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BioC 2.14: BUILD BIN report for COMPASS on petty

This page was generated on 2014-10-08 09:01:38 -0700 (Wed, 08 Oct 2014).

Package 182/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
COMPASS 1.2.1
Kevin Ushey
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/COMPASS
Last Changed Rev: 90176 / Revision: 95116
Last Changed Date: 2014-05-09 15:54:26 -0700 (Fri, 09 May 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  WARNINGS 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS [ OK ]
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK 

Summary

Package: COMPASS
Version: 1.2.1
Command: rm -rf COMPASS.buildbin-libdir && mkdir COMPASS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh COMPASS_1.2.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R COMPASS.buildbin-libdir
StartedAt: 2014-10-08 01:18:34 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 01:18:53 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 19.1 seconds
RetCode: 0
Status:  OK 
PackageFile: COMPASS_1.2.1.tgz
PackageFileSize: 1013 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf COMPASS.buildbin-libdir && mkdir COMPASS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh COMPASS_1.2.1.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_1.2.1.tar.gz'
>>>>>>> 

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

R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin10.8.0 (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
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c COMPASS_c.c -o COMPASS_c.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c COMPASS_cpp.cpp -o COMPASS_cpp.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c COMPASS_init.c -o COMPASS_init.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/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/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-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/3.1/Resources/lib/libgcc_s.1.dylib" "COMPASS.buildbin-libdir/COMPASS/libs//COMPASS.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libgfortran.2.dylib" "COMPASS.buildbin-libdir/COMPASS/libs//COMPASS.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.1/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/3.1/Resources/lib/libreadline.dylib" "COMPASS.buildbin-libdir/COMPASS/libs//COMPASS.so"