##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ReportingTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ReportingTools_2.45.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ReportingTools.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ReportingTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ReportingTools’ version ‘2.45.0’
* 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 ... 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 code 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 ... NOTE
checkRd: (-1) ReportHandlers-class.Rd:50: Lost braces
    50 |       connection as elements are added to the report. code{finish} completes the page and closes the connection.}
       |                                                           ^
* 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 sizes of PDF files under ‘inst/doc’ ... 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 ... 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-3.20-bioc/meat/ReportingTools.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ReportingTools
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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

Attaching package: 'BiocGenerics'

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, aperm, 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, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, 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:utils':

    findMatches

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

    I, expand.grid, unname

Loading required package: org.Hs.eg.db


Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


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

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

    rowMedians

Loading required package: DEXSeq
Loading required package: BiocParallel
Loading required package: RColorBrewer
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
2024-10-28 00:10:39.829 R[9695:40651301] XType: Using static font registry.
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: testRmd.Rmd
output file: testRmd.knit.md

/opt/homebrew/bin/pandoc +RTS -K512m -RTS testRmd.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /Users/biocbuild/bbs-3.20-bioc/meat/ReportingTools.Rcheck/tests/reports/testRmd.html --lua-filter /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T//RtmpDkwOUx/rmarkdown-str25df5b389d00.html 
[WARNING] This document format requires a nonempty <title> element.
  Defaulting to 'testRmd.knit' as the title.
  To specify a title, use 'title' in metadata or --metadata title="...".

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


RUNIT TEST PROTOCOL -- Mon Oct 28 00:11:42 2024 
*********************************************** 
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 
Warning messages:
1: In DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
2: In DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
> 
> proc.time()
   user  system elapsed 
 66.756   6.634  73.514