Back to Multiple platform build/check report for BioC 3.11
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

CHECK report for savR on machv2

This page was generated on 2020-10-17 11:59:30 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE savR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1576/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
savR 1.26.0
R. Brent Calder
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/savR
Branch: RELEASE_3_11
Last Commit: 70d9d86
Last Changed Date: 2020-04-27 14:38:08 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: savR
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:savR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings savR_1.26.0.tar.gz
StartedAt: 2020-10-17 05:00:01 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:02:15 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 134.2 seconds
RetCode: 0
Status:  OK 
CheckDir: savR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:savR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings savR_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/savR.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘savR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘savR’ version ‘1.26.0’
* 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 ‘savR’ 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 ... NOTE
buildReports,savProject-character: no visible global function
  definition for ‘dev.off’
qualityHeatmap,savProject-integer-integer-logical: no visible global
  function definition for ‘quantile’
Undefined global functions or variables:
  dev.off quantile
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("stats", "quantile")
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
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
cycles               5.591  0.023   5.754
correctedIntensities 5.452  0.034   5.503
errorMetrics         5.363  0.022   5.450
tileMetrics          5.354  0.014   5.373
location             5.297  0.021   5.324
run                  5.186  0.021   5.215
savR                 5.151  0.016   5.177
directions           5.121  0.023   5.164
extractionMetrics    5.017  0.019   5.051
* 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-3.11-bioc/meat/savR.Rcheck/00check.log’
for details.



Installation output

savR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL savR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘savR’ ...
** using staged installation
** R
** 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 (savR)

Tests output

savR.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-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(savR)
Loading required package: ggplot2
> 
> test_check("savR")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 8 | SKIPPED: 7 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 13.740   0.261  14.023 

Example timings

savR.Rcheck/savR-Ex.timings

nameusersystemelapsed
buildReports000
clusterQualityGtN0.0000.0010.000
clusters0.0000.0000.001
correctedIntensities5.4520.0345.503
cycles5.5910.0235.754
directions5.1210.0235.164
errorMetrics5.3630.0225.450
extractionMetrics5.0170.0195.051
flowcellLayout4.8670.0214.895
location5.2970.0215.324
pfClusters0.0000.0010.001
qualityMetrics4.9540.0154.974
reads4.9560.0214.988
run5.1860.0215.215
savR5.1510.0165.177
tileMetrics5.3540.0145.373