| Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:47:31 -0400 (Wed, 16 Oct 2019).
| Package 1389/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Arnaud Droit
| 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 | |||||||
| Package: rMAT |
| Version: 3.34.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rMAT |
| StartedAt: 2019-10-15 18:21:04 -0400 (Tue, 15 Oct 2019) |
| EndedAt: 2019-10-15 18:21:32 -0400 (Tue, 15 Oct 2019) |
| EllapsedTime: 28.4 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rMAT
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘rMAT’ ...
** using staged installation
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
config.status: src/config.h is unchanged
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c BARFileData.cpp -o BARFileData.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c BARFileWriter.cpp -o BARFileWriter.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c BARWriter.cpp -o BARWriter.o
BARWriter.cpp:94:9: warning: unused variable 'curListPtr' [-Wunused-variable]
int curListPtr = 0, startListPtr = 0;
^
BARWriter.cpp:93:10: warning: unused variable 'lengthList' [-Wunused-variable]
int *lengthList = new int[NUM_SEQ];
^
BARWriter.cpp:90:9: warning: unused variable 'signal2Length' [-Wunused-variable]
int signal2Length = length(pValue);
^
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:274:6: warning: unused variable 'addPos' [-Wunused-variable]
int addPos = 0;
^
7 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c BPMAPfunctions.cpp -o BPMAPfunctions.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c DeclareAll.c -o DeclareAll.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c FileIO.cpp -o FileIO.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c FileWriter.cpp -o FileWriter.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c NormalizeProbes.c -o NormalizeProbes.o
NormalizeProbes.c:91:13: warning: unused variable 'j' [-Wunused-variable]
int j=0,nVariables;
^
NormalizeProbes.c:133:9: warning: variable 'yVector' is uninitialized when captured by block [-Wuninitialized]
DO_NORMALIZE(normArray(seq, y, yNormalized, nProbes,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./config.h:34:20: note: expanded from macro 'DO_NORMALIZE'
^(size_t counter_name) { task; });
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NormalizeProbes.c:85:9: note: variable 'yVector' is declared here
gsl_vector_view yVector,copyNumberVector;
^
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))
^~
=
3 warnings generated.
clang++ -std=gnu++11 -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 /Library/Frameworks/R.framework/Versions/3.6/Resources/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)