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CHECK report for msgbsR on merida1

This page was generated on 2019-04-16 12:00:40 -0400 (Tue, 16 Apr 2019).

Package 1005/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
msgbsR 1.6.1
Benjamin Mayne
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/msgbsR
Branch: RELEASE_3_8
Last Commit: 411f316
Last Changed Date: 2019-01-04 13:40:29 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: msgbsR
Version: 1.6.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:msgbsR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings msgbsR_1.6.1.tar.gz
StartedAt: 2019-04-16 01:26:03 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:33:16 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 433.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: msgbsR.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:msgbsR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings msgbsR_1.6.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/msgbsR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘msgbsR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘msgbsR’ version ‘1.6.1’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘msgbsR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 15.9Mb
  sub-directories of 1Mb or more:
    extdata  15.2Mb
* 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 ... NOTE
Namespace in Imports field not imported from: 'utils'
  All declared Imports should be used.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
               old_size new_size compress
  ratdata.rda     318Kb    125Kb       xz
  ratdata2.rda    287Kb    116Kb       xz
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
rawCounts 8.861  0.304    9.26
* 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/msgbsR.Rcheck/00check.log’
for details.



Installation output

msgbsR.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL msgbsR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘msgbsR’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘IRanges’ for request: ‘rev’ when loading ‘easyRNASeq’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in package ‘IRanges’ for request: ‘rev’ when loading ‘easyRNASeq’
* DONE (msgbsR)

Tests output


Example timings

msgbsR.Rcheck/msgbsR-Ex.timings

nameusersystemelapsed
checkCuts2.6250.5833.569
diffMeth2.5300.0652.616
plotCircos1.8620.0791.959
plotCounts0.4240.0090.433
rawCounts8.8610.3049.260