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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### rm -rf rMAT.buildbin-libdir && mkdir rMAT.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh rMAT_3.23.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R rMAT.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=rMAT.buildbin-libdir rMAT_3.23.0.tar.gz'
>>>>>>>
* installing *source* package ‘rMAT’ ...
R_HOME: /Library/Frameworks/R.framework/Resources
checking for gcc... clang
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 clang accepts -g... yes
checking for clang option to accept ISO C89... none needed
checking how to run the C preprocessor... clang -E
checking for pkg-config... /usr/local/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... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
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... yes
checking dispatch/dispatch.h presence... yes
checking for dispatch/dispatch.h... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/config.h
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c BARFileData.cpp -o BARFileData.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c BARFileWriter.cpp -o BARFileWriter.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c BARReader.cpp -o BARReader.o
BARReader.cpp:259:6: warning: unused variable 'buf' [-Wunused-variable]
char buf[MAX_SIZE];
^
BARReader.cpp:474:49: warning: unused variable 'p_region' [-Wunused-variable]
int *p_chromosome = NULL, *p_position = NULL, *p_region = NULL;
^
BARReader.cpp:473:42: warning: unused variable 'regionR' [-Wunused-variable]
SEXP chromosomeR, positionR, matScoreR, regionR, pValueR;
^
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c BARWriter.cpp -o BARWriter.o
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: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: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:274:6: warning: unused variable 'addPos' [-Wunused-variable]
int addPos = 0;
^
7 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c BPMAPFileData.cpp -o BPMAPFileData.o
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);
^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c BPMAPfunctions.cpp -o BPMAPfunctions.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c DeclareAll.c -o DeclareAll.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c FileIO.cpp -o FileIO.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c FileWriter.cpp -o FileWriter.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c NormalizeProbes.c -o NormalizeProbes.o
NormalizeProbes.c:91:13: warning: unused variable 'j' [-Wunused-variable]
int j=0,nVariables;
^
NormalizeProbes.c:1109:18: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if((*MATScaling==1))
˜˜˜˜˜˜˜˜˜˜˜^˜˜
NormalizeProbes.c:1109:18: note: remove extraneous parentheses around the comparison to silence this warning
if((*MATScaling==1))
˜ ^ ˜
NormalizeProbes.c:1109:18: note: use '=' to turn this equality comparison into an assignment
if((*MATScaling==1))
^˜
=
2 warnings generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -L/usr/local/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-bioc/meat/rMAT.buildbin-libdir/rMAT/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rMAT)
>>>>>>>
>>>>>>> FIXING LINKS FOR rMAT.buildbin-libdir/rMAT/libs//rMAT.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libgcc_s.1.dylib" "rMAT.buildbin-libdir/rMAT/libs//rMAT.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libgfortran.3.dylib" "rMAT.buildbin-libdir/rMAT/libs//rMAT.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libreadline.5.2.dylib" "rMAT.buildbin-libdir/rMAT/libs//rMAT.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libreadline.dylib" "rMAT.buildbin-libdir/rMAT/libs//rMAT.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libquadmath.0.dylib" "rMAT.buildbin-libdir/rMAT/libs//rMAT.so"