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This page was generated on 2023-10-20 09:38:03 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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

Package 892/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GSEAlm 1.60.0  (landing page)
Assaf Oron
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/GSEAlm
git_branch: RELEASE_3_17
git_last_commit: f133f94
git_last_commit_date: 2023-04-25 09:46:30 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for GSEAlm on kjohnson2


To the developers/maintainers of the GSEAlm package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: GSEAlm
Version: 1.60.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GSEAlm.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GSEAlm_1.60.0.tar.gz
StartedAt: 2023-10-17 23:46:15 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 23:47:16 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 60.7 seconds
RetCode: 0
Status:   OK  
CheckDir: GSEAlm.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GSEAlm.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GSEAlm_1.60.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/GSEAlm.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GSEAlm/DESCRIPTION’ ... OK
* this is package ‘GSEAlm’ version ‘1.60.0’
* 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
checkRd: (-1) dfbetasPerGene.Rd:32: Escaped LaTeX specials: \_
checkRd: (-1) dfbetasPerGene.Rd:37: Escaped LaTeX specials: \_
checkRd: (-1) dfbetasPerGene.Rd:46: Escaped LaTeX specials: \_ \_
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-3.17-bioc-mac-arm64/meat/GSEAlm.Rcheck/00check.log’
for details.



Installation output

GSEAlm.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GSEAlm
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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
GSNormalize0.1540.0130.254
dfbetasPerGene0.2480.0280.408
getResidPerGene0.1170.0130.198
gsealmPerm2.8460.0484.446
lmPerGene0.0590.0060.098
resplot0.1580.0140.262