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CHECK report for RCM on malbec2

This page was generated on 2020-10-17 11:55:32 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE RCM PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1435/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RCM 1.4.0
Joris Meys
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/RCM
Branch: RELEASE_3_11
Last Commit: 9436a06
Last Changed Date: 2020-04-27 15:22:26 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: RCM
Version: 1.4.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:RCM.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings RCM_1.4.0.tar.gz
StartedAt: 2020-10-17 04:33:18 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:37:21 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 243.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: RCM.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:RCM.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings RCM_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/RCM.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.4.0’
* 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 ... OK
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
  Warning: 'loge' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
plotRespFun       16.015  0.047  16.073
plot.RCM           7.705  0.000   7.705
RCM                7.639  0.032   7.671
addOrthProjection  7.242  0.007   7.250
liks               6.119  0.000   6.223
RCM_NB             5.919  0.008   5.928
extractCoord       5.096  0.012   5.109
* 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 WARNING
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/RCM.Rcheck/00check.log’
for details.

Installation output

RCM.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL RCM
###
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* installing to library ‘/home/biocbuild/bbs-3.11-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 version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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)
> 
> test_check("RCM")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 12 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 16.690   0.266  16.942

Example timings

RCM.Rcheck/RCM-Ex.timings

nameusersystemelapsed
RCM7.6390.0327.671
RCM_NB5.9190.0085.928
addOrthProjection7.2420.0077.250
extractCoord5.0960.0125.109
inertia4.9790.0004.978
liks6.1190.0006.223
plot.RCM7.7050.0007.705
plotRespFun16.015 0.04716.073
residualPlot3.0800.0043.085