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CHECK report for Rsubread on celaya2

This page was generated on 2019-04-09 13:00:33 -0400 (Tue, 09 Apr 2019).

Package 1398/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rsubread 1.33.33
Wei Shi , Yang Liao and Gordon K Smyth
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/Rsubread
Branch: master
Last Commit: 8a60064
Last Changed Date: 2019-04-08 01:22:04 -0400 (Mon, 08 Apr 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK YES, new version is higher than in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 ...NOT SUPPORTED...
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK YES, new version is higher than in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: Rsubread
Version: 1.33.33
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_1.33.33.tar.gz
StartedAt: 2019-04-09 05:10:18 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 05:11:56 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 97.8 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_1.33.33.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Rsubread.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.33.33’
* 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 ... OK
* 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 34.0Mb
  sub-directories of 1Mb or more:
    annot  28.5Mb
    qualf   3.4Mb
* 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 ... OK
* 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 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
* 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    15.917  6.967  21.092
align       7.775  6.116  14.091
propmapped  7.748  5.906  14.517
buildindex  5.991  3.459   9.529
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-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/3.6/Resources/library’
* installing *source* package ‘Rsubread’ ...
** using staged installation
@@@@@ 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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -fPIC  -Wall -g -O2  -c RsimReads.c -o RsimReads.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -fPIC  -Wall -g -O2  -c gen_rand_reads.c -o gen_rand_reads.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include -DMAKE_FOR_EXON -D MACOS  -D SUBREAD_VERSION="\"Rsubread 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 1.33.33\""  -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 RsimReads.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 gen_rand_reads.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/3.6/Resources/library/00LOCK-Rsubread/00new/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 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 (Rsubread)

Tests output


Example timings

Rsubread.Rcheck/Rsubread-Ex.timings

nameusersystemelapsed
align 7.775 6.11614.091
buildindex5.9913.4599.529
featureCounts0.0010.0010.001
findCommonVariants0.0000.0000.001
getInBuiltAnnotation0.4750.0530.555
promoterRegions1.4650.1111.690
propmapped 7.748 5.90614.517
qualityScores0.0860.0340.121
simReads0.0010.0000.000
sublong15.917 6.96721.092