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BioC 3.4: BUILD BIN report for ShortRead on morelia

This page was generated on 2017-04-15 16:22:44 -0400 (Sat, 15 Apr 2017).

Package 1137/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ShortRead 1.32.1
Bioconductor Package Maintainer
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/ShortRead
Last Changed Rev: 127452 / Revision: 128728
Last Changed Date: 2017-03-15 22:03:50 -0400 (Wed, 15 Mar 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: ShortRead
Version: 1.32.1
Command: rm -rf ShortRead.buildbin-libdir && mkdir ShortRead.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ShortRead_1.32.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R ShortRead.buildbin-libdir
StartedAt: 2017-04-15 11:02:55 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 11:03:19 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 23.5 seconds
RetCode: 0
Status:  OK 
PackageFile: ShortRead_1.32.1.tgz
PackageFileSize: 4.514 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ShortRead.buildbin-libdir && mkdir ShortRead.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ShortRead_1.32.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R ShortRead.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ShortRead.buildbin-libdir ShortRead_1.32.1.tar.gz'
>>>>>>> 

* installing *source* package ‘ShortRead’ ...
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for gzeof in -lz... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking size of unsigned long... 8
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c Biostrings_stubs.c -o Biostrings_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c R_init_ShortRead.c -o R_init_ShortRead.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c XVector_stubs.c -o XVector_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c alphabet.c -o alphabet.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c io.c -o io.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c io_bowtie.c -o io_bowtie.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c io_soap.c -o io_soap.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include"  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fPIC  -Wall -mtune=core2 -g -O2  -c readBfaToc.cc -o readBfaToc.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include"  -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fPIC  -Wall -mtune=core2 -g -O2  -c read_maq_map.cc -o read_maq_map.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c sampler.c -o sampler.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c trim.c -o trim.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c util.c -o util.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Biostrings/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c xsnap.c -o xsnap.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 ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o S4Vectors_stubs.o XVector_stubs.o alphabet.o io.o io_bowtie.o io_soap.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-bioc/meat/ShortRead.buildbin-libdir/ShortRead/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 (ShortRead)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libgcc_s.1.dylib" "ShortRead.buildbin-libdir/ShortRead/libs//ShortRead.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libgfortran.3.dylib" "ShortRead.buildbin-libdir/ShortRead/libs//ShortRead.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libreadline.5.2.dylib" "ShortRead.buildbin-libdir/ShortRead/libs//ShortRead.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libreadline.dylib" "ShortRead.buildbin-libdir/ShortRead/libs//ShortRead.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libquadmath.0.dylib" "ShortRead.buildbin-libdir/ShortRead/libs//ShortRead.so"