Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-09-22 15:04:49 -0400 (Wed, 22 Sep 2021).

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? 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 467/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEGreport 1.28.0  (landing page)
Lorena Pantano
Snapshot Date: 2021-09-21 04:50:12 -0400 (Tue, 21 Sep 2021)
git_url: https://git.bioconductor.org/packages/DEGreport
git_branch: RELEASE_3_13
git_last_commit: c9d2eef
git_last_commit_date: 2021-05-19 12:05:35 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: 1.28.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:DEGreport.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings DEGreport_1.28.0.tar.gz
StartedAt: 2021-09-21 09:35:00 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 09:41:12 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 371.7 seconds
RetCode: 0
Status:   OK  
CheckDir: DEGreport.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:DEGreport.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings DEGreport_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/DEGreport.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 ‘DEGreport/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DEGreport’ version ‘1.28.0’
* 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 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 binding for global variable
  ‘gene’
Undefined global functions or variables:
  .x FDR base_mean boxplot cluster comp compare count counts covar
  cutoff desc enrichGO fdr fdrtool gene genes itemConsensus k keys lm
  log2FoldChange log2fc logFC 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
degMV        10.049  0.096  12.541
degResults    9.825  0.092   9.918
degComps      9.496  0.140   9.636
degPlot       8.885  0.064   8.949
degPlotWide   8.682  0.112   8.794
degDefault    8.554  0.196   8.800
degQC         7.763  0.056   7.820
significants  7.662  0.032   7.694
degVB         7.288  0.036   7.324
degMB         7.164  0.116   7.281
degMean       7.185  0.040   7.228
DEGSet        6.788  0.160   6.950
degVar        6.897  0.048   6.945
degSummary    6.568  0.036   6.608
degMA         5.160  0.048   5.295
* 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-3.13-bioc/meat/DEGreport.Rcheck/00check.log’
for details.



Installation output

DEGreport.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL DEGreport
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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 4.1.1 (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(edgeR)
Loading required package: limma
> 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 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 19 | SKIP 0 | PASS 64 ]
> 
> proc.time()
   user  system elapsed 
 43.663   1.391  45.036 

Example timings

DEGreport.Rcheck/DEGreport-Ex.timings

nameusersystemelapsed
DEGSet6.7880.1606.950
degCheckFactors1.6580.0601.718
degColors4.7060.0884.794
degComps9.4960.1409.636
degCorCov0.8040.0160.820
degCovariates1.6740.0681.742
degDefault8.5540.1968.800
degFilter0.5760.0040.580
degMA5.1600.0485.295
degMB7.1640.1167.281
degMDS0.8180.0160.834
degMV10.049 0.09612.541
degMean7.1850.0407.228
degObj0.3230.0120.335
degPCA0.8430.0120.855
degPatterns1.5290.0121.541
degPlot8.8850.0648.949
degPlotCluster1.8840.0131.897
degPlotWide8.6820.1128.794
degQC7.7630.0567.820
degResults9.8250.0929.918
degSignature0.5160.0160.531
degSummary6.5680.0366.608
degVB7.2880.0367.324
degVar6.8970.0486.945
degVolcano3.4780.0123.491
geom_cor0.4440.0120.456
significants7.6620.0327.694