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This page was generated on 2024-03-04 11:37:38 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 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

Package 1425/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
npGSEA 1.38.0  (landing page)
Jessica Larson
Snapshot Date: 2024-03-03 14:05:05 -0500 (Sun, 03 Mar 2024)
git_url: https://git.bioconductor.org/packages/npGSEA
git_branch: RELEASE_3_18
git_last_commit: 3157813
git_last_commit_date: 2023-10-24 09:58:39 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for npGSEA on lconway


To the developers/maintainers of the npGSEA package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/npGSEA.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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: 1.38.0
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_1.38.0.tar.gz
StartedAt: 2024-03-03 22:14:05 -0500 (Sun, 03 Mar 2024)
EndedAt: 2024-03-03 22:16:14 -0500 (Sun, 03 Mar 2024)
EllapsedTime: 129.2 seconds
RetCode: 0
Status:   OK  
CheckDir: npGSEA.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* 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

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-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

npGSEA.Rcheck/npGSEA-Ex.timings

nameusersystemelapsed
DF-methods0.0120.0020.013
alphaValue-methods0.0050.0010.004
betaHats-methods0.0030.0010.004
betaStat-methods0.0030.0010.003
betaValue-methods0.0030.0000.004
chiSqStat-methods0.0050.0010.006
geneSetName-methods0.0030.0010.003
getIncidence0.0010.0010.001
npGSEA0.0030.0010.004
npGSEAPlot-methods0.0020.0010.003
npGSEAResultBeta-class0.0010.0010.001
npGSEAResultBetaCollection-class0.0000.0010.001
npGSEAResultChiSq-class0.0010.0000.000
npGSEAResultChiSqCollection-class0.0010.0000.002
npGSEAResultNorm-class0.0000.0000.001
npGSEAResultNormCollection-class0.0010.0000.002
pLeft-methods0.0030.0000.004
pRight-methods0.0030.0010.003
pTwoSided-methods0.0030.0010.004
pValues-methods0.0020.0010.003
show-methods0.0020.0010.002
sigmaSq-methods0.0030.0010.003
stat-methods0.0020.0010.003
xSet-methods0.0040.0010.005
zStat-methods0.0020.0000.003