Back to Multiple platform build/check report for BioC 3.14
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-07-24 12:06:25 -0400 (Sat, 24 Jul 2021).

CHECK results for combi on merida1

To the developers/maintainers of the combi package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/combi.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 357/2008HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
combi 1.5.0  (landing page)
Joris Meys
Snapshot Date: 2021-07-23 14:50:08 -0400 (Fri, 23 Jul 2021)
URL: https://git.bioconductor.org/packages/combi
Branch: master
Last Commit: 9f97750
Last Changed Date: 2021-05-19 12:50:35 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: combi
Version: 1.5.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:combi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings combi_1.5.0.tar.gz
StartedAt: 2021-07-24 00:57:10 -0400 (Sat, 24 Jul 2021)
EndedAt: 2021-07-24 01:03:36 -0400 (Sat, 24 Jul 2021)
EllapsedTime: 386.1 seconds
RetCode: 0
Status:   OK  
CheckDir: combi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:combi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings combi_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/combi.Rcheck’
* using R version 4.1.0 RC (2021-05-16 r80304)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘combi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘combi’ version ‘1.5.0’
* 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 ‘combi’ 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 ... NOTE
Foreign function call to a different package:
  .C("spline_value", ..., PACKAGE = "cobs")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
addLink: no visible binding for global variable ‘species’
convPlot: no visible binding for global variable ‘Iteration’
convPlot: no visible binding for global variable ‘Value’
convPlot: no visible binding for global variable ‘Variable’
convPlot: no visible binding for global variable ‘Colour’
inflPlot: no visible binding for global variable ‘h’
inflPlot: no visible binding for global variable ‘LatentVariable’
inflPlot: no visible binding for global variable ‘value’
Undefined global functions or variables:
  Colour Iteration LatentVariable Value Variable h species value
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
checkMeanVarTrend 6.725  0.112   6.846
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/combi.Rcheck/00check.log’
for details.



Installation output

combi.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘combi’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning in .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
** testing if installed package can be loaded from final location
Warning in .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
** testing if installed package keeps a record of temporary installation path
* DONE (combi)

Tests output

combi.Rcheck/tests/testthat.Rout


R version 4.1.0 RC (2021-05-16 r80304) -- "Camp Pontanezen"
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(combi)
Warning message:
In .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
> test_check("combi")
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 15 ]
> 
> proc.time()
   user  system elapsed 
 65.452   3.573  69.064 

Example timings

combi.Rcheck/combi-Ex.timings

nameusersystemelapsed
addLink0.7620.0760.840
checkMeanVarTrend6.7250.1126.846
combi0.0350.0020.036
convPlot1.1140.0081.123
extractCoords0.0680.0110.079
extractData0.0480.0020.049
inflPlot2.0990.0152.117
plot.combi2.6140.0782.696
print.combi0.0580.0030.061