BioC 3.4: CHECK report for DASiR on zin1

Package: DASiR

Version: 1.11.2

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings DASiR_1.11.2.tar.gz

StartedAt: 2016-05-01 21:03:53 -0700 (Sun, 01 May 2016)

EndedAt: 2016-05-01 21:05:31 -0700 (Sun, 01 May 2016)

EllapsedTime: 98.1 seconds

RetCode: 1

Status:  ERROR

CheckDir: DASiR.Rcheck

Warnings: NA

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings DASiR_1.11.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/DASiR.Rcheck’
* using R version 3.3.0 RC (2016-04-28 r70561)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DASiR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DASiR’ version ‘1.11.2’
* 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 ‘DASiR’ can be installed ... [6s/7s] WARNING
Found the following significant warnings:
  Warning: Package 'DASiR' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.4-bioc/meat/DASiR.Rcheck/00install.out’ for details.
* 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 loading without being on the library search path ... 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
getDasStructure: no visible global function definition for
  ‘download.file’
plotFeatures: no visible binding for global variable ‘plot.default’
plotFeatures: no visible global function definition for ‘dev.cur’
plotFeatures: no visible global function definition for ‘rainbow’
plotFeatures: no visible global function definition for ‘rect’
plotFeatures: no visible global function definition for ‘text’
Undefined global functions or variables:
  dev.cur download.file plot.default rainbow rect text
Consider adding
  importFrom("grDevices", "dev.cur", "rainbow")
  importFrom("graphics", "plot.default", "rect", "text")
  importFrom("utils", "download.file")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘DASiR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DASiR-package
> ### Title: Distributed Annotation System in R
> ### Aliases: DASiR-package DASiR
> ### Keywords: package
> 
> ### ** Examples
> 
>     setDasServer(server="http://www.ensembl.org/das")
DAS server for this session is: http://www.ensembl.org/das
>     print(getDasServer())
[1] "http://www.ensembl.org/das"
> 
>     # See the sources (supported organisms)
>     sources <- getDasSource()
Querying url: http://www.ensembl.org/das/sources
Error: could not find function "xmlStructuredStop"...
>     head(sources)
NULL
> 
>     dsn_sources <- getDasDsn()
Querying url: http://www.ensembl.org/das/dsn
failed to load external entity "http://www.ensembl.org/das/dsn"
Error: 1: failed to load external entity "http://www.ensembl.org/das/dsn"
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 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/DASiR.Rcheck/00check.log’
for details.

* installing *source* package ‘DASiR’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: Package 'DASiR' is deprecated and will be removed from Bioconductor
  version 3.3
* DONE (DASiR)

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