Jason A. Hackney
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/ReportingTools |
| Branch: RELEASE_3_9 |
| Last Commit: d114c65 |
| Last Changed Date: 2019-05-02 11:53:38 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:50:36 -0400 (Wed, 16 Oct 2019).
| Package 1356/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ReportingTools 2.24.0 Jason A. Hackney
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: ReportingTools |
| Version: 2.24.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ReportingTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ReportingTools_2.24.0.tar.gz |
| StartedAt: 2019-10-16 06:10:13 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:26:46 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 992.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReportingTools.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ReportingTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ReportingTools_2.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ReportingTools.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-apple-darwin15.6.0 (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 ‘2.24.0’ * 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 :: no visible binding for global variable 'tags' custHeaderPanel : : 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 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 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 ‘/Users/biocbuild/bbs-3.9-bioc/meat/ReportingTools.Rcheck/00check.log’ for details.
ReportingTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ReportingTools ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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)
ReportingTools.Rcheck/tests/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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.
> 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, 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, 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
processing file: /Library/Frameworks/R.framework/Versions/3.6/Resources/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 -- Wed Oct 16 06:26:38 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
423.426 56.286 482.347
ReportingTools.Rcheck/ReportingTools-Ex.timings
| name | user | system | elapsed | |
| BaseReportType-class | 0.003 | 0.001 | 0.004 | |
| CSVFile-class | 0.001 | 0.000 | 0.002 | |
| CSVFile | 0.009 | 0.002 | 0.011 | |
| DataPackage-class | 0.015 | 0.004 | 0.019 | |
| DataPackage | 0.007 | 0.002 | 0.009 | |
| HTMLReport | 0.038 | 0.019 | 0.065 | |
| HTMLReportRef-class | 0.001 | 0.001 | 0.002 | |
| Link | 0.016 | 0.001 | 0.016 | |
| ReportHandlers-class | 0.001 | 0.001 | 0.002 | |
| finish-methods | 0.001 | 0.001 | 0.001 | |
| makeDESeqDF | 0.000 | 0.000 | 0.001 | |
| mockRnaSeqData | 0.031 | 0.002 | 0.034 | |
| publish-methods | 0.001 | 0.001 | 0.002 | |
| reporting.theme | 0.027 | 0.001 | 0.028 | |
| reporting.theme.alternate | 0.035 | 0.001 | 0.036 | |
| validConnection | 0.144 | 0.025 | 0.169 | |