| Back to Build/check report for BioC 3.13 on Apple's new arm64 arch |
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This page was generated on 2021-01-31 03:53:37 -0500 (Sun, 31 Jan 2021).
| These are experimental builds on Apple's new arm64 arch. See here for more information. |
|
To the developers/maintainers of the ShortRead package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1666/1938 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ShortRead 1.49.1 Bioconductor Package Maintainer
| taxco | macOS 11.0.1 Big Sur / arm64 | OK | NA | NA | |||||||||
| Package: ShortRead |
| Version: 1.49.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ShortRead |
| StartedAt: 2021-01-30 16:57:59 -0500 (Sat, 30 Jan 2021) |
| EndedAt: 2021-01-30 16:59:47 -0500 (Sat, 30 Jan 2021) |
| EllapsedTime: 107.8 seconds |
| RetCode: 0 |
| Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ShortRead ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library’ * installing *source* package ‘ShortRead’ ... ** using staged installation checking for gcc... clang 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 clang accepts -g... yes checking for clang option to accept ISO C89... none needed checking for gzeof in -lz... yes checking how to run the C preprocessor... clang -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/4.1-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -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/4.1-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -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/4.1-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -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/4.1-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -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/4.1-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -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/4.1-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c alphabet.c -o alphabet.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c count.c -o count.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c io.c -o io.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -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/4.1-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c io_soap.c -o io_soap.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/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 -falign-functions=64 -Wall -g -O2 -c readBfaToc.cc -o readBfaToc.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/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 -falign-functions=64 -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/4.1-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sampler.c -o sampler.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c trim.c -o trim.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c util.c -o util.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c xsnap.c -o xsnap.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/opt/R/arm64/lib -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o S4Vectors_stubs.o XVector_stubs.o alphabet.o count.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 /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/00LOCK-ShortRead/00new/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 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 (ShortRead)