BioC 3.2: CHECK report for KEGGprofile on oaxaca

Package: KEGGprofile

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings KEGGprofile_1.12.0.tar.gz

StartedAt: 2016-04-23 01:32:14 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 01:38:30 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 376.6 seconds

RetCode: 1

Status:  ERROR

CheckDir: KEGGprofile.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 KEGGprofile_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/KEGGprofile.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘KEGGprofile/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘KEGGprofile’ version ‘1.12.0’
* 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 ‘KEGGprofile’ can be installed ... [10s/11s] 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 ... OK
* 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 ... ERROR
Running examples in ‘KEGGprofile-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_pathway
> ### Title: plot_pathway
> ### Aliases: plot_pathway
> 
> ### ** Examples
> 
> data(pro_pho_expr)
> data(pho_sites_count)
> #type='lines'
> col<-col_by_value(pho_sites_count,col=colorRampPalette(c('white','khaki2'))(4),breaks=c(0,1,4,10,Inf))
> temp<-plot_pathway(pro_pho_expr,bg_col=col,line_col=c("brown1","seagreen3"),groups=c(rep("Proteome ",6),rep("Phosphoproteome ",6)),magnify=1.2,species='hsa',database_dir=system.file("extdata",package="KEGGprofile"),pathway_id="04110",max_dist=5)
[1] "Downloading files: 1/1"
trying URL 'http://www.genome.jp/kegg-bin/download?entry=hsa04110&format=kgml'
Content type 'text/xml' length unknown
.......... .......... .......... .......... 
downloaded 40 KB

trying URL 'http://www.genome.jp/kegg/pathway/hsa/hsa04110.png'
Content type 'image/png' length 32599 bytes (31 KB)
==================================================
downloaded 31 KB

trying URL 'http://www.genome.jp/kegg/pathway/map/map04110.png'
Content type 'image/png' length 30938 bytes (30 KB)
==================================================
downloaded 30 KB

attributes construct error
Couldn't find end of Start Tag subtype line 789
Premature end of data in tag relation line 788
Premature end of data in tag pathway line 4
Error: 1: attributes construct error
2: Couldn't find end of Start Tag subtype line 789
3: Premature end of data in tag relation line 788
4: Premature end of data in tag pathway line 4
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
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/KEGGprofile.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
col_by_value	0.030	0.002	0.033
convertId	0.566	0.011	19.659
download_KEGGfile	0.003	0.005	23.785
download_latest_pathway	0.001	0.000	0.000
find_enriched_pathway	2.784	0.072	2.935
newIdMatrix	0.002	0.000	0.003
parse_XMLfile	0.078	0.001	0.079