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BioC 3.5: INSTALL report for Rsubread on toluca2

This page was generated on 2017-04-23 14:35:40 -0400 (Sun, 23 Apr 2017).

Package 1151/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rsubread 1.25.2
Wei Shi
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rsubread
Last Changed Rev: 127407 / Revision: 129046
Last Changed Date: 2017-03-15 00:12:59 -0400 (Wed, 15 Mar 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...
toluca2 Mac OS X Mavericks (10.9.5) / x86_64 [ OK ] OK  OK  OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Rsubread
Version: 1.25.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rsubread
StartedAt: 2017-04-22 17:57:22 -0400 (Sat, 22 Apr 2017)
EndedAt: 2017-04-22 17:57:36 -0400 (Sat, 22 Apr 2017)
EllapsedTime: 13.7 seconds
RetCode: 0
Status:  OK 

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rsubread
###
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##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library’
* installing *source* package ‘Rsubread’ ...
@@@@@ The operating system is Darwin.
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c HelperFunctions.c -o HelperFunctions.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c R_wrapper.c -o R_wrapper.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c SNPCalling.c -o SNPCalling.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c aligner.c -o aligner.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c atgcContent.c -o atgcContent.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c build-sam-index.c -o build-sam-index.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c core-bigtable.c -o core-bigtable.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c core-indel.c -o core-indel.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c core-interface-aligner.c -o core-interface-aligner.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c core-interface-subjunc.c -o core-interface-subjunc.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c core-junction.c -o core-junction.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c core.c -o core.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c detectionCall.c -o detectionCall.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c detectionCallAnnotation.c -o detectionCallAnnotation.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c exon-algorithms.c -o exon-algorithms.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c exon-align-indel.c -o exon-align-indel.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c exon-align.c -o exon-align.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c fullscan.c -o fullscan.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c fusion-align.c -o fusion-align.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c gene-algorithms.c -o gene-algorithms.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c gene-value-index.c -o gene-value-index.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c hashtable.c -o hashtable.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c index-builder.c -o index-builder.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c input-files.c -o input-files.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c interval_merge.c -o interval_merge.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c long-hashtable.c -o long-hashtable.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c mergeVCF.c -o mergeVCF.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c processExons.c -o processExons.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c propmapped.c -o propmapped.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c qualityScores.c -o qualityScores.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c read-repair.c -o read-repair.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c readSummary.c -o readSummary.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c removeDupReads.c -o removeDupReads.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c sam2bed.c -o sam2bed.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c sambam-file.c -o sambam-file.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c seek-zlib.c -o seek-zlib.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c sorted-hashtable.c -o sorted-hashtable.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.25.2\"" -fPIC  -Wall -mtune=core2 -g -O2  -c sublog.c -o sublog.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 Rsubread.so HelperFunctions.o R_wrapper.o SNPCalling.o aligner.o atgcContent.o build-sam-index.o core-bigtable.o core-indel.o core-interface-aligner.o core-interface-subjunc.o core-junction.o core.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align-indel.o exon-align.o fullscan.o fusion-align.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-files.o interval_merge.o long-hashtable.o mergeVCF.o processExons.o propmapped.o qualityScores.o read-repair.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o seek-zlib.o sorted-hashtable.o sublog.o -lpthread -DMAKE_FOR_EXON -D MACOS -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rsubread/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rsubread)