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CHECK report for DEGreport on tokay1

This page was generated on 2019-04-13 11:23:58 -0400 (Sat, 13 Apr 2019).

Package 386/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DEGreport 1.18.1
Lorena Pantano
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/DEGreport
Branch: RELEASE_3_8
Last Commit: 9d5c08e
Last Changed Date: 2019-01-04 13:05:10 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DEGreport
Version: 1.18.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEGreport.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DEGreport_1.18.1.tar.gz
StartedAt: 2019-04-13 01:41:32 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 01:49:54 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 502.4 seconds
RetCode: 0
Status:  OK  
CheckDir: DEGreport.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DEGreport.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings DEGreport_1.18.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/DEGreport.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.18.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'knitr'
A package should be listed in only one of these fields.
* 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
.convertIDs: no visible global function definition for 'keys'
.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'
.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'
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'
degPatterns: no visible global function definition for 'n'
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 desc
  enrichGO fdr gene genes itemConsensus k keys lm log2FoldChange log2fc
  logFC max_sd min_median n p.value 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 or elapsed time > 5s
           user system elapsed
degResults 6.70   0.02    6.71
degComps   5.56   0.55    6.11
degPlot    5.62   0.01    5.64
degColors  5.50   0.05    5.54
DEGSet     4.97   0.25    5.22
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
degResults 6.84   0.03    6.87
degColors  6.66   0.11    6.76
degComps   5.56   0.05    5.61
degPlot    5.50   0.02    5.53
DEGSet     4.95   0.10    5.05
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/DEGreport.Rcheck/00check.log'
for details.



Installation output

DEGreport.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/DEGreport_1.18.1.tar.gz && rm -rf DEGreport.buildbin-libdir && mkdir DEGreport.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DEGreport.buildbin-libdir DEGreport_1.18.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL DEGreport_1.18.1.zip && rm DEGreport_1.18.1.tar.gz DEGreport_1.18.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 17.7M  100 17.7M    0     0  89.0M      0 --:--:-- --:--:-- --:--:-- 90.7M

install for i386

* installing *source* package 'DEGreport' ...
** 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
In R CMD INSTALL

install for x64

* installing *source* package 'DEGreport' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DEGreport' as DEGreport_1.18.1.zip
* DONE (DEGreport)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'DEGreport' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

DEGreport.Rcheck/tests_i386/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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
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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

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

    expand.grid

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: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply

> library(DEGreport)
> 
> test_check("DEGreport")
== testthat results  ===========================================================
OK: 61 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  25.93    0.93   26.85 

DEGreport.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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
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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

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

    expand.grid

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: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply

> library(DEGreport)
> 
> test_check("DEGreport")
== testthat results  ===========================================================
OK: 61 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  27.04    0.56   27.62 

Example timings

DEGreport.Rcheck/examples_i386/DEGreport-Ex.timings

nameusersystemelapsed
DEGSet4.970.255.22
degCheckFactors0.780.070.92
degColors5.500.055.54
degComps5.560.556.11
degCorCov0.750.040.80
degCovariates1.980.052.03
degFilter0.370.020.39
degMA2.490.062.55
degMB2.90.02.9
degMDS0.600.010.61
degMV3.070.023.10
degMean2.970.053.01
degObj0.300.040.34
degPCA0.660.000.66
degPatterns1.420.071.49
degPlot5.620.015.64
degPlotCluster1.470.001.46
degPlotWide3.020.113.13
degQC3.820.063.89
degResults6.700.026.71
degSignature0.610.000.61
degSummary2.630.052.67
degVB3.550.003.54
degVar3.000.013.02
degVolcano1.780.031.81
geom_cor0.510.020.53
significants4.320.004.32

DEGreport.Rcheck/examples_x64/DEGreport-Ex.timings

nameusersystemelapsed
DEGSet4.950.105.05
degCheckFactors0.970.061.03
degColors6.660.116.76
degComps5.560.055.61
degCorCov0.780.030.81
degCovariates3.140.033.17
degFilter0.320.000.31
degMA2.670.022.69
degMB3.040.033.06
degMDS0.660.010.67
degMV3.480.053.53
degMean3.560.023.58
degObj0.350.010.36
degPCA0.670.020.69
degPatterns1.430.031.47
degPlot5.500.025.53
degPlotCluster1.770.031.82
degPlotWide2.920.042.96
degQC4.110.054.18
degResults6.840.036.87
degSignature0.610.030.64
degSummary2.850.002.85
degVB3.120.003.12
degVar4.310.034.34
degVolcano1.970.001.97
geom_cor0.570.000.57
significants4.540.004.54