CALIB 1.36.0
Hui Zhao
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/CALIB | | Last Changed Rev: 109589 / Revision: 116712 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | [ OK ] | |
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### Running command:
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### rm -rf CALIB.buildbin-libdir && mkdir CALIB.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CALIB_1.36.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CALIB.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CALIB.buildbin-libdir CALIB_1.36.0.tar.gz'
>>>>>>>
* installing *source* package ‘CALIB’ ...
** 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 Design.cpp -o Design.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 Estimation.cpp -o Estimation.o
Estimation.cpp:144:19: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
^
Estimation.cpp:144:25: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
^
Estimation.cpp:144:30: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
^
Estimation.cpp:144:35: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
^
Estimation.cpp:144:40: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
^
Estimation.cpp:144:49: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
^
Estimation.cpp:144:58: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
^
Estimation.cpp:144:67: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
char *name[8] = {"MuS","Ka","P1","P2","SigmaA","SigmaM","SigmaS","SpotError"};
^
Estimation.cpp:223:30: warning: 'readinparlist' has C-linkage specified, but returns incomplete type 'vector<ParameterofOneArray>' which could be incompatible with C [-Wreturn-type-c-linkage]
vector <ParameterofOneArray> readinparlist(SEXP parlist, int ncol)
^
9 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 NormalizedData.cpp -o NormalizedData.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 ParameterofOneArray.cpp -o ParameterofOneArray.o
In file included from ParameterofOneArray.cpp:4:
./ParameterofOneArray.h:11:9: warning: private field 'SpotErrorofOneSpot' is not used [-Wunused-private-field]
double SpotErrorofOneSpot;
^
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 RawDataofOneArray.cpp -o RawDataofOneArray.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 SpikeofOneArray.cpp -o SpikeofOneArray.o
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 CALIB.so Design.o Estimation.o NormalizedData.o ParameterofOneArray.o RawDataofOneArray.o SpikeofOneArray.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/CALIB.buildbin-libdir/CALIB/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CALIB)
>>>>>>>
>>>>>>> FIXING LINKS FOR CALIB.buildbin-libdir/CALIB/libs//CALIB.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgcc_s.1.dylib" "CALIB.buildbin-libdir/CALIB/libs//CALIB.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgfortran.3.dylib" "CALIB.buildbin-libdir/CALIB/libs//CALIB.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.5.2.dylib" "CALIB.buildbin-libdir/CALIB/libs//CALIB.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.dylib" "CALIB.buildbin-libdir/CALIB/libs//CALIB.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libquadmath.0.dylib" "CALIB.buildbin-libdir/CALIB/libs//CALIB.so"