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CHECK report for DEqMS on malbec1

This page was generated on 2019-04-16 11:53:46 -0400 (Tue, 16 Apr 2019).

Package 393/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEqMS 1.0.1
Yafeng Zhu
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/DEqMS
Branch: RELEASE_3_8
Last Commit: f13e048
Last Changed Date: 2019-01-04 13:28:45 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DEqMS
Version: 1.0.1
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:DEqMS.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings DEqMS_1.0.1.tar.gz
StartedAt: 2019-04-15 23:25:12 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:28:56 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 224.2 seconds
RetCode: 0
Status:  OK 
CheckDir: DEqMS.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:DEqMS.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings DEqMS_1.0.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/DEqMS.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.0.1’
* 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 ‘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
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’
Undefined global functions or variables:
  PSM_id Peptide value variable
* 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 or elapsed time > 5s
                           user system elapsed
medpolishSummary         99.328  0.048  99.782
farmsSummary             37.248  0.200  37.862
equalMedianNormalization 13.388  0.416  14.469
plotFitCurve              7.600  0.028   7.686
medianSweeping            7.392  0.052   7.629
spectraCounteBayes        7.396  0.044   7.691
medianSummary             7.356  0.072   7.705
outputResult              7.036  0.040   7.283
* 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-3.8-bioc/meat/DEqMS.Rcheck/00check.log’
for details.



Installation output

DEqMS.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL DEqMS
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘DEqMS’ ...
** 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
* DONE (DEqMS)

Tests output


Example timings

DEqMS.Rcheck/DEqMS-Ex.timings

nameusersystemelapsed
equalMedianNormalization13.388 0.41614.469
farmsSummary37.248 0.20037.862
medianSummary7.3560.0727.705
medianSweeping7.3920.0527.629
medpolishSummary99.328 0.04899.782
outputResult7.0360.0407.283
peptideProfilePlot2.5080.0242.736
plotFitCurve7.6000.0287.686
spectraCounteBayes7.3960.0447.691