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This page was generated on 2021-10-16 15:51:46 -0400 (Sat, 16 Oct 2021).

CHECK results for microbiomeDataSets on nebbiolo2

To the developers/maintainers of the microbiomeDataSets package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 225/404HostnameOS / ArchINSTALLBUILDCHECK
microbiomeDataSets 1.1.5  (landing page)
Leo Lahti
Snapshot Date: 2021-10-16 09:30:02 -0400 (Sat, 16 Oct 2021)
git_url: https://git.bioconductor.org/packages/microbiomeDataSets
git_branch: master
git_last_commit: 6269e63
git_last_commit_date: 2021-09-07 17:55:15 -0400 (Tue, 07 Sep 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: microbiomeDataSets
Version: 1.1.5
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:microbiomeDataSets.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings microbiomeDataSets_1.1.5.tar.gz
StartedAt: 2021-10-16 12:23:08 -0400 (Sat, 16 Oct 2021)
EndedAt: 2021-10-16 12:28:35 -0400 (Sat, 16 Oct 2021)
EllapsedTime: 326.8 seconds
RetCode: 0
Status:   OK  
CheckDir: microbiomeDataSets.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:microbiomeDataSets.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings microbiomeDataSets_1.1.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-data-experiment/meat/microbiomeDataSets.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 ‘microbiomeDataSets/DESCRIPTION’ ... OK
* this is package ‘microbiomeDataSets’ 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 ... NOTE
Found the following non-portable file path:
  microbiomeDataSets/docs/articles/microbiomeDataSets_files/accessible-code-block-0.0.1/empty-anchor.js

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘microbiomeDataSets’ 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
LahtiMLData       13.442  0.164  15.213
GrieneisenTSData  11.306  0.376  12.961
HintikkaXOData     9.526  0.176  10.589
SprockettTHData    9.454  0.148  10.510
SilvermanAGutData  9.021  0.184   9.975
SongQAData         8.187  0.136   9.179
LahtiWAData        6.134  0.108   6.788
OKeefeDSData       5.578  0.136   6.354
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.14-data-experiment/meat/microbiomeDataSets.Rcheck/00check.log’
for details.



Installation output

microbiomeDataSets.Rcheck/00install.out

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

Tests output

microbiomeDataSets.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(microbiomeDataSets)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

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
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

Loading required package: TreeSummarizedExperiment
Loading required package: SingleCellExperiment
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: MultiAssayExperiment
> 
> test_check("microbiomeDataSets")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
> 
> proc.time()
   user  system elapsed 
 92.600   2.356 102.616 

Example timings

microbiomeDataSets.Rcheck/microbiomeDataSets-Ex.timings

nameusersystemelapsed
GrieneisenTSData11.306 0.37612.961
HintikkaXOData 9.526 0.17610.589
LahtiMLData13.442 0.16415.213
LahtiWAData6.1340.1086.788
OKeefeDSData5.5780.1366.354
SilvermanAGutData9.0210.1849.975
SongQAData8.1870.1369.179
SprockettTHData 9.454 0.14810.510
availableDataSets0.0030.0000.003