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CHECK report for GSEAlm on machv2

This page was generated on 2020-10-17 11:58:39 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE GSEAlm PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 787/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GSEAlm 1.48.0
Assaf Oron
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/GSEAlm
Branch: RELEASE_3_11
Last Commit: 6228177
Last Changed Date: 2020-04-27 14:16:42 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: GSEAlm
Version: 1.48.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GSEAlm.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GSEAlm_1.48.0.tar.gz
StartedAt: 2020-10-17 01:53:38 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 01:54:22 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 43.7 seconds
RetCode: 0
Status:  OK 
CheckDir: GSEAlm.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:GSEAlm.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GSEAlm_1.48.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/GSEAlm.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GSEAlm/DESCRIPTION’ ... OK
* this is package ‘GSEAlm’ version ‘1.48.0’
* 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 ‘GSEAlm’ 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
Package in Depends field not imported from: ‘Biobase’
  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
pvalFromPermMat: warning in matrix(as.double(NA), nr = nrow(perms),
  ncol = 2): partial argument match of 'nr' to 'nrow'
CooksDPerGene: no visible global function definition for ‘exprs’
dfbetasPerGene: no visible global function definition for ‘exprs’
dfbetasPerGene: no visible global function definition for
  ‘featureNames’
dfbetasPerGene: no visible global function definition for ‘sampleNames’
dffitsPerGene: no visible global function definition for ‘exprs’
dffitsPerGene: no visible global function definition for ‘featureNames’
dffitsPerGene : <anonymous>: no visible global function definition for
  ‘exprs’
getResidPerGene: no visible global function definition for ‘exprs’
getResidPerGene: no visible global function definition for ‘new’
getResidPerGene: no visible global function definition for ‘phenoData’
gsealmPerm: no visible global function definition for ‘pData’
gsealmPerm: no visible global function definition for ‘pData<-’
lmPerGene: no visible global function definition for ‘varLabels’
lmPerGene: no visible global function definition for ‘pData’
lmPerGene: no visible global function definition for ‘model.matrix’
lmPerGene: no visible global function definition for ‘exprs’
mnDiffPlot: no visible global function definition for ‘layout’
mnDiffPlot: no visible binding for global variable ‘var’
mnDiffPlot: no visible global function definition for ‘abline’
mnDiffPlot: no visible global function definition for ‘lines’
mnDiffPlot: no visible global function definition for ‘predict’
mnDiffPlot: no visible global function definition for ‘loess’
resplot: no visible global function definition for ‘layout’
resplot: no visible global function definition for ‘boxplot’
resplot: no visible global function definition for ‘lines’
restrip: no visible global function definition for ‘layout’
restrip: no visible global function definition for ‘stripchart’
restrip: no visible global function definition for ‘title’
restrip: no visible global function definition for ‘lines’
Undefined global functions or variables:
  abline boxplot exprs featureNames layout lines loess model.matrix new
  pData pData<- phenoData predict sampleNames stripchart title var
  varLabels
Consider adding
  importFrom("graphics", "abline", "boxplot", "layout", "lines",
             "stripchart", "title")
  importFrom("methods", "new")
  importFrom("stats", "loess", "model.matrix", "predict", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: gsealmPerm.Rd:62: Dropping empty section \references
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following files contain a license that requires
distribution of original sources:
  ‘crop.sty’
Please ensure that you have complied with it.
* checking examples ... OK
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/GSEAlm.Rcheck/00check.log’
for details.



Installation output

GSEAlm.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GSEAlm
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘GSEAlm’ ...
** using staged installation
** R
** 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 (GSEAlm)

Tests output


Example timings

GSEAlm.Rcheck/GSEAlm-Ex.timings

nameusersystemelapsed
GSNormalize0.1560.0190.176
dfbetasPerGene0.3220.0300.353
getResidPerGene0.1620.0100.173
gsealmPerm3.5290.0393.572
lmPerGene0.0800.0060.087
resplot0.1980.0090.209