Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:06:26 -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 tokay2


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: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEGreport.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings DEGreport_1.30.3.tar.gz
StartedAt: 2022-04-12 18:22:33 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 18:34:25 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 712.8 seconds
RetCode: 0
Status:   OK  
CheckDir: DEGreport.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEGreport.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings DEGreport_1.30.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/DEGreport.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
degResults   12.58   0.03   12.63
degComps     10.36   0.03   10.39
degPlot       9.53   0.01    9.55
degVB         8.94   0.02    8.96
degQC         8.78   0.03    8.83
degMV         8.67   0.03    8.70
significants  8.70   0.00    8.70
degPlotWide   8.47   0.01    8.48
degMB         8.38   0.03    8.40
degMean       8.34   0.00    8.34
degSummary    8.11   0.00    8.11
degVar        7.72   0.03    7.78
DEGSet        6.67   0.59    7.26
degMA         5.67   0.03    5.71
degDefault    5.52   0.04    5.56
degColors     4.92   0.11    5.03
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
degComps     12.05   0.08   12.12
degMV        12.01   0.12   13.39
degPlot      11.98   0.05   12.55
degVar       11.86   0.00   12.01
degResults   11.67   0.04   11.72
degPlotWide  11.08   0.01   11.09
degMB         9.71   0.05    9.82
degMean       9.72   0.02    9.79
degQC         9.05   0.02    9.06
significants  8.69   0.01    8.70
DEGSet        7.94   0.16    8.09
degVB         7.95   0.00    7.95
degSummary    7.90   0.04    7.94
degMA         7.66   0.01    7.74
degDefault    7.53   0.03    7.67
degColors     5.77   0.09    5.86
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/DEGreport.Rcheck/00check.log'
for details.



Installation output

DEGreport.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/DEGreport_1.30.3.tar.gz && rm -rf DEGreport.buildbin-libdir && mkdir DEGreport.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DEGreport.buildbin-libdir DEGreport_1.30.3.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL DEGreport_1.30.3.zip && rm DEGreport_1.30.3.tar.gz DEGreport_1.30.3.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  1 18.0M    1  329k    0     0   731k      0  0:00:25 --:--:--  0:00:25  731k
  9 18.0M    9 1805k    0     0  1246k      0  0:00:14  0:00:01  0:00:13 1246k
 21 18.0M   21 3982k    0     0  1631k      0  0:00:11  0:00:02  0:00:09 1631k
 38 18.0M   38 7208k    0     0  2096k      0  0:00:08  0:00:03  0:00:05 2096k
 61 18.0M   61 11.0M    0     0  2560k      0  0:00:07  0:00:04  0:00:03 2560k
 88 18.0M   88 16.0M    0     0  3025k      0  0:00:06  0:00:05  0:00:01 3232k
100 18.0M  100 18.0M    0     0  3198k      0  0:00:05  0:00:05 --:--:-- 3851k

install for i386

* installing *source* package 'DEGreport' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DEGreport'
    finding HTML links ... done
    DEGSet                                  html  
    DEGreport-deprecated                    html  
    createReport                            html  
    deg                                     html  
    degCheckFactors                         html  
    degColors                               html  
    degComps                                html  
    degCorCov                               html  
    degCovariates                           html  
    degDefault                              html  
    degFilter                               html  
    degMA                                   html  
    finding level-2 HTML links ... done

    degMB                                   html  
    degMDS                                  html  
    degMV                                   html  
    degMean                                 html  
    degMerge                                html  
    degObj                                  html  
    degPCA                                  html  
    degPatterns                             html  
    degPlot                                 html  
    degPlotCluster                          html  
    degPlotWide                             html  
    degQC                                   html  
    degResults                              html  
    degSignature                            html  
    degSummary                              html  
    degVB                                   html  
    degVar                                  html  
    degVolcano                              html  
    geneInfo                                html  
    geom_cor                                html  
    humanGender                             html  
    significants                            html  
** 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

install for x64

* installing *source* package 'DEGreport' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DEGreport' as DEGreport_1.30.3.zip
* DONE (DEGreport)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'DEGreport' successfully unpacked and MD5 sums checked

Tests output

DEGreport.Rcheck/tests_i386/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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

Attaching package: 'IRanges'

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

    windows

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 
  52.04    1.93   54.37 

DEGreport.Rcheck/tests_x64/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-w64-mingw32/x64 (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

Attaching package: 'IRanges'

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

    windows

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 
  49.04    0.68   49.73 

Example timings

DEGreport.Rcheck/examples_i386/DEGreport-Ex.timings

nameusersystemelapsed
DEGSet6.670.597.26
degCheckFactors1.590.021.61
degColors4.920.115.03
degComps10.36 0.0310.39
degCorCov0.910.010.93
degCovariates2.170.042.20
degDefault5.520.045.56
degFilter0.390.020.40
degMA5.670.035.71
degMB8.380.038.40
degMDS0.830.020.85
degMV8.670.038.70
degMean8.340.008.34
degObj0.390.010.41
degPCA0.860.050.91
degPatterns1.720.051.76
degPlot9.530.019.55
degPlotCluster1.960.021.98
degPlotWide8.470.018.48
degQC8.780.038.83
degResults12.58 0.0312.63
degSignature0.650.000.65
degSummary8.110.008.11
degVB8.940.028.96
degVar7.720.037.78
degVolcano3.950.013.97
geom_cor0.580.020.60
significants8.70.08.7

DEGreport.Rcheck/examples_x64/DEGreport-Ex.timings

nameusersystemelapsed
DEGSet7.940.168.09
degCheckFactors1.580.021.59
degColors5.770.095.86
degComps12.05 0.0812.12
degCorCov1.180.011.21
degCovariates2.30.02.3
degDefault7.530.037.67
degFilter0.380.040.40
degMA7.660.017.74
degMB9.710.059.82
degMDS1.050.051.16
degMV12.01 0.1213.39
degMean9.720.029.79
degObj0.510.030.55
degPCA1.090.031.13
degPatterns2.160.012.28
degPlot11.98 0.0512.55
degPlotCluster1.920.021.95
degPlotWide11.08 0.0111.09
degQC9.050.029.06
degResults11.67 0.0411.72
degSignature0.590.040.63
degSummary7.900.047.94
degVB7.950.007.95
degVar11.86 0.0012.01
degVolcano4.280.024.32
geom_cor0.390.000.39
significants8.690.018.70