rMAT 3.23.0
Arnaud Droit and Raphael Gottardo
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rMAT | | Last Changed Rev: 117081 / Revision: 121152 | | Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | [ ERROR ] | skipped | | |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |  |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data rMAT
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* checking for file ‘rMAT/DESCRIPTION’ ... OK
* preparing ‘rMAT’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* installing the package to build vignettes
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* installing *source* package ‘rMAT’ ...
R_HOME: /home/biocbuild/bbs-3.4-bioc/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/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c BARFileData.cpp -o BARFileData.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c BARFileWriter.cpp -o BARFileWriter.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c BARReader.cpp -o BARReader.o
BARReader.cpp: In function ‘SEXPREC* Parser(SEXP)’:
BARReader.cpp:259:6: warning: unused variable ‘buf’ [-Wunused-variable]
char buf[MAX_SIZE];
^
BARReader.cpp: In function ‘SEXPREC* ParseMATBar(SEXP)’:
BARReader.cpp:473:42: warning: unused variable ‘regionR’ [-Wunused-variable]
SEXP chromosomeR, positionR, matScoreR, regionR, pValueR;
^
BARReader.cpp:474:49: warning: unused variable ‘p_region’ [-Wunused-variable]
int *p_chromosome = NULL, *p_position = NULL, *p_region = NULL;
^
BARReader.cpp: In function ‘SEXPREC* ParseNormalizeBar(SEXP)’:
BARReader.cpp:587:10: warning: variable ‘p_signal’ set but not used [-Wunused-but-set-variable]
double *p_signal = NULL;
^
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/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c BARWriter.cpp -o BARWriter.o
BARWriter.cpp: In function ‘SEXPREC* WriteBAR(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
BARWriter.cpp:90:9: warning: unused variable ‘signal2Length’ [-Wunused-variable]
int signal2Length = length(pValue);
^
BARWriter.cpp:93:10: warning: unused variable ‘lengthList’ [-Wunused-variable]
int *lengthList = new int[NUM_SEQ];
^
BARWriter.cpp:94:9: warning: unused variable ‘curListPtr’ [-Wunused-variable]
int curListPtr = 0, startListPtr = 0;
^
BARWriter.cpp:94:25: warning: unused variable ‘startListPtr’ [-Wunused-variable]
int curListPtr = 0, startListPtr = 0;
^
BARWriter.cpp:95:9: warning: unused variable ‘curChromosome’ [-Wunused-variable]
int curChromosome = INTEGER(chNos)[0];
^
BARWriter.cpp:96:9: warning: unused variable ‘i’ [-Wunused-variable]
int i;
^
BARWriter.cpp: In function ‘SEXPREC* WriteNormalizedBAR(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
BARWriter.cpp:274:6: warning: unused variable ‘addPos’ [-Wunused-variable]
int addPos = 0;
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c BPMAPFileData.cpp -o BPMAPFileData.o
BPMAPFileData.cpp: In member function ‘bool affxbpmap::CBPMAPFileData::ReadDataSection()’:
BPMAPFileData.cpp:379:7: warning: unused variable ‘hitSize’ [-Wunused-variable]
int hitSize=(m_SequenceItems[iSeq].m_ProbePairs == PM_MM ? HIT_ITEM_SIZE_WITH_PROBE_PAIRS : HIT_ITEM_SIZE_WITH_PM_ONLY);
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c BPMAPfunctions.cpp -o BPMAPfunctions.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c DeclareAll.c -o DeclareAll.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c FileIO.cpp -o FileIO.o
FileIO.cpp: In function ‘float MmGetFloat_I(float*)’:
FileIO.cpp:362:22: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
return *((float*)&v);
^
In file included from FileIO.cpp:27:0:
FileIO.cpp: In function ‘void MmSetFloat_I(float*, float)’:
FileIO.cpp:367:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
*(uint32_t*)ptr=htoil(*(uint32_t*)&val);
^
FileIO.h:90:19: note: in definition of macro ‘htoil’
#define htoil(x) (x)
^
FileIO.cpp: In function ‘float MmGetFloat_N(float*)’:
FileIO.cpp:373:22: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
return *((float*)&v);
^
In file included from FileIO.cpp:36:0:
FileIO.cpp: In function ‘void MmSetFloat_N(float*, float)’:
FileIO.cpp:378:38: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
*(uint32_t*)ptr=htonl(*(uint32_t*)&val);
^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c FileWriter.cpp -o FileWriter.o
FileWriter.cpp: In function ‘void WriteFloat_I(std::ofstream&, float)’:
FileWriter.cpp:108:42: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
WriteUInt32_I(outstr,*(uint32_t *)(&fval));
^
FileWriter.cpp: In function ‘void WriteFloat_N(std::ofstream&, float)’:
FileWriter.cpp:113:42: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
WriteUInt32_N(outstr,*(uint32_t *)(&fval));
^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c NormalizeProbes.c -o NormalizeProbes.o
NormalizeProbes.c: In function ‘NormalizeProbes’:
NormalizeProbes.c:91:13: warning: unused variable ‘j’ [-Wunused-variable]
int j=0,nVariables;
^
NormalizeProbes.c: In function ‘normArray’:
NormalizeProbes.c:1030:18: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
else if(k==iterMax & i>=(*nProbes))
^
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -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/biocbuild/bbs-3.4-bioc/R/lib -lR
/usr/bin/ld: cannot find -lm-lgomp
collect2: error: ld returned 1 exit status
/home/biocbuild/bbs-3.4-bioc/R/share/make/shlib.mk:6: recipe for target 'rMAT.so' failed
make: *** [rMAT.so] Error 1
ERROR: compilation failed for package ‘rMAT’
* removing ‘/tmp/Rtmp4IwmaH/Rinst3e8e64527bcd/rMAT’
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ERROR: package installation failed