Package: DEGreport

Version: 1.19.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DEGreport.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DEGreport_1.19.1.tar.gz

StartedAt: 2019-04-09 00:21:55 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:28:06 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 370.3 seconds

RetCode: 0

Status:  OK

CheckDir: DEGreport.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DEGreport.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DEGreport_1.19.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/DEGreport.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.19.1’
* 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’
.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
  cutoff 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 ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
degComps     9.992  0.042  10.132
degResults   9.460  0.062   9.594
significants 8.148  0.026   8.271
degPlot      7.597  0.042   7.730
degColors    6.731  0.092   6.893
DEGSet       6.464  0.219   6.732
degMV        6.273  0.060   9.196
degQC        5.998  0.065   6.114
degMB        5.459  0.101   5.618
degMean      5.450  0.048   5.560
degVar       5.058  0.042   5.158
* 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-3.9-bioc/meat/DEGreport.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DEGreport
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘DEGreport’ ...
** 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
* DONE (DEGreport)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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
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, 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
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, rowsum

> library(DEGreport)
> 
> test_check("DEGreport")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 63 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 42.145   0.971  43.516 

name	user	system	elapsed
DEGSet	6.464	0.219	6.732
degCheckFactors	1.091	0.093	1.194
degColors	6.731	0.092	6.893
degComps	9.992	0.042	10.132
degCorCov	0.671	0.016	0.696
degCovariates	2.335	0.023	2.385
degFilter	0.357	0.012	0.371
degMA	4.222	0.021	4.277
degMB	5.459	0.101	5.618
degMDS	0.755	0.019	0.789
degMV	6.273	0.060	9.196
degMean	5.450	0.048	5.560
degObj	0.352	0.019	0.375
degPCA	0.755	0.018	0.781
degPatterns	2.637	0.025	2.697
degPlot	7.597	0.042	7.730
degPlotCluster	3.808	0.027	3.880
degPlotWide	4.084	0.036	4.174
degQC	5.998	0.065	6.114
degResults	9.460	0.062	9.594
degSignature	0.811	0.012	0.831
degSummary	4.416	0.024	4.485
degVB	4.837	0.063	4.956
degVar	5.058	0.042	5.158
degVolcano	2.841	0.015	2.886
geom_cor	0.533	0.015	0.554
significants	8.148	0.026	8.271