Back to Mac ARM64 build report for BioC 3.17
ABCDEFGHIJKLM[N]OPQRSTUVWXYZ

This page was generated on 2023-10-20 09:38:07 -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 1396/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
npGSEA 1.36.0  (landing page)
Jessica Larson
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/npGSEA
git_branch: RELEASE_3_17
git_last_commit: 09d8486
git_last_commit_date: 2023-04-25 10:31:40 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for npGSEA on kjohnson2


To the developers/maintainers of the npGSEA 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: npGSEA
Version: 1.36.0
Command: /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_1.36.0.tar.gz
StartedAt: 2023-10-18 11:52:56 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 11:55:57 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 181.6 seconds
RetCode: 0
Status:   OK  
CheckDir: npGSEA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /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_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/npGSEA.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 ‘npGSEA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘npGSEA’ version ‘1.36.0’
* 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-3.17-bioc-mac-arm64/meat/npGSEA.Rcheck/00check.log’
for details.



Installation output

npGSEA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL npGSEA
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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

npGSEA.Rcheck/npGSEA-Ex.timings

nameusersystemelapsed
DF-methods0.0130.0010.022
alphaValue-methods0.0050.0000.006
betaHats-methods0.0030.0010.005
betaStat-methods0.0030.0010.005
betaValue-methods0.0030.0010.007
chiSqStat-methods0.0050.0010.011
geneSetName-methods0.0030.0000.005
getIncidence0.0010.0000.002
npGSEA0.0020.0000.004
npGSEAPlot-methods0.0020.0010.004
npGSEAResultBeta-class0.0010.0010.002
npGSEAResultBetaCollection-class0.0010.0010.001
npGSEAResultChiSq-class0.0010.0010.000
npGSEAResultChiSqCollection-class0.0010.0000.001
npGSEAResultNorm-class0.0000.0000.001
npGSEAResultNormCollection-class0.0000.0000.001
pLeft-methods0.0030.0010.004
pRight-methods0.0030.0010.006
pTwoSided-methods0.0020.0000.003
pValues-methods0.0020.0000.005
show-methods0.0030.0000.005
sigmaSq-methods0.0020.0000.003
stat-methods0.0020.0000.003
xSet-methods0.0040.0010.008
zStat-methods0.0030.0000.003