Package: COMPASS

Version: 1.16.2

Command: rm -rf COMPASS.buildbin-libdir && mkdir COMPASS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh COMPASS_1.16.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R COMPASS.buildbin-libdir

StartedAt: 2018-04-12 11:17:37 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 11:17:50 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 12.4 seconds

RetCode: 0

Status:  OK

PackageFile: COMPASS_1.16.2.tgz

PackageFileSize: 1024 KiB

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf COMPASS.buildbin-libdir && mkdir COMPASS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh COMPASS_1.16.2.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_1.16.2.tar.gz'
>>>>>>> 

* installing *source* package ‘COMPASS’ ...

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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   -fPIC  -Wall -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   -fPIC  -Wall -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   -fPIC  -Wall -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/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-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"
install_name_tool -change "/usr/local/gfortran/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/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "COMPASS.buildbin-libdir/COMPASS/libs//COMPASS.so"