rMAT 3.34.0
Arnaud Droit and Raphael Gottardo
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/rMAT |
| Branch: RELEASE_3_9 |
| Last Commit: 71c1a2e |
| Last Changed Date: 2019-05-02 11:53:11 -0400 (Thu, 02 May 2019) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | [ OK ] | ERROR | skipped | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | ...NOT SUPPORTED... |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | ERROR | skipped | skipped | |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL rMAT
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘rMAT’ ...
** using staged installation
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++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c BARFileData.cpp -o BARFileData.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c BARFileWriter.cpp -o BARFileWriter.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-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;
^~~~~~~~
BARReader.cpp: In function ‘SEXPREC* Parser(SEXP)’:
BARReader.cpp:46:8: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 4 [-Wformat-truncation=]
SEXP Parser (SEXP fileName)
^~~~~~
BARReader.cpp:46:8: note: directive argument in the range [1, 2147483646]
In file included from /usr/include/stdio.h:862:0,
from /usr/include/c++/7/cstdio:42,
from /usr/include/c++/7/ext/string_conversions.h:43,
from /usr/include/c++/7/bits/basic_string.h:6361,
from /usr/include/c++/7/string:52,
from /usr/include/c++/7/bits/locale_classes.h:40,
from /usr/include/c++/7/bits/ios_base.h:41,
from /usr/include/c++/7/ios:42,
from /usr/include/c++/7/ostream:38,
from /usr/include/c++/7/iostream:39,
from BARReader.cpp:26:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:65:44: note: ‘__builtin___snprintf_chk’ output between 8 and 17 bytes into a destination of size 10
__bos (__s), __fmt, __va_arg_pack ());
^
In function ‘int snprintf(char*, size_t, const char*, ...)’,
inlined from ‘SEXPREC* Parser(SEXP)’ at BARReader.cpp:260:9:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:65:44: warning: ‘int __builtin___snprintf_chk(char*, long unsigned int, int, long unsigned int, const char*, ...)’: specified bound 255 exceeds the size 10 of the destination [-Wstringop-overflow=]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-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++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-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++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c BPMAPfunctions.cpp -o BPMAPfunctions.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c DeclareAll.c -o DeclareAll.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-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++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-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-3.9-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++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-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-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-rMAT/00new/rMAT/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'rMAT' is deprecated and will be removed from Bioconductor
version 3.10
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: Package 'rMAT' is deprecated and will be removed from Bioconductor
version 3.10
** testing if installed package keeps a record of temporary installation path
* DONE (rMAT)