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This page was generated on 2021-12-03 13:04:45 -0500 (Fri, 03 Dec 2021).

CHECK results for chromswitch on nebbiolo2

To the developers/maintainers of the chromswitch package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/chromswitch.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 315/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromswitch 1.16.0  (landing page)
Selin Jessa
Snapshot Date: 2021-12-02 01:55:06 -0500 (Thu, 02 Dec 2021)
git_url: https://git.bioconductor.org/packages/chromswitch
git_branch: RELEASE_3_14
git_last_commit: 0d65abe
git_last_commit_date: 2021-10-26 12:39:46 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: chromswitch
Version: 1.16.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:chromswitch.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings chromswitch_1.16.0.tar.gz
StartedAt: 2021-12-02 06:35:39 -0500 (Thu, 02 Dec 2021)
EndedAt: 2021-12-02 06:39:36 -0500 (Thu, 02 Dec 2021)
EllapsedTime: 237.3 seconds
RetCode: 0
Status:   OK  
CheckDir: chromswitch.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:chromswitch.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings chromswitch_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/chromswitch.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘chromswitch/DESCRIPTION’ ... OK
* this is package ‘chromswitch’ version ‘1.16.0’
* 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 ‘chromswitch’ 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 LazyData ... 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: OK


Installation output

chromswitch.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL chromswitch
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘chromswitch’ ...
** 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 (chromswitch)

Tests output

chromswitch.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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(chromswitch)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
> 
> test_check("chromswitch")
[ FAIL 0 | WARN 5 | SKIP 0 | PASS 93 ]
> 
> proc.time()
   user  system elapsed 
 41.854  10.752  40.713 

Example timings

chromswitch.Rcheck/chromswitch-Ex.timings

nameusersystemelapsed
GRangesToCoord0.0490.0040.053
LocalPeaks-class0.3350.0720.406
NMI0.0020.0000.003
binarizePeaks1.4380.0641.502
callBinary4.2450.1844.429
callSummary3.4820.6844.166
classEntropy0.0010.0000.002
cluster0.7980.1600.959
clusterEntropy0.0010.0000.001
completeness0.0010.0000.001
conditionalClassEntropy0.0010.0000.001
conditionalClusterEntropy0.0010.0000.000
coordToGRanges0.0250.0040.029
filterPeaks0.3730.0080.381
homogeneity0.0010.0000.001
makeBrowserCoord000
normalizePeaks0.2860.0040.290
pReciprocalOverlap0.0590.0000.059
purity0.0000.0010.001
readNarrowPeak0.5130.0140.526
reducePeaks0.3370.0000.336
retrievePeaks0.2840.0000.284
summarizePeaks0.5390.0040.543
vMeasure0.0010.0000.001
winsorNorm0.0010.0000.001