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CHECK report for sSeq on merida1

This page was generated on 2021-05-06 12:36:57 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the sSeq package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1789/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sSeq 1.28.0  (landing page)
Danni Yu
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/sSeq
Branch: RELEASE_3_12
Last Commit: 401f680
Last Changed Date: 2020-10-27 10:50:42 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: sSeq
Version: 1.28.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:sSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings sSeq_1.28.0.tar.gz
StartedAt: 2021-05-06 06:36:20 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:40:59 -0400 (Thu, 06 May 2021)
EllapsedTime: 279.3 seconds
RetCode: 0
Status:   OK  
CheckDir: sSeq.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:sSeq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings sSeq_1.28.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/sSeq.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sSeq’ version ‘1.28.0’
* 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 ‘sSeq’ can be installed ... OK
* checking installed package size ... OK
* 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
'library' or 'require' call to ‘caTools’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RColorBrewer’ ‘caTools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
drawMA_vol: no visible global function definition for ‘par’
drawMA_vol: no visible global function definition for ‘points’
drawMA_vol: no visible global function definition for ‘abline’
ecdfAUC: no visible global function definition for ‘ecdf’
ecdfAUC: no visible global function definition for ‘trapz’
ecdfAUC: no visible global function definition for ‘mtext’
ecdfAUC: no visible global function definition for ‘axis’
ecdfAUC: no visible global function definition for ‘box’
ecdfAUC: no visible global function definition for ‘lines’
ecdfAUC: no visible global function definition for ‘abline’
ecdfAUC: no visible global function definition for ‘legend’
exactNBtest1: no visible global function definition for ‘dnbinom’
getAdjustDisp: no visible global function definition for ‘quantile’
getAdjustDisp: no visible global function definition for ‘var’
getNormFactor : <anonymous>: no visible global function definition for
  ‘median’
getQ: no visible global function definition for ‘quantile’
getQ: no visible global function definition for ‘cov’
getQ: no visible global function definition for ‘var’
getQ: no visible global function definition for ‘abline’
getQ: no visible global function definition for ‘mtext’
getT: no visible global function definition for ‘quantile’
getT: no visible global function definition for ‘sd’
getT: no visible global function definition for ‘cov’
getT: no visible global function definition for ‘var’
getT: no visible global function definition for ‘mtext’
getT: no visible global function definition for ‘axis’
getT: no visible global function definition for ‘abline’
getTgroup: no visible global function definition for ‘quantile’
getTgroup: no visible global function definition for ‘cov’
getTgroup: no visible global function definition for ‘var’
getTgroup: no visible global function definition for ‘mtext’
getTgroup: no visible global function definition for ‘box’
getTgroup: no visible global function definition for ‘axis’
getTgroup: no visible global function definition for ‘abline’
nbinomTestForMatricesSH : int.func: no visible global function
  definition for ‘median’
nbinomTestForMatricesSH: no visible global function definition for
  ‘dnbinom’
nbinomTestForMatricesSH: no visible global function definition for
  ‘pchisq’
plotDispersion: no visible global function definition for ‘brewer.pal’
plotDispersion: no visible global function definition for
  ‘smoothScatter’
plotDispersion: no visible binding for global variable ‘blues9’
plotDispersion: no visible global function definition for ‘points’
plotDispersion: no visible global function definition for ‘legend’
rnbinomMV: no visible global function definition for ‘rnbinom’
rowVars: no visible binding for global variable ‘var’
sim: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline axis blues9 box brewer.pal cov dnbinom ecdf legend lines
  median mtext par pchisq points quantile rnbinom rnorm sd
  smoothScatter trapz var
Consider adding
  importFrom("grDevices", "blues9")
  importFrom("graphics", "abline", "axis", "box", "legend", "lines",
             "mtext", "par", "points", "smoothScatter")
  importFrom("stats", "cov", "dnbinom", "ecdf", "median", "pchisq",
             "quantile", "rnbinom", "rnorm", "sd", "var")
to your NAMESPACE file.
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
getTgroup    79.805  1.311  81.219
nbTestSH     77.891  1.167  79.174
sSeq-package 74.848  1.056  76.001
* 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-3.12-bioc/meat/sSeq.Rcheck/00check.log’
for details.



Installation output

sSeq.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL sSeq
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘sSeq’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (sSeq)

Tests output


Example timings

sSeq.Rcheck/sSeq-Ex.timings

nameusersystemelapsed
Hammer2months0.0590.0070.066
Sultan0.0640.0040.069
Tuch0.0300.0030.032
countsTable0.0170.0020.019
drawMA_vol0.4560.0080.467
ecdfAUC0.0680.0040.073
equalSpace0.3550.0060.362
exactNBtest10.0010.0000.000
getAdjustDisp0.3070.0030.311
getNormFactor0.0210.0020.024
getQ1.3460.1761.524
getT1.0750.0771.154
getTgroup79.805 1.31181.219
nbTestSH77.891 1.16779.174
plotDispersion2.8170.3223.147
rnbinomMV0.0020.0000.003
rowVars0.0000.0000.001
sSeq-package74.848 1.05676.001
sim0.3320.0300.363