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This page was generated on 2021-09-22 15:04:48 -0400 (Wed, 22 Sep 2021).

CHECK results for chromswitch on nebbiolo1

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 308/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromswitch 1.14.0  (landing page)
Selin Jessa
Snapshot Date: 2021-09-21 04:50:12 -0400 (Tue, 21 Sep 2021)
git_url: https://git.bioconductor.org/packages/chromswitch
git_branch: RELEASE_3_13
git_last_commit: e364a04
git_last_commit_date: 2021-05-19 12:31:47 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: 1.14.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:chromswitch.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings chromswitch_1.14.0.tar.gz
StartedAt: 2021-09-21 09:17:12 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 09:21:24 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 251.4 seconds
RetCode: 0
Status:   OK  
CheckDir: chromswitch.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:chromswitch.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings chromswitch_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/chromswitch.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.14.0’
* 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-3.13-bioc/R/bin/R CMD INSTALL chromswitch
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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 4.1.1 (2021-08-10) -- "Kick Things"
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
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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 
 39.488   9.072  38.295 

Example timings

chromswitch.Rcheck/chromswitch-Ex.timings

nameusersystemelapsed
GRangesToCoord0.0480.0080.056
LocalPeaks-class0.3540.0640.419
NMI0.0020.0000.003
binarizePeaks2.3570.0522.408
callBinary4.0420.0604.102
callSummary1.6380.0321.670
classEntropy0.0010.0000.001
cluster0.6540.0080.662
clusterEntropy0.0020.0000.001
completeness0.0020.0000.001
conditionalClassEntropy0.0020.0000.001
conditionalClusterEntropy0.0010.0000.001
coordToGRanges0.0240.0030.027
filterPeaks0.4560.0160.471
homogeneity0.0020.0000.001
makeBrowserCoord000
normalizePeaks0.310.020.33
pReciprocalOverlap0.0610.0000.060
purity0.0000.0010.001
readNarrowPeak0.4940.0100.505
reducePeaks0.310.000.31
retrievePeaks0.2830.0000.282
summarizePeaks0.8330.0120.846
vMeasure0.0020.0000.002
winsorNorm0.0040.0000.004