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

BUILD BIN report for cancerclass on machv2

This page was generated on 2020-10-17 11:58:09 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE cancerclass PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 225/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cancerclass 1.32.0
Daniel Kosztyla
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/cancerclass
Branch: RELEASE_3_11
Last Commit: c811d2c
Last Changed Date: 2020-04-27 14:29:45 -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  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: cancerclass
Version: 1.32.0
Command: rm -rf cancerclass.buildbin-libdir && mkdir cancerclass.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh cancerclass_1.32.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R cancerclass.buildbin-libdir
StartedAt: 2020-10-17 06:43:46 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:44:02 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 15.9 seconds
RetCode: 0
Status:  OK 
PackageFile: cancerclass_1.32.0.tgz
PackageFileSize: 1.584 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf cancerclass.buildbin-libdir && mkdir cancerclass.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh cancerclass_1.32.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R cancerclass.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=cancerclass.buildbin-libdir cancerclass_1.32.0.tar.gz'
>>>>>>> 

* installing *source* package ‘cancerclass’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c copa.c -o copa.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c cor.c -o cor.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c fc.c -o fc.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c help.c -o help.o
help.c:335:7: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
   var=var; ///(to-from-1); R=var(N-1) => /(count-1)
   ~~~^~~~
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c ort.c -o ort.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c os.c -o os.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c shift.c -o shift.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c statistics.c -o statistics.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c student.c -o student.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c throw.c -o throw.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c welch.c -o welch.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c wilcox.c -o wilcox.o
clang -mmacosx-version-min=10.13 -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 cancerclass.so copa.o cor.o fc.o help.o ort.o os.o shift.o statistics.o student.o throw.o welch.o wilcox.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.11-bioc/meat/cancerclass.buildbin-libdir/00LOCK-cancerclass/00new/cancerclass/libs
** R
** data
** 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 (cancerclass)


>>>>>>> 
>>>>>>> FIXING LINKS FOR cancerclass.buildbin-libdir/cancerclass/libs/cancerclass.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" "cancerclass.buildbin-libdir/cancerclass/libs/cancerclass.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.5.dylib" "cancerclass.buildbin-libdir/cancerclass/libs/cancerclass.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "cancerclass.buildbin-libdir/cancerclass/libs/cancerclass.so"