BioC 3.5: CHECK report for ReportingTools on oaxaca

Package: ReportingTools

Version: 2.15.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ReportingTools_2.15.1.tar.gz

StartedAt: 2017-03-04 08:01:46 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 08:14:00 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 734.4 seconds

RetCode: 1

Status:  ERROR

CheckDir: ReportingTools.Rcheck

Warnings: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ReportingTools_2.15.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ReportingTools.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘2.15.1’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  Test files with failing tests
  
     test_DESeqDataSet.R 
       test_2coefs 
  
     test_DESeqResults.R 
       test_1dataframe 
       test_2objectToHTML 
       test_4publish 
       test_5modifyDF 
  
  
  Error in BiocGenerics:::testPackage("ReportingTools") : 
    unit tests failed for package ReportingTools
  Execution halted
* 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 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/ReportingTools.Rcheck/00check.log’
for details.

R Under development (unstable) (2017-02-15 r72177) -- "Unsuffered Consequences"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, 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
matrixStats v0.51.0 (2016-10-08) successfully loaded. See ?matrixStats for help.

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

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

    colMaxs, rowMaxs

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

    apply


Attaching package: 'SummarizedExperiment'

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

    rowRanges

estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
Timing stopped at: 0.234 0.001 0.235
Error : subscript contains invalid names
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
Timing stopped at: 0.005 0 0.005
Error in .local(object, ...) : No features meet selection criteria.
Try changing the log-fold change or p-value cutoff.
Timing stopped at: 0.007 0 0.007
Error in .local(object, ...) : No features meet selection criteria.
Try changing the log-fold change or p-value cutoff.
Timing stopped at: 0.029 0.003 0.032
Error in .local(object, ...) : No features meet selection criteria.
Try changing the log-fold change or p-value cutoff.
Timing stopped at: 0.018 0.002 0.021
Error in .local(object, ...) : No features meet selection criteria.
Try changing the log-fold change or p-value cutoff.
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: /Users/biocbuild/bbs-3.5-bioc/meat/ReportingTools.Rcheck/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 -- Sat Mar  4 08:13:57 2017 
*********************************************** 
Number of test functions: 45 
Number of errors: 5 
Number of failures: 0 

 
1 Test Suite : 
ReportingTools RUnit Tests - 45 test functions, 5 errors, 0 failures
ERROR in test_2coefs: Error : subscript contains invalid names
ERROR in test_1dataframe: Error in .local(object, ...) : No features meet selection criteria.
Try changing the log-fold change or p-value cutoff.
ERROR in test_2objectToHTML: Error in .local(object, ...) : No features meet selection criteria.
Try changing the log-fold change or p-value cutoff.
ERROR in test_4publish: Error in .local(object, ...) : No features meet selection criteria.
Try changing the log-fold change or p-value cutoff.
ERROR in test_5modifyDF: Error in .local(object, ...) : No features meet selection criteria.
Try changing the log-fold change or p-value cutoff.

Test files with failing tests

   test_DESeqDataSet.R 
     test_2coefs 

   test_DESeqResults.R 
     test_1dataframe 
     test_2objectToHTML 
     test_4publish 
     test_5modifyDF 


Error in BiocGenerics:::testPackage("ReportingTools") : 
  unit tests failed for package ReportingTools
Execution halted

* 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)

name	user	system	elapsed
BaseReportType-class	0.001	0.000	0.002
CSVFile-class	0.001	0.000	0.001
CSVFile	0.005	0.000	0.005
DataPackage-class	0.054	0.001	0.204
DataPackage	0.003	0.000	0.011
HTMLReport	0.117	0.011	1.615
HTMLReportRef-class	0.000	0.001	0.001
Link	0.171	0.000	0.172
ReportHandlers-class	0.001	0.001	0.002
finish-methods	0.001	0.000	0.001
makeDESeqDF	0.001	0.000	0.000
mockRnaSeqData	0.018	0.001	0.019
publish-methods	0.001	0.000	0.002
reporting.theme	0.023	0.001	0.053
reporting.theme.alternate	0.027	0.001	0.027
validConnection	0.786	0.014	0.915