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BUILD BIN report for CSSP on machv2

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

TO THE DEVELOPERS/MAINTAINERS OF THE CSSP PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 399/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CSSP 1.26.0
Chandler Zuo
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/CSSP
Branch: RELEASE_3_11
Last Commit: 9ec7a00
Last Changed Date: 2020-04-27 14:35:29 -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  OK  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: CSSP
Version: 1.26.0
Command: rm -rf CSSP.buildbin-libdir && mkdir CSSP.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CSSP_1.26.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CSSP.buildbin-libdir
StartedAt: 2020-10-17 06:52:53 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:53:12 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 19.0 seconds
RetCode: 0
Status:  OK 
PackageFile: CSSP_1.26.0.tgz
PackageFileSize: 867.6 KiB

Command output

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###
### Running command:
###
###   rm -rf CSSP.buildbin-libdir && mkdir CSSP.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CSSP_1.26.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CSSP.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CSSP.buildbin-libdir CSSP_1.26.0.tar.gz'
>>>>>>> 

* installing *source* package ‘CSSP’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c bincount.c -o bincount.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c binpower.c -o binpower.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c gridLogMean.c -o gridLogMean.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c gridMGC.c -o gridMGC.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c gridMean.c -o gridMean.o
gridMean.c:10:63: warning: unused variable 'counter' [-Wunused-variable]
  R_len_t ng=REAL(ngrid)[0],k,i,j,l,ind[4],n=length(map),newG,counter;
                                                              ^
gridMean.c:177:63: warning: unused variable 'counter' [-Wunused-variable]
  R_len_t ng=REAL(ngrid)[0],k,i,j,l,ind[2],n=length(map),newG,counter;
                                                              ^
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c gridMode.c -o gridMode.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c gridNonpa.c -o gridNonpa.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c gridSample.c -o gridSample.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c tag2bin.c -o tag2bin.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 CSSP.so bincount.o binpower.o gridLogMean.o gridMGC.o gridMean.o gridMode.o gridNonpa.o gridSample.o tag2bin.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.11-bioc/meat/CSSP.buildbin-libdir/00LOCK-CSSP/00new/CSSP/libs
** R
** data
** 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 (CSSP)


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