ncdfFlow 2.12.0
Mike Jiang
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/ncdfFlow | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | [ OK ] |
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### Running command:
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### rm -rf ncdfFlow.buildbin-libdir && mkdir ncdfFlow.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ncdfFlow_2.12.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R ncdfFlow.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ncdfFlow.buildbin-libdir ncdfFlow_2.12.0.tar.gz'
>>>>>>>
* installing *source* package ‘ncdfFlow’ ...
configure: search for hdf5 library in: /usr/lib
configure: found hdf5 library in: /usr/lib
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -fPIC -Wall -mtune=core2 -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -fPIC -Wall -mtune=core2 -g -O2 -c bitOps.cpp -o bitOps.o
bitOps.cpp:23:11: warning: unused variable 'nByte' [-Wunused-variable]
unsigned nByte = bytes.size();
^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -fPIC -Wall -mtune=core2 -g -O2 -c hdfFlow.c -o hdfFlow.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -fPIC -Wall -mtune=core2 -g -O2 -c init.c -o init.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -fPIC -Wall -mtune=core2 -g -O2 -c readFrame.cpp -o readFrame.o
readFrame.cpp:484:11: warning: variable 'samplePos' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized]
if(it == origSampleVector.end())
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
readFrame.cpp:493:62: note: uninitialized use occurs here
Rcpp::NumericVector mat = readSlice_cpp(file, chIndx, samplePos, nrows);
^˜˜˜˜˜˜˜˜
readFrame.cpp:484:8: note: remove the 'if' if its condition is always false
if(it == origSampleVector.end())
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
readFrame.cpp:474:26: note: initialize the variable 'samplePos' to silence this warning
unsigned samplePos;
^
= 0
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/BH/include" -fPIC -Wall -mtune=core2 -g -O2 -c wrappers.c -o wrappers.o
wrappers.c:535:12: warning: unused variable 'data_out' [-Wunused-variable]
double *data_out = REAL(ans);
^
1 warning 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 ncdfFlow.so RcppExports.o bitOps.o hdfFlow.o init.o readFrame.o wrappers.o -L/usr/lib -lhdf5 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/ncdfFlow.buildbin-libdir/ncdfFlow/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘lapply’ from package ‘base’ in package ‘ncdfFlow’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ncdfFlow)
>>>>>>>
>>>>>>> FIXING LINKS FOR ncdfFlow.buildbin-libdir/ncdfFlow/libs//ncdfFlow.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libgcc_s.1.dylib" "ncdfFlow.buildbin-libdir/ncdfFlow/libs//ncdfFlow.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libgfortran.3.dylib" "ncdfFlow.buildbin-libdir/ncdfFlow/libs//ncdfFlow.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libreadline.5.2.dylib" "ncdfFlow.buildbin-libdir/ncdfFlow/libs//ncdfFlow.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libreadline.dylib" "ncdfFlow.buildbin-libdir/ncdfFlow/libs//ncdfFlow.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libquadmath.0.dylib" "ncdfFlow.buildbin-libdir/ncdfFlow/libs//ncdfFlow.so"