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CHECK report for DEqMS on malbec1

This page was generated on 2021-05-06 12:27:19 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the DEqMS package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 459/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEqMS 1.8.0  (landing page)
Yafeng Zhu
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/DEqMS
Branch: RELEASE_3_12
Last Commit: 39cbf3b
Last Changed Date: 2020-10-27 11:38:32 -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: DEqMS
Version: 1.8.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:DEqMS.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings DEqMS_1.8.0.tar.gz
StartedAt: 2021-05-06 00:51:49 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 00:56:30 -0400 (Thu, 06 May 2021)
EllapsedTime: 281.2 seconds
RetCode: 0
Status:   OK  
CheckDir: DEqMS.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:DEqMS.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings DEqMS_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/DEqMS.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DEqMS/DESCRIPTION’ ... OK
* this is package ‘DEqMS’ version ‘1.8.0’
* 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 ‘DEqMS’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
Residualplot: no visible global function definition for ‘fitted’
Residualplot: no visible global function definition for ‘residuals’
VarianceScatterplot: no visible global function definition for ‘fitted’
peptideProfilePlot: no visible binding for global variable ‘variable’
peptideProfilePlot: no visible binding for global variable ‘value’
peptideProfilePlot: no visible binding for global variable ‘PSM_id’
peptideProfilePlot: no visible binding for global variable ‘Peptide’
spectraCounteBayes: no visible global function definition for ‘fitted’
Undefined global functions or variables:
  PSM_id Peptide fitted residuals value variable
Consider adding
  importFrom("stats", "fitted", "residuals")
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
medpolishSummary         95.996  0.068  96.428
farmsSummary             40.708  0.072  41.130
Residualplot             15.632  0.340  16.733
VarianceBoxplot          11.516  0.116  11.877
equalMedianNormalization 10.680  0.072  13.452
outputResult             10.616  0.072  10.952
medianSummary            10.552  0.064  10.855
spectraCounteBayes       10.412  0.092  10.805
VarianceScatterplot      10.436  0.044  13.362
medianSweeping           10.072  0.060  10.365
peptideProfilePlot        5.184  0.036   5.465
* 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/DEqMS.Rcheck/00check.log’
for details.



Installation output

DEqMS.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL DEqMS
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘DEqMS’ ...
** using staged installation
** R
** inst
** 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 (DEqMS)

Tests output


Example timings

DEqMS.Rcheck/DEqMS-Ex.timings

nameusersystemelapsed
Residualplot15.632 0.34016.733
VarianceBoxplot11.516 0.11611.877
VarianceScatterplot10.436 0.04413.362
equalMedianNormalization10.680 0.07213.452
farmsSummary40.708 0.07241.130
medianSummary10.552 0.06410.855
medianSweeping10.072 0.06010.365
medpolishSummary95.996 0.06896.428
outputResult10.616 0.07210.952
peptideProfilePlot5.1840.0365.465
spectraCounteBayes10.412 0.09210.805