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This page was generated on 2024-04-17 11:37:15 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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 1826/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RUVnormalize 1.36.0  (landing page)
Laurent Jacob
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/RUVnormalize
git_branch: RELEASE_3_18
git_last_commit: 16236e9
git_last_commit_date: 2023-10-24 10:00:36 -0400 (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
merida1macOS 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 RUVnormalize on palomino4


To the developers/maintainers of the RUVnormalize package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RUVnormalize.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: RUVnormalize
Version: 1.36.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RUVnormalize.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings RUVnormalize_1.36.0.tar.gz
StartedAt: 2024-04-16 04:39:21 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 04:40:04 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 42.1 seconds
RetCode: 0
Status:   OK  
CheckDir: RUVnormalize.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RUVnormalize.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings RUVnormalize_1.36.0.tar.gz
###
##############################################################################
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* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/RUVnormalize.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'RUVnormalize/DESCRIPTION' ... OK
* this is package 'RUVnormalize' version '1.36.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'spams'
* 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 'RUVnormalize' 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
'library' or 'require' call to 'spams' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
iterativeRUV: no visible global function definition for 'kmeans'
myPalette: no visible global function definition for 'col2rgb'
myPalette: no visible global function definition for 'rgb'
svdPlot: no visible global function definition for 'pdf'
svdPlot: no visible global function definition for 'par'
svdPlot: no visible global function definition for 'points'
svdPlot: no visible global function definition for 'text'
svdPlot: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  col2rgb dev.off kmeans par pdf points rgb text
Consider adding
  importFrom("grDevices", "col2rgb", "dev.off", "pdf", "rgb")
  importFrom("graphics", "par", "points", "text")
  importFrom("stats", "kmeans")
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: 3 NOTEs
See
  'F:/biocbuild/bbs-3.18-bioc/meat/RUVnormalize.Rcheck/00check.log'
for details.



Installation output

RUVnormalize.Rcheck/00install.out

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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL RUVnormalize
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'RUVnormalize' ...
** using staged installation
** R
** demo
** inst
** 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 (RUVnormalize)

Tests output


Example timings

RUVnormalize.Rcheck/RUVnormalize-Ex.timings

nameusersystemelapsed
clScore2.610.192.89
iterativeRUV0.070.000.08
naiveRandRUV2.560.262.83
naiveReplicateRUV1.650.131.79
svdPlot2.330.232.56