Back to Multiple platform build/check report for BioC 3.15
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2021-11-27 14:05:51 -0500 (Sat, 27 Nov 2021).

CHECK results for RCM on merida1

To the developers/maintainers of the RCM package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RCM.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 1534/2068HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCM 1.11.1  (landing page)
Stijn Hawinkel
Snapshot Date: 2021-11-26 14:50:14 -0500 (Fri, 26 Nov 2021)
git_url: https://git.bioconductor.org/packages/RCM
git_branch: master
git_last_commit: fb5a52e
git_last_commit_date: 2021-11-26 03:22:15 -0500 (Fri, 26 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  YES
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  YES

Summary

Package: RCM
Version: 1.11.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RCM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RCM_1.11.1.tar.gz
StartedAt: 2021-11-27 06:44:09 -0500 (Sat, 27 Nov 2021)
EndedAt: 2021-11-27 06:51:55 -0500 (Sat, 27 Nov 2021)
EllapsedTime: 465.2 seconds
RetCode: 0
Status:   OK  
CheckDir: RCM.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RCM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RCM_1.11.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/RCM.Rcheck’
* using R Under development (unstable) (2021-11-01 r81125)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RCM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCM’ version ‘1.11.1’
* package encoding: UTF-8
* 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 ‘RCM’ 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
Package in Depends field not imported from: ‘DBI’
  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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
plotRespFun       13.643  0.078  13.742
getDevianceRes     9.879  0.496  10.389
addOrthProjection  8.191  0.121   8.329
RCM                7.824  0.210   8.045
liks               7.765  0.054   7.831
extractCoord       7.349  0.077   7.434
inertia            6.465  0.071   6.542
plot.RCM           6.178  0.045   6.235
RCM_NB             5.362  0.316   5.686
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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-3.15-bioc/meat/RCM.Rcheck/00check.log’
for details.



Installation output

RCM.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘RCM’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (RCM)

Tests output

RCM.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-01 r81125) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(RCM)
Loading required package: DBI
> 
> test_check("RCM")
[ FAIL 0 | WARN 10 | SKIP 0 | PASS 37 ]
> 
> proc.time()
   user  system elapsed 
129.238   5.846 135.230 

Example timings

RCM.Rcheck/RCM-Ex.timings

nameusersystemelapsed
RCM7.8240.2108.045
RCM_NB5.3620.3165.686
addOrthProjection8.1910.1218.329
checkAlias0.0100.0010.010
extractCoord7.3490.0777.434
getDevianceRes 9.879 0.49610.389
inertia6.4650.0716.542
liks7.7650.0547.831
plot.RCM6.1780.0456.235
plotRespFun13.643 0.07813.742
residualPlot4.3620.0874.455