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BUILD BIN report for dexus on machv2

This page was generated on 2020-10-17 11:58:22 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE dexus PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 466/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
dexus 1.28.0
Guenter Klambauer
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/dexus
Branch: RELEASE_3_11
Last Commit: 72ae234
Last Changed Date: 2020-04-27 14:33:34 -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: dexus
Version: 1.28.0
Command: rm -rf dexus.buildbin-libdir && mkdir dexus.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh dexus_1.28.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R dexus.buildbin-libdir
StartedAt: 2020-10-17 06:56:43 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:57:02 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 18.7 seconds
RetCode: 0
Status:  OK 
PackageFile: dexus_1.28.0.tgz
PackageFileSize: 3.377 MiB

Command output

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###
### Running command:
###
###   rm -rf dexus.buildbin-libdir && mkdir dexus.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh dexus_1.28.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R dexus.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=dexus.buildbin-libdir dexus_1.28.0.tar.gz'
>>>>>>> 

* installing *source* package ‘dexus’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c dexus.cpp -o dexus.o
dexus.cpp:136:15: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
        if ((innerCyc==maxInnerCyc))
             ~~~~~~~~^~~~~~~~~~~~~
dexus.cpp:136:15: note: remove extraneous parentheses around the comparison to silence this warning
        if ((innerCyc==maxInnerCyc))
            ~        ^            ~
dexus.cpp:136:15: note: use '=' to turn this equality comparison into an assignment
        if ((innerCyc==maxInnerCyc))
                     ^~
                     =
dexus.cpp:193:15: warning: unused variable 'DEFAULT_R' [-Wunused-variable]
        const double DEFAULT_R = 20; // R value used when re-setting clusters
                     ^
dexus.cpp:575:15: warning: unused variable 'DEFAULT_R' [-Wunused-variable]
        const double DEFAULT_R = 20; // R value used when re-setting clusters
                     ^
3 warnings 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 dexus.so dexus.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.11-bioc/meat/dexus.buildbin-libdir/00LOCK-dexus/00new/dexus/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 (dexus)


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