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BioC 3.5: BUILD BIN report for Starr on oaxaca

This page was generated on 2017-03-04 16:38:13 -0500 (Sat, 04 Mar 2017).

Package 1238/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Starr 1.31.0
Benedikt Zacher
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Starr
Last Changed Rev: 122712 / Revision: 127142
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 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
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK [ OK ]

Summary

Package: Starr
Version: 1.31.0
Command: rm -rf Starr.buildbin-libdir && mkdir Starr.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Starr_1.31.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Starr.buildbin-libdir
StartedAt: 2017-03-04 12:28:23 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 12:29:02 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 38.7 seconds
RetCode: 0
Status:  OK 
PackageFile: Starr_1.31.0.tgz
PackageFileSize: 1.615 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf Starr.buildbin-libdir && mkdir Starr.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Starr_1.31.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Starr.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Starr.buildbin-libdir Starr_1.31.0.tar.gz'
>>>>>>> 

* installing *source* package ‘Starr’ ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DHAVE_ZLIB=1   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c ahocorasick.c -o ahocorasick.o
ahocorasick.c:8:1: warning: unused function 'kseq_rewind' [-Wunused-function]
KSEQ_INIT(gzFile, gzread)
^
./kseq.h:220:2: note: expanded from macro 'KSEQ_INIT'
        __KSEQ_BASIC(type_t)                                            \
        ^
./kseq.h:152:21: note: expanded from macro '__KSEQ_BASIC'
        static inline void kseq_rewind(kseq_t *ks)                                                      \
                           ^
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DHAVE_ZLIB=1   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c collect.c -o collect.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DHAVE_ZLIB=1   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c rm_small_peak.c -o rm_small_peak.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DHAVE_ZLIB=1   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c sort_by_genomic.c -o sort_by_genomic.o
clang -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 Starr.so ahocorasick.o collect.o rm_small_peak.o sort_by_genomic.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/Starr.buildbin-libdir/Starr/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Starr)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgcc_s.1.dylib" "Starr.buildbin-libdir/Starr/libs//Starr.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "Starr.buildbin-libdir/Starr/libs//Starr.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.5.2.dylib" "Starr.buildbin-libdir/Starr/libs//Starr.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "Starr.buildbin-libdir/Starr/libs//Starr.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "Starr.buildbin-libdir/Starr/libs//Starr.so"