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BioC 3.5: CHECK report for Rsubread on oaxaca

This page was generated on 2017-03-04 16:40:49 -0500 (Sat, 04 Mar 2017).

Package 1116/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rsubread 1.25.1
Wei Shi
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rsubread
Last Changed Rev: 125005 / Revision: 127142
Last Changed Date: 2016-12-11 22:29:27 -0500 (Sun, 11 Dec 2016)
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 UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: Rsubread
Version: 1.25.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rsubread_1.25.1.tar.gz
StartedAt: 2017-03-04 08:34:44 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 08:35:25 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 40.6 seconds
RetCode: 0
Status:  OK 
CheckDir: Rsubread.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rsubread_1.25.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Rsubread.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rsubread/DESCRIPTION’ ... OK
* this is package ‘Rsubread’ version ‘1.25.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rsubread’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 30.4Mb
  sub-directories of 1Mb or more:
    annot  28.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.findCommonVariants_inner: no visible global function definition for
  ‘read.delim’
atgcContent: no visible global function definition for ‘read.csv’
createAnnotationFile: no visible global function definition for ‘is’
createAnnotationFile: no visible global function definition for
  ‘values’
createAnnotationFile: no visible global function definition for
  ‘seqnames’
createAnnotationFile: no visible global function definition for ‘start’
createAnnotationFile: no visible global function definition for ‘end’
createAnnotationFile: no visible global function definition for
  ‘strand’
detectionCall: no visible global function definition for
  ‘download.file’
detectionCall: no visible global function definition for ‘read.delim’
detectionCall: no visible global function definition for ‘lowess’
detectionCall: no visible global function definition for ‘approxfun’
detectionCall: no visible global function definition for ‘ppois’
detectionCall: no visible global function definition for ‘runif’
detectionCall: no visible global function definition for ‘dpois’
detectionCall: no visible global function definition for ‘pdf’
detectionCall: no visible global function definition for ‘density’
detectionCall: no visible global function definition for ‘dev.off’
featureCounts: no visible global function definition for ‘write.table’
featureCounts: no visible global function definition for ‘read.delim’
findCommonVariants: no visible global function definition for
  ‘read.delim’
getInBuiltAnnotation: no visible binding for global variable
  ‘annot.inbuilt’
getInBuiltAnnotation: no visible global function definition for
  ‘read.delim’
processExons: no visible global function definition for ‘read.delim’
processExons: no visible global function definition for ‘write.table’
propmapped: no visible global function definition for ‘read.delim’
qualityScores: no visible global function definition for ‘read.csv’
write.Rsubread: no visible global function definition for ‘is’
write.Rsubread: no visible global function definition for ‘values’
write.Rsubread: no visible global function definition for ‘seqnames’
write.Rsubread: no visible global function definition for ‘start’
write.Rsubread: no visible global function definition for ‘end’
write.Rsubread: no visible global function definition for ‘strand’
Undefined global functions or variables:
  annot.inbuilt approxfun density dev.off download.file dpois end is
  lowess pdf ppois read.csv read.delim runif seqnames start strand
  values write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("methods", "is")
  importFrom("stats", "approxfun", "density", "dpois", "end", "lowess",
             "ppois", "runif", "start")
  importFrom("utils", "download.file", "read.csv", "read.delim",
             "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘Rsubread/libs/Rsubread.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Objects: ‘HelperFunctions.o’, ‘build-sam-index.o’, ‘core.o’,
      ‘sorted-hashtable.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Objects: ‘HelperFunctions.o’, ‘core-indel.o’, ‘core.o’,
      ‘propmapped.o’
File ‘Rsubread/libs/Rsubread.so’:
  Found non-API call to R: ‘R_CStackLimit’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/Rsubread.Rcheck/00check.log’
for details.


Rsubread.Rcheck/00install.out:

* 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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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 1.25.1\"" -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
warning: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/nm: no name list
warning: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/nm: no name list
warning: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/nm: no name list
warning: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/nm: no name list
warning: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/nm: no name list
installing to /Users/biocbuild/bbs-3.5-bioc/meat/Rsubread.Rcheck/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)

Rsubread.Rcheck/Rsubread-Ex.timings:

nameusersystemelapsed
align1.8481.6243.473
buildindex0.4300.6451.076
createAnnotationFile000
featureCounts0.0010.0000.001
findCommonVariants0.0000.0000.001
getInBuiltAnnotation2.6670.0392.707
propmapped2.0391.4213.481
qualityScores0.0710.0020.073