbes.o -lgsl -lgslcblas -lm-lgomp -L/home/ddbj/local/lib64/R/lib -lR
/usr/bin/ld: cannot find -lm-lgomp
collect2: error: ld returned 1 exit status
/home/ddbj/local/lib64/R/share/make/shlib.mk:6: recipe for target 'rMAT.so' failed
make: *** [rMAT.so] Error 1
ERROR: compilation failed for package 'rMAT'
* removing '/home/ddbj/local/lib64/R/library/rMAT'