COMPASS 1.13.3
Greg Finak
| Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/COMPASS | | Last Changed Rev: 128311 / Revision: 129046 | | Last Changed Date: 2017-04-07 14:25:29 -0400 (Fri, 07 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | ERROR | OK | |
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | [ OK ] | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | ERROR | skipped | skipped | |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf COMPASS.buildbin-libdir && mkdir COMPASS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh COMPASS_1.13.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R COMPASS.buildbin-libdir
###
##############################################################################
##############################################################################
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=COMPASS.buildbin-libdir COMPASS_1.13.3.tar.gz'
>>>>>>>
* installing *source* package ‘COMPASS’ ...
R Under development (unstable) (2017-02-15 r72187) -- "Unsuffered Consequences"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> source('R/cleanup.R'); cleanup()
It looks like this isn't being called from R CMD build; bailing out
>
>
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c COMPASS_c.c -o COMPASS_c.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c COMPASS_cpp.cpp -o COMPASS_cpp.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c COMPASS_init.c -o COMPASS_init.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 COMPASS.so COMPASS_c.o COMPASS_cpp.o COMPASS_init.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/COMPASS.buildbin-libdir/COMPASS/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (COMPASS)
>>>>>>>
>>>>>>> FIXING LINKS FOR COMPASS.buildbin-libdir/COMPASS/libs//COMPASS.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" "COMPASS.buildbin-libdir/COMPASS/libs//COMPASS.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "COMPASS.buildbin-libdir/COMPASS/libs//COMPASS.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" "COMPASS.buildbin-libdir/COMPASS/libs//COMPASS.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "COMPASS.buildbin-libdir/COMPASS/libs//COMPASS.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "COMPASS.buildbin-libdir/COMPASS/libs//COMPASS.so"