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BioC 3.6: CHECK report for KEGGprofile on tokay1

This page was generated on 2017-08-16 13:30:36 -0400 (Wed, 16 Aug 2017).

Package 714/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
KEGGprofile 1.19.1
Shilin Zhao
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/KEGGprofile
Last Changed Rev: 131943 / Revision: 131943
Last Changed Date: 2017-08-15 17:15:44 -0400 (Tue, 15 Aug 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  ERROR 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  ERROR  OK 

Summary

Package: KEGGprofile
Version: 1.19.1
Command: rm -rf KEGGprofile.buildbin-libdir KEGGprofile.Rcheck && mkdir KEGGprofile.buildbin-libdir KEGGprofile.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=KEGGprofile.buildbin-libdir KEGGprofile_1.19.1.tar.gz >KEGGprofile.Rcheck\00install.out 2>&1 && cp KEGGprofile.Rcheck\00install.out KEGGprofile-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=KEGGprofile.buildbin-libdir --install="check:KEGGprofile-install.out" --force-multiarch --no-vignettes --timings KEGGprofile_1.19.1.tar.gz
StartedAt: 2017-08-16 00:27:02 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:29:49 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 167.5 seconds
RetCode: 1
Status:  ERROR  
CheckDir: KEGGprofile.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf KEGGprofile.buildbin-libdir KEGGprofile.Rcheck && mkdir KEGGprofile.buildbin-libdir KEGGprofile.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=KEGGprofile.buildbin-libdir KEGGprofile_1.19.1.tar.gz >KEGGprofile.Rcheck\00install.out 2>&1 && cp KEGGprofile.Rcheck\00install.out KEGGprofile-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=KEGGprofile.buildbin-libdir --install="check:KEGGprofile-install.out" --force-multiarch --no-vignettes --timings KEGGprofile_1.19.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/KEGGprofile.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'KEGGprofile/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'KEGGprofile' version '1.19.1'
* 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 whether package 'KEGGprofile' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
col_by_value: no visible global function definition for 'image'
col_by_value: no visible global function definition for 'box'
col_by_value: no visible global function definition for 'par'
col_by_value: no visible global function definition for 'axis'
convertId: no visible global function definition for 'flush.console'
download_KEGGfile: no visible global function definition for
  'download.file'
find_enriched_pathway: no visible global function definition for
  'phyper'
find_enriched_pathway: no visible global function definition for
  'p.adjust'
newIdMatrix: no visible binding for global variable 'var'
pieGlyph2: no visible global function definition for 'par'
pieGlyph2: no visible global function definition for 'polygon'
pieGlyph2: no visible global function definition for 'text'
plot_pathway_cor : <anonymous>: no visible global function definition
  for 'sd'
plot_pathway_cor : <anonymous>: no visible global function definition
  for 'cor'
plot_pathway_cor : <anonymous> : <anonymous>: no visible global
  function definition for 'cor'
plot_pathway_cor : <anonymous>: no visible global function definition
  for 'median'
plot_pathway_cor: no visible global function definition for
  'wilcox.test'
plot_pathway_cor: no visible global function definition for 'par'
plot_pathway_cor: no visible global function definition for 'boxplot'
plot_pathway_cor: no visible global function definition for 'abline'
plot_polygon: no visible global function definition for 'polygon'
plot_profile: no visible global function definition for 'rainbow'
plot_profile: no visible global function definition for 'png'
plot_profile: no visible global function definition for 'par'
plot_profile: no visible global function definition for 'plot'
plot_profile: no visible global function definition for 'rasterImage'
plot_profile: no visible binding for global variable 'var'
plot_profile: no visible global function definition for 'matplot'
plot_profile: no visible global function definition for 'text'
plot_profile: no visible global function definition for 'legend'
plot_profile: no visible global function definition for 'polygon'
plot_profile: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  abline axis box boxplot cor dev.off download.file flush.console image
  legend matplot median p.adjust par phyper plot png polygon rainbow
  rasterImage sd text var wilcox.test
Consider adding
  importFrom("grDevices", "dev.off", "png", "rainbow")
  importFrom("graphics", "abline", "axis", "box", "boxplot", "image",
             "legend", "matplot", "par", "plot", "polygon",
             "rasterImage", "text")
  importFrom("stats", "cor", "median", "p.adjust", "phyper", "sd", "var",
             "wilcox.test")
  importFrom("utils", "download.file", "flush.console")
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 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 ...
** running examples for arch 'i386' ... 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/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

