Back to the "Multiple platform build/check report" A  B [C] D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.2: BUILD BIN report for COMPASS on oaxaca

This page was generated on 2016-04-23 10:27:35 -0700 (Sat, 23 Apr 2016).

Package 213/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
COMPASS 1.8.1
Greg Finak
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/COMPASS
Last Changed Rev: 111190 / Revision: 116712
Last Changed Date: 2015-12-03 14:15:03 -0800 (Thu, 03 Dec 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: COMPASS
Version: 1.8.1
Command: rm -rf COMPASS.buildbin-libdir && mkdir COMPASS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh COMPASS_1.8.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R COMPASS.buildbin-libdir
StartedAt: 2016-04-23 05:35:07 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 05:35:17 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 10.5 seconds
RetCode: 0
Status:  OK 
PackageFile: COMPASS_1.8.1.tgz
PackageFileSize: 1.069 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf COMPASS.buildbin-libdir && mkdir COMPASS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh COMPASS_1.8.1.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_1.8.1.tar.gz'
>>>>>>> 

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

R version 3.2.4 (2016-03-10) -- "Very Secure Dishes"
Copyright (C) 2016 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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/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/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/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-3.2-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/3.2/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/3.2/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/3.2/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/3.2/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/3.2/Resources/lib/libquadmath.0.dylib" "COMPASS.buildbin-libdir/COMPASS/libs//COMPASS.so"