Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:22:50 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for DEqMS on merida1


To the developers/maintainers of the DEqMS package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DEqMS.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 509/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEqMS 1.14.0  (landing page)
Yafeng Zhu
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/DEqMS
git_branch: RELEASE_3_15
git_last_commit: a30da35
git_last_commit_date: 2022-04-26 11:50:53 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DEqMS
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DEqMS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DEqMS_1.14.0.tar.gz
StartedAt: 2022-10-19 01:33:12 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 01:39:49 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 397.5 seconds
RetCode: 0
Status:   OK  
CheckDir: DEqMS.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DEqMS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DEqMS_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/DEqMS.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DEqMS/DESCRIPTION’ ... OK
* this is package ‘DEqMS’ version ‘1.14.0’
* 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 ... NOTE
Package in Depends field not imported from: ‘matrixStats’
  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
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         151.702  0.436 152.492
farmsSummary              52.569  0.942  54.392
Residualplot              23.347  1.612  36.173
VarianceScatterplot       11.146  0.249  11.819
VarianceBoxplot           10.941  0.318  11.730
spectraCounteBayes        10.552  0.211  10.944
equalMedianNormalization   9.820  0.234  10.321
medianSummary              9.577  0.183  10.068
outputResult               9.550  0.148   9.873
medianSweeping             8.624  0.165   9.062
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/DEqMS.Rcheck/00check.log’
for details.



Installation output

DEqMS.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DEqMS
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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
Residualplot23.347 1.61236.173
VarianceBoxplot10.941 0.31811.730
VarianceScatterplot11.146 0.24911.819
equalMedianNormalization 9.820 0.23410.321
farmsSummary52.569 0.94254.392
medianSummary 9.577 0.18310.068
medianSweeping8.6240.1659.062
medpolishSummary151.702 0.436152.492
outputResult9.5500.1489.873
peptideProfilePlot3.8140.1244.109
spectraCounteBayes10.552 0.21110.944