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BUILD BIN report for ShortRead on merida1

This page was generated on 2021-05-06 12:36:48 -0400 (Thu, 06 May 2021).

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 1697/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ShortRead 1.48.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/ShortRead
Branch: RELEASE_3_12
Last Commit: ba44cd2
Last Changed Date: 2020-10-27 10:33:27 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: ShortRead
Version: 1.48.0
Command: rm -rf ShortRead.buildbin-libdir && mkdir ShortRead.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ShortRead_1.48.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R ShortRead.buildbin-libdir
StartedAt: 2021-05-06 10:00:35 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 10:01:35 -0400 (Thu, 06 May 2021)
EllapsedTime: 60.2 seconds
RetCode: 0
Status:   OK  
PackageFile: ShortRead_1.48.0.tgz
PackageFileSize: 5.339 MiB

Command output

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###
### Running command:
###
###   rm -rf ShortRead.buildbin-libdir && mkdir ShortRead.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ShortRead_1.48.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R ShortRead.buildbin-libdir
###
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##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ShortRead.buildbin-libdir ShortRead_1.48.0.tar.gz'
>>>>>>> 

* installing *source* package ‘ShortRead’ ...
** using staged installation
checking for gcc... clang -mmacosx-version-min=10.13
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 -mmacosx-version-min=10.13 accepts -g... yes
checking for clang -mmacosx-version-min=10.13 option to accept ISO C89... none needed
checking for gzeof in -lz... yes
checking how to run the C preprocessor... clang -mmacosx-version-min=10.13 -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c Biostrings_stubs.c -o Biostrings_stubs.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_init_ShortRead.c -o R_init_ShortRead.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c XVector_stubs.c -o XVector_stubs.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c alphabet.c -o alphabet.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c count.c -o count.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c io.c -o io.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c io_bowtie.c -o io_bowtie.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c io_soap.c -o io_soap.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/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++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c sampler.c -o sampler.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c trim.c -o trim.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c util.c -o util.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c xsnap.c -o xsnap.o
clang++ -mmacosx-version-min=10.13 -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/usr/local/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 /Users/biocbuild/bbs-3.12-bioc/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 "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgcc_s.1.dylib" "ShortRead.buildbin-libdir/ShortRead/libs/ShortRead.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.5.dylib" "ShortRead.buildbin-libdir/ShortRead/libs/ShortRead.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "ShortRead.buildbin-libdir/ShortRead/libs/ShortRead.so"