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BUILD BIN report for flowSpy on merida1

This page was generated on 2021-05-06 12:35:00 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the flowSpy package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 633/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowSpy 1.4.0  (landing page)
Yuting Dai
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/flowSpy
Branch: RELEASE_3_12
Last Commit: e8ba381
Last Changed Date: 2020-10-27 11:50:57 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository

Summary

Package: flowSpy
Version: 1.4.0
Command: rm -rf flowSpy.buildbin-libdir && mkdir flowSpy.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh flowSpy_1.4.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R flowSpy.buildbin-libdir
StartedAt: 2021-05-06 08:38:21 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 08:40:28 -0400 (Thu, 06 May 2021)
EllapsedTime: 126.9 seconds
RetCode: 0
Status:   OK  
PackageFile: flowSpy_1.4.0.tgz
PackageFileSize: 3.705 MiB

Command output

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###
### Running command:
###
###   rm -rf flowSpy.buildbin-libdir && mkdir flowSpy.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh flowSpy_1.4.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R flowSpy.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=flowSpy.buildbin-libdir flowSpy_1.4.0.tar.gz'
>>>>>>> 

* installing *source* package ‘flowSpy’ ...
** 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/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c jaccard_coeff.cpp -o jaccard_coeff.o
In file included from jaccard_coeff.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
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 flowSpy.so RcppExports.o jaccard_coeff.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.12-bioc/meat/flowSpy.buildbin-libdir/00LOCK-flowSpy/00new/flowSpy/libs
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘flowCore’ for requests: ‘action’, ‘assign’, ‘Data’, ‘gate’, ‘tree’ when loading ‘flowUtils’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘flowCore’ for requests: ‘action’, ‘assign’, ‘Data’, ‘gate’, ‘tree’ when loading ‘flowUtils’
Warning: Package 'flowSpy' is deprecated and will be removed from Bioconductor
  version 3.13
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
No methods found in package ‘flowCore’ for requests: ‘action’, ‘assign’, ‘Data’, ‘gate’, ‘tree’ when loading ‘flowUtils’
Warning: Package 'flowSpy' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package keeps a record of temporary installation path
* DONE (flowSpy)


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