Back to Multiple platform build/check report for BioC 3.14
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-11-24 15:05:56 -0500 (Wed, 24 Nov 2021).

BUILD BIN results for biodb on machv2

To the developers/maintainers of the biodb package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodb.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 175/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodb 1.2.1  (landing page)
Pierrick Roger
Snapshot Date: 2021-11-23 04:15:06 -0500 (Tue, 23 Nov 2021)
git_url: https://git.bioconductor.org/packages/biodb
git_branch: RELEASE_3_14
git_last_commit: 8010421
git_last_commit_date: 2021-11-08 03:15:41 -0500 (Mon, 08 Nov 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: biodb
Version: 1.2.1
Command: rm -rf biodb.buildbin-libdir && mkdir biodb.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh biodb_1.2.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R biodb.buildbin-libdir
StartedAt: 2021-11-23 23:42:30 -0500 (Tue, 23 Nov 2021)
EndedAt: 2021-11-23 23:44:52 -0500 (Tue, 23 Nov 2021)
EllapsedTime: 142.5 seconds
RetCode: 0
Status:   OK  
PackageFile: biodb_1.2.1.tgz
PackageFileSize: 4.427 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf biodb.buildbin-libdir && mkdir biodb.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh biodb_1.2.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R biodb.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=biodb.buildbin-libdir biodb_1.2.1.tar.gz'
>>>>>>> 

* installing *source* package ‘biodb’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/testthat/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/testthat/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c closeMatchPpm.cpp -o closeMatchPpm.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/testthat/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c test-100-ms_matching.cpp -o test-100-ms_matching.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/testthat/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c test-runner.cpp -o test-runner.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 biodb.so RcppExports.o closeMatchPpm.o test-100-ms_matching.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.14-bioc/meat/biodb.buildbin-libdir/00LOCK-biodb/00new/biodb/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 (biodb)


>>>>>>> 
>>>>>>> FIXING LINKS FOR biodb.buildbin-libdir/biodb/libs/biodb.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" "biodb.buildbin-libdir/biodb/libs/biodb.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgfortran.5.dylib" "biodb.buildbin-libdir/biodb/libs/biodb.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libquadmath.0.dylib" "biodb.buildbin-libdir/biodb/libs/biodb.so"