Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-26 11:07:20 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4164
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4059
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4001
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4118
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 chromswitch on riesling1


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 312/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromswitch 1.17.0  (landing page)
Selin Jessa
Snapshot Date: 2022-01-25 13:55:17 -0500 (Tue, 25 Jan 2022)
git_url: https://git.bioconductor.org/packages/chromswitch
git_branch: master
git_last_commit: 78d3895
git_last_commit_date: 2021-10-26 12:39:46 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'GenomicRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: chromswitch
Version: 1.17.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:chromswitch.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings chromswitch_1.17.0.tar.gz
StartedAt: 2022-01-25 18:35:22 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 18:38:22 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 180.2 seconds
RetCode: 0
Status:   OK  
CheckDir: chromswitch.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:chromswitch.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings chromswitch_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/chromswitch.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'chromswitch/DESCRIPTION' ... OK
* this is package 'chromswitch' version '1.17.0'
* 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 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

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL chromswitch
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-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
  converting help for package 'chromswitch'
    finding HTML links ... done
    GRangesToCoord                          html  
    H3K4me3                                 html  
    LocalPeaks-class                        html  
    NMI                                     html  
    binarizePeaks                           html  
    callBinary                              html  
    callSummary                             html  
    chromswitch                             html  
    classEntropy                            html  
    cluster                                 html  
    clusterEntropy                          html  
    completeness                            html  
    conditionalClassEntropy                 html  
    conditionalClusterEntropy               html  
    coordToGRanges                          html  
    filterPeaks                             html  
    homogeneity                             html  
    makeBrowserCoord                        html  
    normalizePeaks                          html  
    pReciprocalOverlap                      html  
    purity                                  html  
    readNarrowPeak                          html  
    reducePeaks                             html  
    retrievePeaks                           html  
    summarizePeaks                          html  
    vMeasure                                html  
    winsorNorm                              html  
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'TimiRGeN' is missing or broken
 done

Tests output

chromswitch.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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(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

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
> 
> test_check("chromswitch")
[ FAIL 0 | WARN 4 | SKIP 10 | PASS 55 ]

== Skipped tests ===============================================================
* On Windows (10)

[ FAIL 0 | WARN 4 | SKIP 10 | PASS 55 ]
> 
> proc.time()
   user  system elapsed 
   8.89    0.76    9.65 

Example timings

chromswitch.Rcheck/chromswitch-Ex.timings

nameusersystemelapsed
GRangesToCoord0.030.000.03
LocalPeaks-class0.240.060.30
NMI000
binarizePeaks0.910.131.03
callBinary2.530.032.57
callSummary2.060.012.07
classEntropy000
cluster0.520.000.52
clusterEntropy000
completeness000
conditionalClassEntropy000
conditionalClusterEntropy000
coordToGRanges0.010.000.02
filterPeaks0.250.000.25
homogeneity000
makeBrowserCoord000
normalizePeaks0.210.000.20
pReciprocalOverlap0.030.000.03
purity000
readNarrowPeak0.250.020.27
reducePeaks0.180.000.18
retrievePeaks0.160.000.16
summarizePeaks0.410.000.41
vMeasure000
winsorNorm000