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This page was generated on 2022-06-27 11:09:51 -0400 (Mon, 27 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for combi on nebbiolo1


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? 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 385/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
combi 1.8.0  (landing page)
Stijn Hawinkel
Snapshot Date: 2022-06-26 13:55:11 -0400 (Sun, 26 Jun 2022)
git_url: https://git.bioconductor.org/packages/combi
git_branch: RELEASE_3_15
git_last_commit: 5360215
git_last_commit_date: 2022-04-26 12:03:34 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: combi
Version: 1.8.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:combi.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings combi_1.8.0.tar.gz
StartedAt: 2022-06-26 19:16:56 -0400 (Sun, 26 Jun 2022)
EndedAt: 2022-06-26 19:23:31 -0400 (Sun, 26 Jun 2022)
EllapsedTime: 394.5 seconds
RetCode: 0
Status:   OK  
CheckDir: combi.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:combi.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings combi_1.8.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/combi.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (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 ‘1.8.0’
* 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 ... 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 ... 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
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/combi.Rcheck/00check.log’
for details.



Installation output

combi.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘combi’ ...
** using staged installation
** R
** data
** 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 (combi)

Tests output

combi.Rcheck/tests/testthat.Rout


R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 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(combi)
Loading required package: DBI
> test_check("combi")
[ FAIL 0 | WARN 18 | SKIP 0 | PASS 21 ]

[ FAIL 0 | WARN 18 | SKIP 0 | PASS 21 ]
> 
> proc.time()
   user  system elapsed 
183.708   1.909 185.606 

Example timings

combi.Rcheck/combi-Ex.timings

nameusersystemelapsed
addLink1.1610.0241.187
checkMeanVarTrend4.0690.0804.149
combi0.0190.0040.023
convPlot0.7720.0120.784
extractCoords0.0510.0120.063
extractData0.0260.0040.030
inflPlot1.7850.1361.921
plot.combi1.6650.0521.717
print.combi0.0460.0000.046