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BUILD BIN report for crlmm on machv2

This page was generated on 2020-10-17 11:58:19 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE crlmm PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 394/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
crlmm 1.46.0
Benilton S Carvalho
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/crlmm
Branch: RELEASE_3_11
Last Commit: 162ee9a
Last Changed Date: 2020-04-27 14:19:05 -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  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: crlmm
Version: 1.46.0
Command: rm -rf crlmm.buildbin-libdir && mkdir crlmm.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh crlmm_1.46.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R crlmm.buildbin-libdir
StartedAt: 2020-10-17 06:52:38 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:53:39 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 61.0 seconds
RetCode: 0
Status:  OK 
PackageFile: crlmm_1.46.0.tgz
PackageFileSize: 5.19 MiB

Command output

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###
### Running command:
###
###   rm -rf crlmm.buildbin-libdir && mkdir crlmm.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh crlmm_1.46.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R crlmm.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=crlmm.buildbin-libdir crlmm_1.46.0.tar.gz'
>>>>>>> 

* installing *source* package ‘crlmm’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/preprocessCore/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c gtypeCaller.c -o gtypeCaller.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/preprocessCore/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/preprocessCore/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c trimmed.c -o trimmed.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/preprocessCore/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c utils.c -o utils.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 crlmm.so gtypeCaller.o init.o trimmed.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.11-bioc/meat/crlmm.buildbin-libdir/00LOCK-crlmm/00new/crlmm/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’
** testing if installed package keeps a record of temporary installation path
* DONE (crlmm)


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