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CHECK report for biobroom on malbec1

This page was generated on 2020-11-27 11:52:25 -0500 (Fri, 27 Nov 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE biobroom PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 153/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biobroom 1.22.0
John D. Storey and Andrew J. Bass
Snapshot Date: 2020-11-26 14:42:42 -0500 (Thu, 26 Nov 2020)
URL: https://git.bioconductor.org/packages/biobroom
Branch: RELEASE_3_12
Last Commit: 8fe86f2
Last Changed Date: 2020-10-27 11:09:12 -0500 (Tue, 27 Oct 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: biobroom
Version: 1.22.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:biobroom.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings biobroom_1.22.0.tar.gz
StartedAt: 2020-11-26 23:56:23 -0500 (Thu, 26 Nov 2020)
EndedAt: 2020-11-26 23:57:59 -0500 (Thu, 26 Nov 2020)
EllapsedTime: 96.8 seconds
RetCode: 0
Status:  OK 
CheckDir: biobroom.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:biobroom.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings biobroom_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/biobroom.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biobroom/DESCRIPTION’ ... OK
* this is package ‘biobroom’ version ‘1.22.0’
* 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 ‘biobroom’ 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 ... NOTE
'library' or 'require' call to ‘DESeq2’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Missing or unexported object: ‘dplyr::tbl_dt’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
finish: no visible global function definition for ‘tbl_dt’
glance.DGEExact: no visible global function definition for ‘p.adjust’
glance.GRanges: no visible binding for global variable ‘gr’
glance.GRangesList: no visible binding for global variable ‘gr’
makeExampleDataSet: no visible global function definition for
  ‘estimateSizeFactors’
makeExampleDataSet: no visible global function definition for ‘counts’
makeExampleDataSet: no visible global function definition for ‘colData’
makeExampleDataSet: no visible global function definition for
  ‘seqnames’
makeExampleDataSet: no visible global function definition for
  ‘rowRanges’
makeExampleDataSet: no visible global function definition for ‘start’
makeExampleDataSet: no visible global function definition for ‘end’
makeExampleDataSet: no visible global function definition for ‘DGEList’
makeExampleDataSet: no visible global function definition for
  ‘calcNormFactors’
makeExampleDataSet: no visible global function definition for
  ‘model.matrix’
makeExampleDataSet: no visible global function definition for ‘design’
makeExampleDataSet: no visible global function definition for
  ‘voomWithQualityWeights’
makeExampleDataSet: no visible global function definition for ‘voom’
makeExampleDataSet: no visible global function definition for ‘pData<-’
makeExampleDataSet: no visible global function definition for ‘fData<-’
makeExampleDataSet: no visible global function definition for ‘is’
tidy.DESeqDataSet: no visible binding for global variable ‘term’
tidy.DESeqDataSet: no visible binding for global variable ‘.’
tidy.DESeqDataSet: no visible global function definition for ‘counts’
tidy.DESeqDataSet: no visible binding for global variable ‘gene’
tidy.DGEList: no visible binding for global variable ‘gene’
tidy.EList: no visible global function definition for ‘setNames’
tidy.ExpressionSet: no visible binding for global variable ‘value’
tidy.ExpressionSet: no visible binding for global variable ‘gene’
tidy.ExpressionSet: no visible global function definition for ‘pData’
tidy.MArrayLM: no visible binding for global variable ‘term’
tidy.MArrayLM: no visible binding for global variable ‘estimate’
tidy.MArrayLM: no visible binding for global variable ‘gene’
tidy.MSnSet: no visible binding for global variable ‘sample.id’
tidy.MSnSet: no visible binding for global variable ‘value’
tidy.MSnSet: no visible binding for global variable ‘protein’
tidy.MSnSet: no visible global function definition for ‘pData’
tidy.RangedSummarizedExperiment: no visible binding for global variable
  ‘value’
tidy.RangedSummarizedExperiment: no visible binding for global variable
  ‘gene’
tidy.RangedSummarizedExperiment: no visible global function definition
  for ‘colData’
tidy.deSet: no visible global function definition for ‘exprs<-’
tidy.deSet: no visible binding for global variable ‘value’
tidy.deSet: no visible binding for global variable ‘gene’
tidy.deSet: no visible global function definition for ‘pData’
tidy.qvalue: no visible binding for global variable ‘smoothed’
tidy.qvalue: no visible binding for global variable ‘pi0’
tidy.qvalue: no visible binding for global variable ‘lambda’
tidy_matrix: no visible binding for global variable ‘value’
tidy_matrix: no visible binding for global variable ‘gene’
Undefined global functions or variables:
  . DGEList calcNormFactors colData counts design end estimate
  estimateSizeFactors exprs<- fData<- gene gr is lambda model.matrix
  p.adjust pData pData<- pi0 protein rowRanges sample.id seqnames
  setNames smoothed start tbl_dt term value voom voomWithQualityWeights
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "end", "model.matrix", "p.adjust", "setNames",
             "start")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
DESeq2_tidiers 13.332  0.296  13.656
MSnSet_tidiers  3.184  0.032  10.249
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/biobroom.Rcheck/00check.log’
for details.



