Multiple platform build/check report for BioC 3.9 - CHECK report for ReportingTools on malbec2

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ReportingTools.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ReportingTools_2.23.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ReportingTools.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReportingTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ReportingTools’ version ‘2.23.1’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ReportingTools’ 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
.GeneSetCollection.to.data.frame: no visible binding for global
  variable 'description'
.GeneSetCollection.to.html: no visible binding for global variable
  'description'
.GeneSetCollection.to.html2: no visible binding for global variable
  'description'
.PFAMhyperG.to.html: no visible binding for global variable 'keytype'
.PFAMhyperG.to.html: no visible binding for global variable 'columns'
.make.gene.plots: no visible global function definition for 'exprs'
.marrayLM.to.data.frame: no visible global function definition for
  'featureNames'
.marrayLM.to.data.frame: no visible global function definition for
  'fData'
.marrayLM.to.html: no visible global function definition for
  'featureNames'
.marrayLM.to.html: no visible global function definition for 'fData'
check.ids: no visible binding for global variable 'org.Hs.eg.db'
check.ids: no visible global function definition for 'keys'
custHeaderPanel : <anonymous>: no visible binding for global variable
  'tags'
custHeaderPanel : <anonymous>: no visible global function definition
  for 'HTML'
custHeaderPanel: no visible global function definition for 'tagList'
custHeaderPanel: no visible global function definition for 'tag'
custHeaderPanel: no visible global function definition for 'div'
custHeaderPanel: no visible global function definition for 'h1'
publish,trellis-HTMLReport: no visible binding for global variable
  'htmlRep'
toReportDF,DESeqDataSet: no visible global function definition for
  'mcols'
Undefined global functions or variables:
  HTML columns description div exprs fData featureNames h1 htmlRep keys
  keytype mcols org.Hs.eg.db tag tagList tags
* 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/ReportingTools.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL ReportingTools
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘ReportingTools’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for 'objectToHTML' with signature 'object="ggbio"': no definition for class "ggbio"
** 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 (ReportingTools)

Tests output


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 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.

> require("ReportingTools") || stop("unable to load ReportingTools")
Loading required package: ReportingTools
Loading required package: knitr


[1] TRUE
> BiocGenerics:::testPackage("ReportingTools")
Loading required package: Biobase
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 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

Welcome to Bioconductor

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


Attaching package: 'limma'

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

    plotMA

Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: org.Hs.eg.db


Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
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

estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
Loading required package: annotate
Loading required package: XML
Loading required package: graph

Attaching package: 'graph'

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

    addNode

Loading required package: Category
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand


Attaching package: 'GOstats'

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

    makeGOGraph


'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns

<script language="JavaScript" src="jslib/jquery-1.8.0.min.js"></script>
<script language="JavaScript" src="jslib/jquery.dataTables-1.9.3.js"></script>
<script language="JavaScript" src="jslib/jquery.dataTables.columnFilter.js"></script>
<script language="JavaScript" src="jslib/jquery.dataTables.plugins.js"></script>
<script language="JavaScript" src="jslib/jquery.dataTables.reprise.js"></script>
<script language="JavaScript" src="jslib/bootstrap.js"></script>
<link rel="stylesheet" type="text/css" href="csslib/bootstrap.css" />
<link rel="stylesheet" type="text/css" href="csslib/reprise.table.bootstrap.css" />

processing file: /home/biocbuild/bbs-3.9-bioc/R/library/ReportingTools/examples/testRmd.Rmd
  ordinary text without R code

label: unnamed-chunk-1 (with options) 
List of 2
 $ message: logi FALSE
 $ output : chr "hide"

  ordinary text without R code

label: unnamed-chunk-2 (with options) 
List of 1
 $ results: chr "asis"

  ordinary text without R code

label: unnamed-chunk-3 (with options) 
List of 1
 $ results: chr "asis"

  ordinary text without R code

label: unnamed-chunk-4 (with options) 
List of 1
 $ results: chr "asis"

output file: testRmd.md

Created file named 'testDataPackage/testPkg/man/my.df2.Rd'.
Edit the file and move it to the appropriate directory.


RUNIT TEST PROTOCOL -- Tue Apr  9 03:20:00 2019 
*********************************************** 
Number of test functions: 45 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
ReportingTools RUnit Tests - 45 test functions, 0 errors, 0 failures
Number of test functions: 45 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
258.232   8.270 273.758

name	user	system	elapsed
BaseReportType-class	0.001	0.000	0.001
CSVFile-class	0	0	0
CSVFile	0.008	0.000	0.008
DataPackage-class	0.012	0.000	0.012
DataPackage	0.002	0.004	0.383
HTMLReport	0.020	0.012	0.091
HTMLReportRef-class	0.001	0.000	0.001
Link	0.006	0.004	0.010
ReportHandlers-class	0	0	0
finish-methods	0	0	0
makeDESeqDF	0	0	0
mockRnaSeqData	0.021	0.003	0.025
publish-methods	0.000	0.000	0.001
reporting.theme	0.017	0.003	0.021
reporting.theme.alternate	0.023	0.000	0.022
validConnection	0.095	0.008	0.104

CHECK report for ReportingTools on malbec2

Summary

Command output

Installation output

Tests output

Example timings