Bioconductor Package Maintainer
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/ShortRead |
| Branch: RELEASE_3_8 |
| Last Commit: 0cbe4b6 |
| Last Changed Date: 2018-10-30 11:41:44 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:54:51 -0400 (Tue, 16 Apr 2019).
| Package 1435/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ShortRead 1.40.0 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | [ OK ] | |
| Package: ShortRead |
| Version: 1.40.0 |
| Command: rm -rf ShortRead.buildbin-libdir && mkdir ShortRead.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ShortRead_1.40.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R ShortRead.buildbin-libdir |
| StartedAt: 2019-04-16 04:44:47 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 04:45:30 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 42.9 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: ShortRead_1.40.0.tgz |
| PackageFileSize: 5.313 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf ShortRead.buildbin-libdir && mkdir ShortRead.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ShortRead_1.40.0.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_1.40.0.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"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c Biostrings_stubs.c -o Biostrings_stubs.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c R_init_ShortRead.c -o R_init_ShortRead.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c XVector_stubs.c -o XVector_stubs.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c alphabet.c -o alphabet.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c io.c -o io.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c io_bowtie.c -o io_bowtie.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c io_soap.c -o io_soap.o clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I/usr/local/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 -g -O2 -c readBfaToc.cc -o readBfaToc.o clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I/usr/local/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 -g -O2 -c read_maq_map.cc -o read_maq_map.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c sampler.c -o sampler.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c trim.c -o trim.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c util.c -o util.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Biostrings/include" -I/usr/local/include -fopenmp -fPIC -Wall -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 -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.8-bioc/meat/ShortRead.buildbin-libdir/ShortRead/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 * 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/3.5/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/3.5/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/3.5/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/3.5/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/3.5/Resources/lib/libquadmath.0.dylib" "ShortRead.buildbin-libdir/ShortRead/libs//ShortRead.so"