Installation output

biobroom.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL biobroom
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘biobroom’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (biobroom)

Tests output

biobroom.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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("magrittr")

Attaching package: 'magrittr'

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

    equals, is_less_than, not

> library("dplyr")

Attaching package: 'dplyr'

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

    matches

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

    filter, lag

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

    intersect, setdiff, setequal, union

> library("DESeq2")
Loading required package: S4Vectors
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:dplyr':

    combine, intersect, setdiff, union

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:dplyr':

    first, rename

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

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    collapse, desc, slice

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    count


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: 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

> library("edgeR")
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:DESeq2':

    plotMA

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

    plotMA

> library("Biobase")
> library("biobroom")
Loading required package: broom
Registered S3 methods overwritten by 'biobroom':
  method      from 
  glance.list broom
  tidy.list   broom
> 
> test_check("biobroom")
── Warning (test-DESeq2_tidiers.R:5:5): Basic DESeq2 tidier works as expected ──
`tbl_df()` is deprecated as of dplyr 1.0.0.
Please use `tibble::as_tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.

── Warning (test-limma_tidiers.R:5:5): limma tidier works as expected ──────────
This function is deprecated as of broom 0.7.0 and will be removed from a future release. Please see tibble::as_tibble().

── Warning (test-limma_tidiers.R:6:5): limma tidier works as expected ──────────
This function is deprecated as of broom 0.7.0 and will be removed from a future release. Please see tibble::as_tibble().

── Warning (test-limma_tidiers.R:26:5): voom tidier adds weight column ─────────
This function is deprecated as of broom 0.7.0 and will be removed from a future release. Please see tibble::as_tibble().

── Warning (test-limma_tidiers.R:26:5): voom tidier adds weight column ─────────
This function is deprecated as of broom 0.7.0 and will be removed from a future release. Please see tibble::as_tibble().

── Warning (test-limma_tidiers.R:27:5): voom tidier adds weight column ─────────
This function is deprecated as of broom 0.7.0 and will be removed from a future release. Please see tibble::as_tibble().

── Warning (test-limma_tidiers.R:27:5): voom tidier adds weight column ─────────
This function is deprecated as of broom 0.7.0 and will be removed from a future release. Please see tibble::as_tibble().

── Warning (test-limma_tidiers.R:40:5): voom tidier adds weight column ─────────
This function is deprecated as of broom 0.7.0 and will be removed from a future release. Please see tibble::as_tibble().

── Warning (test-limma_tidiers.R:41:5): voom tidier adds weight column ─────────
This function is deprecated as of broom 0.7.0 and will be removed from a future release. Please see tibble::as_tibble().

── Warning (test-limma_tidiers.R:49:5): voomWithQualityWeights tidier adds weigh
This function is deprecated as of broom 0.7.0 and will be removed from a future release. Please see tibble::as_tibble().

── Warning (test-limma_tidiers.R:49:5): voomWithQualityWeights tidier adds weigh
This function is deprecated as of broom 0.7.0 and will be removed from a future release. Please see tibble::as_tibble().

── Warning (test-limma_tidiers.R:50:5): voomWithQualityWeights tidier adds weigh
This function is deprecated as of broom 0.7.0 and will be removed from a future release. Please see tibble::as_tibble().

── Warning (test-limma_tidiers.R:50:5): voomWithQualityWeights tidier adds weigh
This function is deprecated as of broom 0.7.0 and will be removed from a future release. Please see tibble::as_tibble().

── Warning (test-limma_tidiers.R:67:5): voomWithQualityWeights tidier adds weigh
This function is deprecated as of broom 0.7.0 and will be removed from a future release. Please see tibble::as_tibble().

── Warning (test-limma_tidiers.R:68:5): voomWithQualityWeights tidier adds weigh
This function is deprecated as of broom 0.7.0 and will be removed from a future release. Please see tibble::as_tibble().

══ testthat results  ═══════════════════════════════════════════════════════════
Warning (test-DESeq2_tidiers.R:5:5): Basic DESeq2 tidier works as expected
Warning (test-limma_tidiers.R:5:5): limma tidier works as expected
Warning (test-limma_tidiers.R:6:5): limma tidier works as expected
Warning (test-limma_tidiers.R:26:5): voom tidier adds weight column
Warning (test-limma_tidiers.R:26:5): voom tidier adds weight column
Warning (test-limma_tidiers.R:27:5): voom tidier adds weight column
Warning (test-limma_tidiers.R:27:5): voom tidier adds weight column
Warning (test-limma_tidiers.R:40:5): voom tidier adds weight column
Warning (test-limma_tidiers.R:41:5): voom tidier adds weight column
Warning (test-limma_tidiers.R:49:5): voomWithQualityWeights tidier adds weight and sample.weight columns
Warning (test-limma_tidiers.R:49:5): voomWithQualityWeights tidier adds weight and sample.weight columns
Warning (test-limma_tidiers.R:50:5): voomWithQualityWeights tidier adds weight and sample.weight columns
Warning (test-limma_tidiers.R:50:5): voomWithQualityWeights tidier adds weight and sample.weight columns
Warning (test-limma_tidiers.R:67:5): voomWithQualityWeights tidier adds weight and sample.weight columns
Warning (test-limma_tidiers.R:68:5): voomWithQualityWeights tidier adds weight and sample.weight columns

[ FAIL 0 | WARN 15 | SKIP 0 | PASS 52 ]
> 
> 
> proc.time()
   user  system elapsed 
 19.196   0.368  19.620 

Example timings

biobroom.Rcheck/biobroom-Ex.timings

nameusersystemelapsed
DESeq2_tidiers13.332 0.29613.656
ExpressionSet_tidiers1.1520.0081.160
GRanges_tidiers0.0000.0000.001
MSnSet_tidiers 3.184 0.03210.249
SummarizedExperiment_tidiers0.0000.0000.001
edgeR_tidiers4.8240.0284.864
limma_tidiers0.2720.0000.275
qvalue_tidiers0.8000.0000.944