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BUILD BIN report for IRanges on machv2

This page was generated on 2020-10-17 11:58:45 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE IRanges PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 894/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IRanges 2.22.2
Bioconductor Package Maintainer
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/IRanges
Branch: RELEASE_3_11
Last Commit: 8c5e991
Last Changed Date: 2020-05-20 17:05:42 -0400 (Wed, 20 May 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: IRanges
Version: 2.22.2
Command: rm -rf IRanges.buildbin-libdir && mkdir IRanges.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh IRanges_2.22.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R IRanges.buildbin-libdir
StartedAt: 2020-10-17 07:19:35 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 07:20:57 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 82.0 seconds
RetCode: 0
Status:  OK 
PackageFile: IRanges_2.22.2.tgz
PackageFileSize: 2.186 MiB

Command output

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###
### Running command:
###
###   rm -rf IRanges.buildbin-libdir && mkdir IRanges.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh IRanges_2.22.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R IRanges.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=IRanges.buildbin-libdir IRanges_2.22.2.tar.gz'
>>>>>>> 

* installing *source* package ‘IRanges’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c CompressedList_class.c -o CompressedList_class.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c Grouping_class.c -o Grouping_class.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c IPosRanges_comparison.c -o IPosRanges_comparison.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c IRanges_class.c -o IRanges_class.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c IRanges_constructor.c -o IRanges_constructor.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c NCList.c -o NCList.o
NCList.c:202:22: warning: unused function 'next_top_down' [-Wunused-function]
static const NCList *next_top_down(const NCList *nclist)
                     ^
NCList.c:1173:13: warning: function 'NCList_get_y_overlaps_rec' is not needed and will not be emitted [-Wunneeded-internal-declaration]
static void NCList_get_y_overlaps_rec(const NCList *x_nclist,
            ^
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_init_IRanges.c -o R_init_IRanges.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c Ranges_class.c -o Ranges_class.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RleViews_utils.c -o RleViews_utils.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c coverage_methods.c -o coverage_methods.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c extractListFragments.c -o extractListFragments.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c inter_range_methods.c -o inter_range_methods.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 IRanges.so CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o Grouping_class.o IPosRanges_comparison.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o RleViews_utils.o S4Vectors_stubs.o SimpleIRangesList_class.o coverage_methods.o extractListFragments.o inter_range_methods.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.11-bioc/meat/IRanges.buildbin-libdir/00LOCK-IRanges/00new/IRanges/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘drop’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘chartr’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘toupper’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘tolower’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘sub’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘gsub’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘startsWith’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘endsWith’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘IRanges’
** 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 (IRanges)


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