Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-26 14:06:15 -0400 (Tue, 26 Oct 2021).

CHECK results for airpart on nebbiolo2

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: 2021-10-25 14:50:11 -0400 (Mon, 25 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  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / 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
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  

Summary

Package: airpart
Version: 1.1.5
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:airpart.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings airpart_1.1.5.tar.gz
StartedAt: 2021-10-25 19:05:37 -0400 (Mon, 25 Oct 2021)
EndedAt: 2021-10-25 19:09:55 -0400 (Mon, 25 Oct 2021)
EllapsedTime: 257.7 seconds
RetCode: 0
Status:   OK  
CheckDir: airpart.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:airpart.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings airpart_1.1.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/airpart.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 ‘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
fusedLasso    7.589  3.393   7.337
consensusPart 8.146  0.997   6.294
allelicRatio  6.359  0.097   6.455
makeStep      6.232  0.028   6.259
* 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:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL airpart
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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 (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(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=1533354 on localhost:11829 at 19:09:47.553
starting worker pid=1533355 on localhost:11829 at 19:09:47.572
model-based optimal number of clusters: 3 
[ FAIL 0 | WARN 18 | SKIP 0 | PASS 12 ]
> 
> proc.time()
   user  system elapsed 
 22.655   1.873  23.017 

Example timings

airpart.Rcheck/airpart-Ex.timings

nameusersystemelapsed
allelicRatio6.3590.0976.455
cellQC0.6260.0230.651
consensusPart8.1460.9976.294
estDisp1.7160.1761.892
extractResult4.1460.4004.547
featureQC2.1810.0602.241
fusedLasso7.5893.3937.337
geneCluster0.5780.0040.582
makeForest4.7610.0524.814
makeHeatmap4.7630.0244.787
makeOffByOneAdjMat0.2120.0000.212
makeSimulatedData0.3390.0080.348
makeStep6.2320.0286.259
makeViolin4.1580.0084.166
preprocess0.5000.0160.517
summaryAllelicRatio0.8090.0010.810
wilcoxExt1.9060.0001.906