Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-14 14:38 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
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 1441/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
npGSEA 1.40.0  (landing page)
Jessica Larson
Snapshot Date: 2024-06-12 14:00 -0400 (Wed, 12 Jun 2024)
git_url: https://git.bioconductor.org/packages/npGSEA
git_branch: RELEASE_3_19
git_last_commit: 8ecf0d2
git_last_commit_date: 2024-04-30 10:36:12 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for npGSEA on palomino3

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: 1.40.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:npGSEA.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings npGSEA_1.40.0.tar.gz
StartedAt: 2024-06-13 07:46:05 -0400 (Thu, 13 Jun 2024)
EndedAt: 2024-06-13 07:50:50 -0400 (Thu, 13 Jun 2024)
EllapsedTime: 284.8 seconds
RetCode: 0
Status:   OK  
CheckDir: npGSEA.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:npGSEA.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings npGSEA_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/npGSEA.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'npGSEA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'npGSEA' version '1.40.0'
* 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 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 code 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 ... 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
  'F:/biocbuild/bbs-3.19-bioc/meat/npGSEA.Rcheck/00check.log'
for details.


Installation output

npGSEA.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL npGSEA
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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-methods0.010.000.02
alphaValue-methods000
betaHats-methods000
betaStat-methods0.000.010.02
betaValue-methods000
chiSqStat-methods0.020.000.02
geneSetName-methods000
getIncidence000
npGSEA000
npGSEAPlot-methods0.010.000.01
npGSEAResultBeta-class000
npGSEAResultBetaCollection-class000
npGSEAResultChiSq-class000
npGSEAResultChiSqCollection-class000
npGSEAResultNorm-class000
npGSEAResultNormCollection-class0.020.000.02
pLeft-methods000
pRight-methods000
pTwoSided-methods000
pValues-methods000
show-methods000
sigmaSq-methods000
stat-methods000
xSet-methods000
zStat-methods000