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CHECK report for Rsubread on merida2

This page was generated on 2018-10-17 08:49:10 -0400 (Wed, 17 Oct 2018).

Package 1285/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rsubread 1.30.9
Wei Shi , Yang Liao and Gordon K Smyth
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/Rsubread
Branch: RELEASE_3_7
Last Commit: 75993b5
Last Changed Date: 2018-10-03 22:48:31 -0400 (Wed, 03 Oct 2018)
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...
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: Rsubread
Version: 1.30.9
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Rsubread.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Rsubread_1.30.9.tar.gz
StartedAt: 2018-10-16 23:50:11 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 23:51:31 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 79.2 seconds
RetCode: 0
Status:  OK 
CheckDir: Rsubread.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Rsubread.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Rsubread_1.30.9.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/Rsubread.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rsubread/DESCRIPTION’ ... OK
* this is package ‘Rsubread’ version ‘1.30.9’
* 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 30.6Mb
  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’
.load.delete.summary: no visible global function definition for
  ‘read.delim’
align: no visible global function definition for ‘write.table’
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’
flattenGTF: 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’
subjunc: no visible global function definition for ‘write.table’
txUnique: no visible global function definition for ‘read.delim’
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 ... NOTE
prepare_Rd: flattenGTF.Rd:27: Dropping empty section \examples
* 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 shell scripts ... 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
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rsubread/libs/Rsubread.so’:
  Found ‘_srand’, possibly from ‘srand’ (C)
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 use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
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
Examples with CPU or elapsed time > 5s
             user system elapsed
sublong    23.128  4.276  22.901
align       6.668  3.083   9.884
propmapped  6.215  3.001   9.295
buildindex  6.146  1.999   8.300
* 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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/Rsubread.Rcheck/00check.log’
for details.



Installation output

Rsubread.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/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  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c HelperFunctions.c -o HelperFunctions.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c LRMbase-index.c -o LRMbase-index.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c LRMchro-event.c -o LRMchro-event.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c LRMfile-io.c -o LRMfile-io.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c LRMhashtable.c -o LRMhashtable.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c LRMhelper.c -o LRMhelper.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c LRMseek-zlib.c -o LRMseek-zlib.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c R_wrapper.c -o R_wrapper.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c SNPCalling.c -o SNPCalling.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c aligner.c -o aligner.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c atgcContent.c -o atgcContent.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -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  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c core-bigtable.c -o core-bigtable.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c core-indel.c -o core-indel.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -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  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -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  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c core-junction.c -o core-junction.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c core.c -o core.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c detection-calls.c -o detection-calls.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c detectionCall.c -o detectionCall.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c detectionCallAnnotation.c -o detectionCallAnnotation.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c exon-algorithms.c -o exon-algorithms.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -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  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c exon-align.c -o exon-align.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c flattenAnnotations.c -o flattenAnnotations.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c fullscan.c -o fullscan.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c fusion-align.c -o fusion-align.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c gene-algorithms.c -o gene-algorithms.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -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  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c hashtable.c -o hashtable.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c index-builder.c -o index-builder.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c input-files.c -o input-files.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c interval_merge.c -o interval_merge.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c long-hashtable.c -o long-hashtable.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c longread-mapping.c -o longread-mapping.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c mergeVCF.c -o mergeVCF.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c processExons.c -o processExons.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c propmapped.c -o propmapped.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c qualityScores.c -o qualityScores.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c read-repair.c -o read-repair.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c readSummary.c -o readSummary.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c removeDupReads.c -o removeDupReads.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c sam2bed.c -o sam2bed.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c sambam-file.c -o sambam-file.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c seek-zlib.c -o seek-zlib.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c sorted-hashtable.c -o sorted-hashtable.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c sublog.c -o sublog.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.30.9\""  -fPIC  -Wall -g -O2  -c tx-unique.c -o tx-unique.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 LRMbase-index.o LRMchro-event.o LRMfile-io.o LRMhashtable.o LRMhelper.o LRMseek-zlib.o LRMsorted-hashtable.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 detection-calls.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align-indel.o exon-align.o flattenAnnotations.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 longread-mapping.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 tx-unique.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/3.5/Resources/library/Rsubread/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘Rsubread.Rnw’ 
** testing if installed package can be loaded
* DONE (Rsubread)

Tests output


Example timings

Rsubread.Rcheck/Rsubread-Ex.timings

nameusersystemelapsed
align6.6683.0839.884
buildindex6.1461.9998.300
createAnnotationFile0.0010.0000.002
featureCounts0.0030.0000.004
findCommonVariants0.0010.0000.001
getInBuiltAnnotation0.4590.0250.490
promoterRegions1.4850.0731.573
propmapped6.2153.0019.295
qualityScores0.0590.0030.063
sublong23.128 4.27622.901