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BUILD BIN report for bamsignals on celaya2

This page was generated on 2019-10-16 12:55:13 -0400 (Wed, 16 Oct 2019).

Package 102/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bamsignals 1.16.0
Alessandro Mammana
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/bamsignals
Branch: RELEASE_3_9
Last Commit: dba9a4a
Last Changed Date: 2019-05-02 11:53:53 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: bamsignals
Version: 1.16.0
Command: rm -rf bamsignals.buildbin-libdir && mkdir bamsignals.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh bamsignals_1.16.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R bamsignals.buildbin-libdir
StartedAt: 2019-10-16 08:11:18 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 08:12:02 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 43.6 seconds
RetCode: 0
Status:  OK 
PackageFile: bamsignals_1.16.0.tgz
PackageFileSize: 2.991 MiB

Command output

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###
### Running command:
###
###   rm -rf bamsignals.buildbin-libdir && mkdir bamsignals.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh bamsignals_1.16.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R bamsignals.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=bamsignals.buildbin-libdir bamsignals_1.16.0.tar.gz'
>>>>>>> 

* installing *source* package ‘bamsignals’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/zlibbioc/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c CountSignals.cpp -o CountSignals.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/zlibbioc/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/zlibbioc/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c bamsignals.cpp -o bamsignals.o
bamsignals.cpp:521:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
        bam_write1(out->fp.bgzf, b); // write the alignment to `out'
        ^~~~~~~~~~ ~~~~~~~~~~~~~~~
bamsignals.cpp:516:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
    sam_hdr_write(out, header);
    ^~~~~~~~~~~~~ ~~~~~~~~~~~
bamsignals.cpp:530:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
    bam_index_build(bampath.c_str(), 0);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include/htslib/sam.h:320:41: note: expanded from macro 'bam_index_build'
#define bam_index_build(fn, min_shift) (sam_index_build((fn), (min_shift)))
                                        ^~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~
3 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/zlibbioc/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c bamsignals_init.c -o bamsignals_init.o
clang++ -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 bamsignals.so CountSignals.o RcppExports.o bamsignals.o bamsignals_init.o /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhtslib/usrlib/libhts.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/bamsignals.buildbin-libdir/00LOCK-bamsignals/00new/bamsignals/libs
** R
** 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 (bamsignals)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgcc_s.1.dylib" "bamsignals.buildbin-libdir/bamsignals/libs//bamsignals.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "bamsignals.buildbin-libdir/bamsignals/libs//bamsignals.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.5.2.dylib" "bamsignals.buildbin-libdir/bamsignals/libs//bamsignals.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "bamsignals.buildbin-libdir/bamsignals/libs//bamsignals.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "bamsignals.buildbin-libdir/bamsignals/libs//bamsignals.so"