[1] "The figure was generated in hsa04110_profile_lines.png"
> #type='bg'
> pho_expr<-pro_pho_expr[,7:12]
> temp<-apply(pho_expr,1,function(x) length(which(is.na(x))))
> pho_expr<-pho_expr[which(temp==0),]
> col<-col_by_value(pho_expr,col=colorRampPalette(c('green','black','red'))(1024),range=c(-6,6))
> temp<-plot_pathway(pho_expr,type="bg",bg_col=col,text_col="white",magnify=1.2,species='hsa',database_dir=system.file("extdata",package="KEGGprofile"),pathway_id="04110")
[1] "The figure was generated in hsa04110_profile_bg.png"
> #Compound and gene data
> set.seed(124)
> testData1<-rbind(rnorm(6),rnorm(6),rnorm(6),rnorm(6),rnorm(6),rnorm(6),rnorm(6),rnorm(6))
> row.names(testData1)<-c("4967","55753","1743","8802","47","50","cpd:C15972","cpd:C16255")
> colnames(testData1)<-c("Control0","Control2","Control5","Sample0","Sample2","Sample5")
> temp<-plot_pathway(testData1,type="lines",line_col=c("brown1","seagreen3"),groups=c(rep("Control",3),rep("Sample",3)),magnify=1.2,species='hsa',database_dir=system.file("extdata",package="KEGGprofile"),pathway_id="00020",max_dist=2)
[1] "Downloading files: 1/1"
trying URL 'http://www.genome.jp/kegg/pathway/hsa/hsa00020.png'
Content type 'image/png' length 25459 bytes (24 KB)
==================================================
downloaded 24 KB

trying URL 'http://www.genome.jp/kegg/pathway/map/map00020.png'
Content type 'image/png' length 24592 bytes (24 KB)
==================================================
downloaded 24 KB

Error: XML content does not seem to be XML: 'C:/Users/biocbuild/bbs-3.6-bioc/meat/KEGGprofile.buildbin-libdir/KEGGprofile/extdata/hsa00020.xml'
Execution halted
** running examples for arch 'x64' ... 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] "The figure was generated in hsa04110_profile_lines.png"
> #type='bg'
> pho_expr<-pro_pho_expr[,7:12]
> temp<-apply(pho_expr,1,function(x) length(which(is.na(x))))
> pho_expr<-pho_expr[which(temp==0),]
> col<-col_by_value(pho_expr,col=colorRampPalette(c('green','black','red'))(1024),range=c(-6,6))
> temp<-plot_pathway(pho_expr,type="bg",bg_col=col,text_col="white",magnify=1.2,species='hsa',database_dir=system.file("extdata",package="KEGGprofile"),pathway_id="04110")
[1] "The figure was generated in hsa04110_profile_bg.png"
> #Compound and gene data
> set.seed(124)
> testData1<-rbind(rnorm(6),rnorm(6),rnorm(6),rnorm(6),rnorm(6),rnorm(6),rnorm(6),rnorm(6))
> row.names(testData1)<-c("4967","55753","1743","8802","47","50","cpd:C15972","cpd:C16255")
> colnames(testData1)<-c("Control0","Control2","Control5","Sample0","Sample2","Sample5")
> temp<-plot_pathway(testData1,type="lines",line_col=c("brown1","seagreen3"),groups=c(rep("Control",3),rep("Sample",3)),magnify=1.2,species='hsa',database_dir=system.file("extdata",package="KEGGprofile"),pathway_id="00020",max_dist=2)
[1] "Downloading files: 1/1"
trying URL 'http://www.genome.jp/kegg/pathway/hsa/hsa00020.png'
Content type 'image/png' length 25459 bytes (24 KB)
==================================================
downloaded 24 KB

trying URL 'http://www.genome.jp/kegg/pathway/map/map00020.png'
Content type 'image/png' length 24592 bytes (24 KB)
==================================================
downloaded 24 KB

Error: XML content does not seem to be XML: 'C:/Users/biocbuild/bbs-3.6-bioc/meat/KEGGprofile.buildbin-libdir/KEGGprofile/extdata/hsa00020.xml'
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: 2 ERRORs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/KEGGprofile.Rcheck/00check.log'
for details.

KEGGprofile.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'KEGGprofile' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'KEGGprofile' as KEGGprofile_1.19.1.zip
* DONE (KEGGprofile)

KEGGprofile.Rcheck/examples_i386/KEGGprofile-Ex.timings:

nameusersystemelapsed
col_by_value0.010.000.01
convertId0.520.083.64
download_KEGGfile0.020.014.00
download_latest_pathway0.020.000.01
find_enriched_pathway3.890.053.99
newIdMatrix0.040.000.05
parse_XMLfile0.130.000.12

KEGGprofile.Rcheck/examples_x64/KEGGprofile-Ex.timings:

nameusersystemelapsed
col_by_value0.010.000.01
convertId0.410.042.97
download_KEGGfile0.000.013.89
download_latest_pathway000
find_enriched_pathway2.870.032.91
newIdMatrix0.020.000.02
parse_XMLfile0.180.010.20