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 | |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings KEGGprofile_1.19.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/KEGGprofile.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.19.1’
* 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 for sufficient/correct file permissions ... 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
* 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 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/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: '/Users/biocbuild/bbs-3.6-bioc/meat/KEGGprofile.Rcheck/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: 1 ERROR, 1 NOTE
See
‘/Users/biocbuild/bbs-3.6-bioc/meat/KEGGprofile.Rcheck/00check.log’
for details.