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This page was generated on 2021-10-23 14:06:51 -0400 (Sat, 23 Oct 2021).

CHECK results for airpart on merida1

To the developers/maintainers of the airpart package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/airpart.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 39/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
airpart 1.1.5  (landing page)
Wancen Mu
Snapshot Date: 2021-10-22 14:50:11 -0400 (Fri, 22 Oct 2021)
git_url: https://git.bioconductor.org/packages/airpart
git_branch: master
git_last_commit: cdd43e0
git_last_commit_date: 2021-10-21 23:44:32 -0400 (Thu, 21 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  YES
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  YES
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  YES

Summary

Package: airpart
Version: 1.1.5
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:airpart.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings airpart_1.1.5.tar.gz
StartedAt: 2021-10-23 00:34:14 -0400 (Sat, 23 Oct 2021)
EndedAt: 2021-10-23 00:40:18 -0400 (Sat, 23 Oct 2021)
EllapsedTime: 364.9 seconds
RetCode: 0
Status:   OK  
CheckDir: airpart.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:airpart.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings airpart_1.1.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/airpart.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘airpart/DESCRIPTION’ ... OK
* this is package ‘airpart’ version ‘1.1.5’
* 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 ‘airpart’ 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
consensusPart 13.074  2.301  10.059
fusedLasso     9.951  3.530   8.796
allelicRatio  10.076  0.286  10.383
makeStep       9.893  0.110  10.016
makeHeatmap    8.526  0.049   8.602
makeForest     7.475  0.200   7.685
makeViolin     6.731  0.080   6.820
extractResult  6.034  0.117   6.167
* 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

airpart.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL airpart
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘airpart’ ...
** 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 (airpart)

Tests output

airpart.Rcheck/tests/testthat.Rout


R version 4.1.1 Patched (2021-08-22 r80813) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(airpart)
> 
> test_check("airpart")
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


Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

model-based optimal number of clusters: 3 
model-based optimal number of clusters: 3 
model-based optimal number of clusters: 3 
starting worker pid=399 on localhost:11181 at 00:40:02.723
starting worker pid=405 on localhost:11181 at 00:40:02.735
model-based optimal number of clusters: 3 
[ FAIL 0 | WARN 18 | SKIP 0 | PASS 12 ]
> 
> proc.time()
   user  system elapsed 
 31.564   2.231  31.143 

Example timings

airpart.Rcheck/airpart-Ex.timings

nameusersystemelapsed
allelicRatio10.076 0.28610.383
cellQC1.2090.0611.272
consensusPart13.074 2.30110.059
estDisp2.5440.1462.695
extractResult6.0340.1176.167
featureQC3.4480.0373.488
fusedLasso9.9513.5308.796
geneCluster0.8250.0060.832
makeForest7.4750.2007.685
makeHeatmap8.5260.0498.602
makeOffByOneAdjMat0.3430.0010.345
makeSimulatedData0.5260.0110.536
makeStep 9.893 0.11010.016
makeViolin6.7310.0806.820
preprocess0.8070.0120.820
summaryAllelicRatio1.3670.0091.378
wilcoxExt2.5370.0172.558