Multiple platform build/check report for BioC 3.18 - CHECK results for npGSEA on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes"	4692
palomino4	Windows Server 2022 Datacenter	x64	4.3.2 (2023-10-31 ucrt) -- "Eye Holes"	4445
lconway	macOS 12.7.1 Monterey	x86_64	4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"	4466
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*

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:npGSEA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings npGSEA_1.38.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/npGSEA.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘npGSEA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘npGSEA’ version ‘1.38.0’
* 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 ‘npGSEA’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.prepXYZ: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/npGSEA.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL npGSEA
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘npGSEA’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘BiocGenerics’ for request: ‘unlist’ when loading ‘npGSEA’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘BiocGenerics’ for request: ‘unlist’ when loading ‘npGSEA’
** testing if installed package can be loaded from final location
No methods found in package ‘BiocGenerics’ for request: ‘unlist’ when loading ‘npGSEA’
** testing if installed package keeps a record of temporary installation path
* DONE (npGSEA)

Tests output

Example timings

name	user	system	elapsed
DF-methods	0.012	0.002	0.013
alphaValue-methods	0.005	0.001	0.004
betaHats-methods	0.003	0.001	0.004
betaStat-methods	0.003	0.001	0.003
betaValue-methods	0.003	0.000	0.004
chiSqStat-methods	0.005	0.001	0.006
geneSetName-methods	0.003	0.001	0.003
getIncidence	0.001	0.001	0.001
npGSEA	0.003	0.001	0.004
npGSEAPlot-methods	0.002	0.001	0.003
npGSEAResultBeta-class	0.001	0.001	0.001
npGSEAResultBetaCollection-class	0.000	0.001	0.001
npGSEAResultChiSq-class	0.001	0.000	0.000
npGSEAResultChiSqCollection-class	0.001	0.000	0.002
npGSEAResultNorm-class	0.000	0.000	0.001
npGSEAResultNormCollection-class	0.001	0.000	0.002
pLeft-methods	0.003	0.000	0.004
pRight-methods	0.003	0.001	0.003
pTwoSided-methods	0.003	0.001	0.004
pValues-methods	0.002	0.001	0.003
show-methods	0.002	0.001	0.002
sigmaSq-methods	0.003	0.001	0.003
stat-methods	0.002	0.001	0.003
xSet-methods	0.004	0.001	0.005
zStat-methods	0.002	0.000	0.003

CHECK results for npGSEA on lconway

Summary

Command output

Installation output

Tests output

Example timings