Back to Mac ARM64 build report for BioC 3.16
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This page was generated on 2023-04-19 11:01:58 -0400 (Wed, 19 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnsonmacOS 13.0 Venturaarm644.2.2 (2022-10-31) -- "Innocent and Trusting" 4256
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BUILD BIN results for ShortRead on kjohnson


To the developers/maintainers of the ShortRead package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1861/2183HostnameOS / ArchINSTALLBUILDBUILD BIN
ShortRead 1.56.1  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2023-04-12 13:00:02 -0400 (Wed, 12 Apr 2023)
git_url: https://git.bioconductor.org/packages/ShortRead
git_branch: RELEASE_3_16
git_last_commit: e5758ff
git_last_commit_date: 2022-11-16 07:57:29 -0400 (Wed, 16 Nov 2022)
kjohnsonmacOS 13.0 Ventura / arm64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ShortRead
Version: 1.56.1
Command: rm -rf ShortRead.buildbin-libdir && mkdir ShortRead.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ShortRead_1.56.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R ShortRead.buildbin-libdir
StartedAt: 2023-04-18 19:33:12 -0400 (Tue, 18 Apr 2023)
EndedAt: 2023-04-18 19:35:20 -0400 (Tue, 18 Apr 2023)
EllapsedTime: 128.7 seconds
RetCode: 0
Status:   OK  
PackageFile: ShortRead_1.56.1.tgz
PackageFileSize: 5.396 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ShortRead.buildbin-libdir && mkdir ShortRead.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ShortRead_1.56.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R ShortRead.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ShortRead.buildbin-libdir ShortRead_1.56.1.tar.gz'
>>>>>>> 

* 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
ld: warning: -undefined dynamic_lookup may not work with chained fixups
installing to /Volumes/External/bbs-3.16-bioc-m1/meat/ShortRead.buildbin-libdir/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)


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

install_name_tool -change "/opt/R/arm64/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgcc_s.1.1.dylib" "ShortRead.buildbin-libdir/ShortRead/libs/ShortRead.so"
install_name_tool -change "/opt/R/arm64/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgfortran.5.dylib" "ShortRead.buildbin-libdir/ShortRead/libs/ShortRead.so"
install_name_tool -change "/opt/R/arm64/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libquadmath.0.dylib" "ShortRead.buildbin-libdir/ShortRead/libs/ShortRead.so"