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This page was generated on 2023-03-27 11:05:52 -0400 (Mon, 27 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" 4547
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" 4308
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" 4300
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 katdetectr on palomino3


To the developers/maintainers of the katdetectr package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/katdetectr.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 1028/2195HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
katdetectr 1.1.3  (landing page)
Daan Hazelaar
Snapshot Date: 2023-03-26 14:00:09 -0400 (Sun, 26 Mar 2023)
git_url: https://git.bioconductor.org/packages/katdetectr
git_branch: devel
git_last_commit: ac76967
git_last_commit_date: 2023-03-13 13:01:09 -0400 (Mon, 13 Mar 2023)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / 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: katdetectr
Version: 1.1.3
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:katdetectr.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings katdetectr_1.1.3.tar.gz
StartedAt: 2023-03-27 03:11:30 -0400 (Mon, 27 Mar 2023)
EndedAt: 2023-03-27 03:16:51 -0400 (Mon, 27 Mar 2023)
EllapsedTime: 321.4 seconds
RetCode: 0
Status:   OK  
CheckDir: katdetectr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:katdetectr.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings katdetectr_1.1.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/katdetectr.Rcheck'
* using R Under development (unstable) (2023-03-15 r83984 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'katdetectr/DESCRIPTION' ... OK
* this is package 'katdetectr' version '1.1.3'
* 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 whether package 'katdetectr' 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
rainfallPlot 6.88   0.31    7.24
* 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: OK


Installation output

katdetectr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL katdetectr
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'katdetectr' ...
** 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 (katdetectr)

Tests output

katdetectr.Rcheck/tests/testthat.Rout


R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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(katdetectr)
> 
> test_check("katdetectr")
[ FAIL 0 | WARN 91 | SKIP 0 | PASS 187 ]

[ FAIL 0 | WARN 91 | SKIP 0 | PASS 187 ]
> 
> proc.time()
   user  system elapsed 
  51.87    2.09   54.98 

Example timings

katdetectr.Rcheck/katdetectr-Ex.timings

nameusersystemelapsed
KatDetect4.610.354.95
constructKatdetect0.040.000.05
detectKataegis4.370.314.72
generateSyntheticData2.310.392.93
getGenomicVariants0.080.000.08
getInfo0.060.000.06
getKataegisFoci0.060.000.07
getSegments0.050.000.04
rainfallPlot6.880.317.24