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This page was generated on 2021-12-04 12:32:20 -0500 (Sat, 04 Dec 2021).

CHECK results for RCM on nebbiolo1

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: 2021-12-03 13:55:11 -0500 (Fri, 03 Dec 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  UNNEEDED, same version is already published

Summary

Package: RCM
Version: 1.11.1
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:RCM.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings RCM_1.11.1.tar.gz
StartedAt: 2021-12-03 20:47:54 -0500 (Fri, 03 Dec 2021)
EndedAt: 2021-12-03 20:52:14 -0500 (Fri, 03 Dec 2021)
EllapsedTime: 260.3 seconds
RetCode: 0
Status:   OK  
CheckDir: RCM.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:RCM.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings RCM_1.11.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/RCM.Rcheck’
* using R Under development (unstable) (2021-11-10 r81171)
* using platform: x86_64-pc-linux-gnu (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    6.982  0.064   7.046
getDevianceRes 5.659  0.036   5.696
plot.RCM       5.587  0.023   5.611
liks           5.060  0.032   5.092
* 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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/RCM.Rcheck/00check.log’
for details.



Installation output

RCM.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL RCM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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) (2021-11-10 r81171) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
 71.214   1.137  72.342 

Example timings

RCM.Rcheck/RCM-Ex.timings

nameusersystemelapsed
RCM4.5180.0434.562
RCM_NB3.5550.0153.571
addOrthProjection3.7650.0373.801
checkAlias0.0050.0030.009
extractCoord3.3530.0333.387
getDevianceRes5.6590.0365.696
inertia4.4300.0204.451
liks5.0600.0325.092
plot.RCM5.5870.0235.611
plotRespFun6.9820.0647.046
residualPlot1.9520.0111.965