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This page was generated on 2021-11-26 15:06:03 -0500 (Fri, 26 Nov 2021).

CHECK results for RefPlus on machv2

To the developers/maintainers of the RefPlus package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RefPlus.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1571/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RefPlus 1.64.0  (landing page)
Kai-Ming Chang
Snapshot Date: 2021-11-25 04:15:05 -0500 (Thu, 25 Nov 2021)
git_url: https://git.bioconductor.org/packages/RefPlus
git_branch: RELEASE_3_14
git_last_commit: 9930f72
git_last_commit_date: 2021-10-26 11:50:39 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: RefPlus
Version: 1.64.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RefPlus.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RefPlus_1.64.0.tar.gz
StartedAt: 2021-11-25 20:36:11 -0500 (Thu, 25 Nov 2021)
EndedAt: 2021-11-25 20:38:14 -0500 (Thu, 25 Nov 2021)
EllapsedTime: 123.4 seconds
RetCode: 0
Status:   OK  
CheckDir: RefPlus.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RefPlus.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RefPlus_1.64.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/RefPlus.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RefPlus/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RefPlus’ version ‘1.64.0’
* 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 ‘RefPlus’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
Package in Depends field not imported from: ‘affyPLM’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
rma.para: no visible global function definition for ‘rmaPLM’
rma.para: no visible global function definition for ‘coefs.probe’
rma.para: no visible global function definition for ‘coefs’
Undefined global functions or variables:
  coefs coefs.probe rmaPLM
* checking Rd files ... NOTE
prepare_Rd: colMedians.Rd:19: Dropping empty section \references
prepare_Rd: rmaref.predict.Rd:29-30: Dropping empty section \examples
* 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
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
RefPlus-package 11.540  0.382  11.944
rmaplus          7.503  0.156   7.665
rma.para         5.744  0.128   5.882
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/RefPlus.Rcheck/00check.log’
for details.



Installation output

RefPlus.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RefPlus
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘RefPlus’ ...
** using staged installation
** R
** 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 (RefPlus)

Tests output


Example timings

RefPlus.Rcheck/RefPlus-Ex.timings

nameusersystemelapsed
RefPlus-package11.540 0.38211.944
colMedians000
normalize.quantiles20.0010.0010.001
rma.para5.7440.1285.882
rmaplus7.5030.1567.665