| Back to Multiple platform build/check report for BioC 3.16 |
|
This page was generated on 2022-07-11 11:06:57 -0400 (Mon, 11 Jul 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4148 |
| lconway | macOS 12.2.1 Monterey | x86_64 | 4.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" | 4168 |
| kjohnson | macOS 12.4 Monterey | arm64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 3545 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the ShortRead package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ShortRead.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1820/2130 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ShortRead 1.55.0 (landing page) Bioconductor Package Maintainer
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| lconway | macOS 12.2.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson | macOS 12.4 Monterey / arm64 | OK | NA | NA | NA | |||||||||
| Package: ShortRead |
| Version: 1.55.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ShortRead |
| StartedAt: 2022-07-10 18:17:23 -0400 (Sun, 10 Jul 2022) |
| EndedAt: 2022-07-10 18:20:28 -0400 (Sun, 10 Jul 2022) |
| EllapsedTime: 185.1 seconds |
| RetCode: 0 |
| Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ShortRead ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library’ * installing *source* package ‘ShortRead’ ... ** using staged installation checking for gcc... clang -arch arm64 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 -arch arm64 accepts -g... yes checking for clang -arch arm64 option to accept ISO C89... none needed checking for gzeof in -lz... yes checking how to run the C preprocessor... clang -arch arm64 -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 -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-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 -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-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 -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-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 -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-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 -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-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 -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c alphabet.c -o alphabet.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c count.c -o count.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c io.c -o io.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-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 -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-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++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-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++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-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 -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sampler.c -o sampler.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c trim.c -o trim.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c util.c -o util.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c xsnap.c -o xsnap.o clang++ -arch arm64 -std=gnu++14 -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/4.2-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)