ReportingTools 2.11.0
Jason A. Hackney , Gabriel Becker , Jessica L. Larson
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ReportingTools | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings ReportingTools_2.11.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/ReportingTools.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘2.11.0’
* 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 ... [32s/32s] 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’
.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’
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 description div exprs fData featureNames h1 htmlRep mcols 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [14s/14s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [137s/147s]
[137s/147s] 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-3.3-bioc/meat/ReportingTools.Rcheck/00check.log’
for details.
* installing *source* package ‘ReportingTools’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘objectToHTML’ with signature ‘object="ggbio"’: no definition for class “ggbio”
Note: no visible binding for '<<-' assignment to '.reportDirectory'
Note: no visible binding for '<<-' assignment to '.reportDirectory'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ReportingTools)