Back to Multiple platform build/check report for BioC 3.15
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-10-19 13:20:10 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 nebbiolo1


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 494/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEGreport 1.32.0  (landing page)
Lorena Pantano
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/DEGreport
git_branch: RELEASE_3_15
git_last_commit: 34bf061
git_last_commit_date: 2022-04-26 11:20:09 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / 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

Summary

Package: DEGreport
Version: 1.32.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:DEGreport.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings DEGreport_1.32.0.tar.gz
StartedAt: 2022-10-18 19:21:52 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 19:27:30 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 338.0 seconds
RetCode: 0
Status:   OK  
CheckDir: DEGreport.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:DEGreport.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings DEGreport_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/DEGreport.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (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 ‘1.32.0’
* 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
degComps    6.996  0.212   7.207
degResults  7.026  0.040   7.066
degMV       6.532  0.152   7.060
degPlot     6.362  0.040   6.402
degPlotWide 6.295  0.092   6.388
degVB       5.316  0.128   5.444
DEGSet      5.174  0.227   5.402
degMB       5.173  0.040   5.213
degQC       5.090  0.032   5.122
* 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-3.15-bioc/meat/DEGreport.Rcheck/00check.log’
for details.



Installation output

DEGreport.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL DEGreport
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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(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 
 33.832   1.120  34.940 

Example timings

DEGreport.Rcheck/DEGreport-Ex.timings

nameusersystemelapsed
DEGSet5.1740.2275.402
degCheckFactors1.8580.1472.006
degColors4.9280.0514.982
degComps6.9960.2127.207
degCorCov0.8080.0160.824
degCovariates1.7390.0081.747
degDefault2.9810.0092.989
degFilter0.3800.0110.391
degMA3.1220.0873.211
degMB5.1730.0405.213
degMDS1.2050.0281.233
degMV6.5320.1527.060
degMean4.6500.0364.686
degObj0.3240.0120.337
degPCA0.6780.0040.682
degPatterns1.6230.0241.647
degPlot6.3620.0406.402
degPlotCluster3.5680.0803.648
degPlotWide6.2950.0926.388
degQC5.0900.0325.122
degResults7.0260.0407.066
degSignature0.6480.0080.655
degSummary4.7110.0124.722
degVB5.3160.1285.444
degVar4.4970.0244.523
degVolcano2.2680.0202.288
geom_cor0.5280.0080.536
significants4.7400.0324.772