VariantFiltering 1.12.1
Robert Castelo
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/VariantFiltering | | Last Changed Rev: 129348 / Revision: 131943 | | Last Changed Date: 2017-05-02 14:06:49 -0400 (Tue, 02 May 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | [ OK ] | |
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### Running command:
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### rm -rf VariantFiltering.buildbin-libdir && mkdir VariantFiltering.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh VariantFiltering_1.12.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R VariantFiltering.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=VariantFiltering.buildbin-libdir VariantFiltering_1.12.1.tar.gz'
>>>>>>>
* installing *source* package ‘VariantFiltering’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I/usr/local/include -fPIC -Wall -g -O2 -c Biostrings_stubs.c -o Biostrings_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I/usr/local/include -fPIC -Wall -g -O2 -c R_init_VariantFiltering.c -o R_init_VariantFiltering.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Biostrings/include" -I/usr/local/include -fPIC -Wall -g -O2 -c methods-WeightMatrix.c -o methods-WeightMatrix.o
methods-WeightMatrix.c:99:7: warning: unused variable 'nsco' [-Wunused-variable]
int nsco = INTEGER(nscoR)[0];
^
methods-WeightMatrix.c:100:11: warning: unused variable 'scores' [-Wunused-variable]
double* scores;
^
methods-WeightMatrix.c:129:7: warning: unused variable 'nsco' [-Wunused-variable]
int nsco = INTEGER(nscoR)[0];
^
methods-WeightMatrix.c:131:11: warning: unused variable 'scores' [-Wunused-variable]
double* scores;
^
4 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 VariantFiltering.so Biostrings_stubs.o R_init_VariantFiltering.o methods-WeightMatrix.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/VariantFiltering.buildbin-libdir/VariantFiltering/libs
** R
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* DONE (VariantFiltering)
>>>>>>>
>>>>>>> FIXING LINKS FOR VariantFiltering.buildbin-libdir/VariantFiltering/libs//VariantFiltering.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgcc_s.1.dylib" "VariantFiltering.buildbin-libdir/VariantFiltering/libs//VariantFiltering.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "VariantFiltering.buildbin-libdir/VariantFiltering/libs//VariantFiltering.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.5.2.dylib" "VariantFiltering.buildbin-libdir/VariantFiltering/libs//VariantFiltering.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "VariantFiltering.buildbin-libdir/VariantFiltering/libs//VariantFiltering.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "VariantFiltering.buildbin-libdir/VariantFiltering/libs//VariantFiltering.so"