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This page was generated on 2021-12-06 13:05:51 -0500 (Mon, 06 Dec 2021).

BUILD BIN results for Cardinal on machv2

To the developers/maintainers of the Cardinal package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Cardinal.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 246/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Cardinal 2.12.0  (landing page)
Kylie A. Bemis
Snapshot Date: 2021-12-05 01:55:05 -0500 (Sun, 05 Dec 2021)
git_url: https://git.bioconductor.org/packages/Cardinal
git_branch: RELEASE_3_14
git_last_commit: a9cad46
git_last_commit_date: 2021-10-26 12:18:42 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Cardinal
Version: 2.12.0
Command: rm -rf Cardinal.buildbin-libdir && mkdir Cardinal.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Cardinal_2.12.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Cardinal.buildbin-libdir
StartedAt: 2021-12-05 21:34:45 -0500 (Sun, 05 Dec 2021)
EndedAt: 2021-12-05 21:35:58 -0500 (Sun, 05 Dec 2021)
EllapsedTime: 73.5 seconds
RetCode: 0
Status:   OK  
PackageFile: Cardinal_2.12.0.tgz
PackageFileSize: 5.078 MiB

Command output

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###
### Running command:
###
###   rm -rf Cardinal.buildbin-libdir && mkdir Cardinal.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Cardinal_2.12.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Cardinal.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Cardinal.buildbin-libdir Cardinal_2.12.0.tar.gz'
>>>>>>> 

* installing *source* package ‘Cardinal’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c DIP.cpp -o DIP.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c dynAlign.cpp -o dynAlign.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c imzML.cpp -o imzML.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.cpp -o init.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c pugixml.cpp -o pugixml.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c spatial.cpp -o spatial.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c utils.cpp -o utils.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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 Cardinal.so DIP.o dynAlign.o imzML.o init.o pugixml.o spatial.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.14-bioc/meat/Cardinal.buildbin-libdir/00LOCK-Cardinal/00new/Cardinal/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 (Cardinal)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgcc_s.1.dylib" "Cardinal.buildbin-libdir/Cardinal/libs/Cardinal.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgfortran.5.dylib" "Cardinal.buildbin-libdir/Cardinal/libs/Cardinal.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libquadmath.0.dylib" "Cardinal.buildbin-libdir/Cardinal/libs/Cardinal.so"