Back to Multiple platform build/check report for BioC 3.16
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-06-24 11:07:36 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

BUILD BIN results for CelliD on lconway


To the developers/maintainers of the CelliD package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CelliD.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 271/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CelliD 1.5.0  (landing page)
Akira Cortal
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/CelliD
git_branch: master
git_last_commit: 27bcc3d
git_last_commit_date: 2022-04-26 12:13:53 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: CelliD
Version: 1.5.0
Command: rm -rf CelliD.buildbin-libdir && mkdir CelliD.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CelliD_1.5.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CelliD.buildbin-libdir
StartedAt: 2022-06-23 23:30:14 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 23:31:48 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 93.3 seconds
RetCode: 0
Status:   OK  
PackageFile: CelliD_1.5.0.tgz
PackageFileSize: 3.079 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf CelliD.buildbin-libdir && mkdir CelliD.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CelliD_1.5.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CelliD.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CelliD.buildbin-libdir CelliD_1.5.0.tar.gz'
>>>>>>> 

* installing *source* package ‘CelliD’ ...
** 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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/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/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c dist.cpp -o dist.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c mca.cpp -o mca.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c order.cpp -o order.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 CelliD.so RcppExports.o dist.o mca.o order.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0'
ld: warning: dylib (/usr/local/gfortran/lib/libgfortran.dylib) was built for newer macOS version (12.0) than being linked (10.13)
ld: warning: dylib (/usr/local/gfortran/lib/libquadmath.dylib) was built for newer macOS version (12.0) than being linked (10.13)
installing to /Users/biocbuild/bbs-3.16-bioc/meat/CelliD.buildbin-libdir/00LOCK-CelliD/00new/CelliD/libs
** R
** data
*** moving datasets to lazyload DB
Warning: namespace ‘rgdal’ is not available and has been replaced
by .GlobalEnv when processing object ‘seuratPbmc’
Warning: namespace ‘rgdal’ is not available and has been replaced
by .GlobalEnv when processing object ‘seuratPbmc’
Warning: namespace ‘rgdal’ is not available and has been replaced
by .GlobalEnv when processing object ‘seuratPbmc’
Warning: namespace ‘rgdal’ is not available and has been replaced
by .GlobalEnv when processing object ‘seuratPbmc’
Warning: namespace ‘rgdal’ is not available and has been replaced
by .GlobalEnv when processing object ‘seuratPbmc’
Warning: namespace ‘rgdal’ is not available and has been replaced
by .GlobalEnv when processing object ‘seuratPbmc’
Warning: namespace ‘rgdal’ is not available and has been replaced
by .GlobalEnv when processing object ‘seuratPbmc’
Warning: namespace ‘rgdal’ is not available and has been replaced
by .GlobalEnv when processing object ‘seuratPbmc’
Warning: namespace ‘rgdal’ is not available and has been replaced
by .GlobalEnv when processing object ‘seuratPbmc’
Warning: namespace ‘rgdal’ is not available and has been replaced
by .GlobalEnv when processing object ‘seuratPbmc’
Warning: namespace ‘rgdal’ is not available and has been replaced
by .GlobalEnv when processing object ‘seuratPbmc’
Warning: namespace ‘rgdal’ is not available and has been replaced
by .GlobalEnv when processing object ‘seuratPbmc’
Warning: namespace ‘rgdal’ is not available and has been replaced
by .GlobalEnv when processing object ‘seuratPbmc’
Warning: namespace ‘rgdal’ is not available and has been replaced
by .GlobalEnv when processing object ‘seuratPbmc’
Warning: namespace ‘rgdal’ is not available and has been replaced
by .GlobalEnv when processing object ‘seuratPbmc’
Warning: namespace ‘rgdal’ is not available and has been replaced
by .GlobalEnv when processing object ‘seuratPbmc’
Warning: namespace ‘rgdal’ is not available and has been replaced
by .GlobalEnv when processing object ‘seuratPbmc’
Warning: namespace ‘rgdal’ is not available and has been replaced
by .GlobalEnv when processing object ‘seuratPbmc’
Warning: namespace ‘rgdal’ is not available and has been replaced
by .GlobalEnv when processing object ‘seuratPbmc’
Warning: namespace ‘rgdal’ is not available and has been replaced
by .GlobalEnv when processing object ‘seuratPbmc’
Warning: namespace ‘rgdal’ is not available and has been replaced
by .GlobalEnv when processing object ‘seuratPbmc’
Warning: namespace ‘rgdal’ is not available and has been replaced
by .GlobalEnv when processing object ‘seuratPbmc’
** 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 (CelliD)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib" "CelliD.buildbin-libdir/CelliD/libs/CelliD.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "CelliD.buildbin-libdir/CelliD/libs/CelliD.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "CelliD.buildbin-libdir/CelliD/libs/CelliD.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgfortran.5.dylib" "CelliD.buildbin-libdir/CelliD/libs/CelliD.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libquadmath.0.dylib" "CelliD.buildbin-libdir/CelliD/libs/CelliD.so"