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BioC 3.5: CHECK report for pcaExplorer on malbec2

This page was generated on 2017-08-16 13:17:31 -0400 (Wed, 16 Aug 2017).

Package 959/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pcaExplorer 2.2.0
Federico Marini
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/pcaExplorer
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ ERROR ]
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 

Summary

Package: pcaExplorer
Version: 2.2.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings pcaExplorer_2.2.0.tar.gz
StartedAt: 2017-08-16 01:11:22 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:16:06 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 283.5 seconds
RetCode: 1
Status:  ERROR 
CheckDir: pcaExplorer.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings pcaExplorer_2.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/pcaExplorer.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pcaExplorer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pcaExplorer’ version ‘2.2.0’
* 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 ‘pcaExplorer’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
* 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
pcaExplorer: no visible binding for '<<-' assignment to
  ‘pcaexplorer_env’
pcaExplorer : <anonymous>: no visible binding for global variable
  ‘airway’
pcaExplorer : <anonymous>: no visible binding for global variable
  ‘pcaexplorer_env’
Undefined global functions or variables:
  airway pcaexplorer_env
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘pcaExplorer-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pcaplot3d
> ### Title: Sample PCA plot for transformed data
> ### Aliases: pcaplot3d
> 
> ### ** Examples
> 
> dds <- makeExampleDESeqDataSet_multifac(betaSD_condition = 3,betaSD_tissue = 1)
> rlt <- DESeq2::rlogTransformation(dds)
> pcaplot3d(rlt, ntop=200)
Error in scatterplot3js(d[, 1:3], color = cols, renderer = "canvas", size = 1.3,  : 
  (list) object cannot be coerced to type 'double'
Calls: pcaplot3d -> scatterplot3js
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/pcaExplorer.Rcheck/00check.log’
for details.

pcaExplorer.Rcheck/00install.out:

* installing *source* package ‘pcaExplorer’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (pcaExplorer)

pcaExplorer.Rcheck/pcaExplorer-Ex.timings:

nameusersystemelapsed
correlatePCs2.6960.0482.759
distro_expr3.6080.0043.611
geneprofiler1.7200.0001.722
genespca3.3520.0043.361
get_annotation3.9120.0243.970
get_annotation_orgdb2.2560.0122.270
hi_loadings1.6800.0001.681
limmaquickpca2go1.6720.0321.703
makeExampleDESeqDataSet_multifac0.1000.0000.098
pair_corr1.7400.0201.763
pca2go1.9480.0001.953
pcaExplorer2.0920.0042.097
pcaplot2.4840.0002.491