Back to Multiple platform build/check report for BioC 3.11
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

BUILD BIN report for cydar on machv2

This page was generated on 2020-10-17 11:58:20 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE cydar PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 410/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cydar 1.12.0
Aaron Lun
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/cydar
Branch: RELEASE_3_11
Last Commit: 84e89cc
Last Changed Date: 2020-04-27 15:06:26 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  ERROR [ OK ]

Summary

Package: cydar
Version: 1.12.0
Command: rm -rf cydar.buildbin-libdir && mkdir cydar.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh cydar_1.12.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R cydar.buildbin-libdir
StartedAt: 2020-10-17 06:53:29 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:54:41 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 72.3 seconds
RetCode: 0
Status:  OK 
PackageFile: cydar_1.12.0.tgz
PackageFileSize: 1.097 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf cydar.buildbin-libdir && mkdir cydar.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh cydar_1.12.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R cydar.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=cydar.buildbin-libdir cydar_1.12.0.tar.gz'
>>>>>>> 

* installing *source* package ‘cydar’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c compute_density.cpp -o compute_density.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c count_cells.cpp -o count_cells.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c drop_redundant.cpp -o drop_redundant.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c median_int_by_sample.cpp -o median_int_by_sample.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c weighted_median_int.cpp -o weighted_median_int.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -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 cydar.so RcppExports.o compute_density.o count_cells.o drop_redundant.o median_int_by_sample.o weighted_median_int.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.11-bioc/meat/cydar.buildbin-libdir/00LOCK-cydar/00new/cydar/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cydar)


>>>>>>> 
>>>>>>> FIXING LINKS FOR cydar.buildbin-libdir/cydar/libs/cydar.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgcc_s.1.dylib" "cydar.buildbin-libdir/cydar/libs/cydar.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.5.dylib" "cydar.buildbin-libdir/cydar/libs/cydar.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "cydar.buildbin-libdir/cydar/libs/cydar.so"