Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:07:53 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 DEGreport on machv2


To the developers/maintainers of the DEGreport package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DEGreport.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 475/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEGreport 1.30.3  (landing page)
Lorena Pantano
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/DEGreport
git_branch: RELEASE_3_14
git_last_commit: 3554bce
git_last_commit_date: 2022-03-26 19:02:40 -0400 (Sat, 26 Mar 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: DEGreport
Version: 1.30.3
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DEGreport.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DEGreport_1.30.3.tar.gz
StartedAt: 2022-04-12 12:22:12 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 12:33:38 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 686.8 seconds
RetCode: 0
Status:   OK  
CheckDir: DEGreport.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DEGreport.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DEGreport_1.30.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/DEGreport.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DEGreport/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DEGreport’ version ‘1.30.3’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DEGreport’ 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 ... NOTE
.benckmark_cutoff: no visible binding for global variable ‘cutoff’
.benckmark_cutoff: no visible binding for global variable ‘cluster’
.convertIDs: no visible global function definition for ‘keys’
.correct_fdr: no visible global function definition for ‘fdrtool’
.generate_scatter_plot: no visible binding for global variable
  ‘compare’
.generate_scatter_plot: no visible binding for global variable ‘covar’
.get_counts: no visible global function definition for ‘counts’
.model: no visible global function definition for ‘lm’
.plot_raw: no visible binding for global variable ‘.x’
.plot_shrunken: no visible binding for global variable ‘.x’
.process: no visible binding for global variable ‘genes’
.process: no visible binding for global variable ‘cluster’
.reduce : <anonymous> : <anonymous>: no visible global function
  definition for ‘boxplot’
.reduce_covariates : <anonymous>: no visible binding for global
  variable ‘fdr’
.reduce_covariates : <anonymous>: no visible binding for global
  variable ‘compare’
.reduce_covariates : <anonymous>: no visible binding for global
  variable ‘r’
.reduce_covariates : <anonymous>: no visible binding for global
  variable ‘p.value’
.run_cluster_profiler: no visible global function definition for
  ‘enrichGO’
.run_cluster_profiler: no visible global function definition for
  ‘simplify’
.select_concensus_genes: no visible global function definition for
  ‘desc’
.select_concensus_genes: no visible binding for global variable ‘score’
.select_concensus_genes: no visible binding for global variable ‘k’
.select_concensus_genes: no visible binding for global variable
  ‘itemConsensus’
.summarise_res: no visible global function definition for ‘matches’
.summarise_res: no visible binding for global variable ‘comparison’
.summarise_res: no visible binding for global variable ‘gene’
.summarise_res: no visible binding for global variable ‘value_fdr’
.summarise_res: no visible binding for global variable ‘value_fc’
.table_w_fc: no visible binding for global variable ‘comp’
.table_w_fc: no visible binding for global variable ‘log2FoldChange’
degCheckFactors: no visible binding for global variable ‘ratios’
degCorCov: no visible binding for global variable ‘compare’
degCovariates: no visible binding for global variable ‘x’
degCovariates: no visible binding for global variable ‘y’
degCovariates: no visible binding for global variable ‘xend’
degCovariates: no visible binding for global variable ‘yend’
degCovariates: no visible binding for global variable ‘pvalue’
degMA: no visible binding for global variable ‘base_mean’
degMA: no visible binding for global variable ‘log2fc’
degMV: no visible binding for global variable ‘min_median’
degMV: no visible binding for global variable ‘max_sd’
degPatterns: no visible global function definition for ‘rowMedians’
degPatterns: no visible binding for global variable ‘genes’
degPlotCluster: no visible binding for global variable ‘genes’
degPlotCluster: no visible binding for global variable ‘cluster’
degPlotWide : <anonymous>: no visible binding for global variable
  ‘count’
significants,TopTags: no visible binding for global variable ‘FDR’
significants,TopTags: no visible binding for global variable ‘logFC’
significants,list : <anonymous>: no visible global function definition
  for ‘matches’
Undefined global functions or variables:
  .x FDR base_mean boxplot cluster comp compare comparison count counts
  covar cutoff desc enrichGO fdr fdrtool gene genes itemConsensus k
  keys lm log2FoldChange log2fc logFC matches max_sd min_median p.value
  pvalue r ratios rowMedians score simplify value_fc value_fdr x xend y
  yend
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "lm")
to your NAMESPACE file.
* 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
degResults   21.803  0.085  25.867
degComps     19.867  0.081  20.015
degPlot      18.153  0.080  18.298
degQC        16.909  0.066  17.082
degPlotWide  16.581  0.057  16.864
significants 16.073  0.038  16.126
degMean      15.735  0.042  15.795
degSummary   15.212  0.072  19.094
degMV        14.796  0.074  17.903
degVar       14.817  0.050  14.877
degMB        14.257  0.067  14.377
degVB        13.541  0.053  13.616
DEGSet       12.649  0.266  14.689
degDefault   10.395  0.036  10.453
degMA        10.257  0.044  10.321
degColors     9.872  0.091   9.985
degVolcano    7.283  0.023   7.312
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/DEGreport.Rcheck/00check.log’
for details.



Installation output

DEGreport.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘DEGreport’ ...
** using staged installation
** R
** data
** 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 (DEGreport)

Tests output

DEGreport.Rcheck/tests/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(edgeR)
Loading required package: limma
> library(DESeq2)
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

    plotMA

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

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
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: 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(DEGreport)
> 
> test_check("DEGreport")
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 64 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 64 ]
> 
> proc.time()
   user  system elapsed 
 87.276   1.182  88.520 

Example timings

DEGreport.Rcheck/DEGreport-Ex.timings

nameusersystemelapsed
DEGSet12.649 0.26614.689
degCheckFactors2.2310.0722.305
degColors9.8720.0919.985
degComps19.867 0.08120.015
degCorCov1.5210.0281.561
degCovariates4.0940.0314.134
degDefault10.395 0.03610.453
degFilter0.5280.0160.545
degMA10.257 0.04410.321
degMB14.257 0.06714.377
degMDS1.4250.0201.447
degMV14.796 0.07417.903
degMean15.735 0.04215.795
degObj0.5240.0170.541
degPCA1.5300.0221.573
degPatterns2.7840.0323.002
degPlot18.153 0.08018.298
degPlotCluster3.2520.0363.290
degPlotWide16.581 0.05716.864
degQC16.909 0.06617.082
degResults21.803 0.08525.867
degSignature1.0520.0081.062
degSummary15.212 0.07219.094
degVB13.541 0.05313.616
degVar14.817 0.05014.877
degVolcano7.2830.0237.312
geom_cor0.7830.0190.802
significants16.073 0.03816.126