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BioC 3.4: CHECK report for SVM2CRM on morelia

This page was generated on 2017-04-15 16:26:27 -0400 (Sat, 15 Apr 2017).

Package 1215/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SVM2CRM 1.6.0
Guidantonio Malagoli Tagliazucchi
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/SVM2CRM
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  ERROR  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ ERROR ] OK 

Summary

Package: SVM2CRM
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SVM2CRM_1.6.0.tar.gz
StartedAt: 2017-04-15 08:43:09 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 08:49:06 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 356.9 seconds
RetCode: 1
Status:  ERROR 
CheckDir: SVM2CRM.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SVM2CRM_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/SVM2CRM.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SVM2CRM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SVM2CRM’ version ‘1.6.0’
* 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 ‘SVM2CRM’ 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 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
cisREfindbed: no visible global function definition for ‘as’
createBed: no visible global function definition for ‘write.table’
featSelectionWithKmeans: no visible global function definition for
  ‘kmeans’
featSelectionWithKmeans: no visible global function definition for
  ‘dist’
featSelectionWithKmeans: no visible global function definition for
  ‘hclust’
featSelectionWithKmeans: no visible global function definition for
  ‘pdf’
featSelectionWithKmeans: no visible global function definition for
  ‘par’
featSelectionWithKmeans: no visible global function definition for
  ‘axis’
featSelectionWithKmeans: no visible global function definition for
  ‘abline’
featSelectionWithKmeans: no visible global function definition for
  ‘dev.off’
getSignal: no visible global function definition for ‘read.table’
getSignal: no visible global function definition for ‘as’
plotROC: no visible global function definition for ‘predict’
plotROC: no visible global function definition for ‘pdf’
plotROC: no visible global function definition for ‘dev.off’
predictionGW: no visible global function definition for ‘predict’
smoothInputFS: no visible global function definition for ‘na.omit’
tuningParametersCombROC: no visible global function definition for
  ‘combn’
tuningParametersCombROC: no visible global function definition for
  ‘txtProgressBar’
tuningParametersCombROC: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  abline as axis combn dev.off dist hclust kmeans na.omit par pdf
  predict read.table setTxtProgressBar txtProgressBar write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "axis", "par")
  importFrom("methods", "as")
  importFrom("stats", "dist", "hclust", "kmeans", "na.omit", "predict")
  importFrom("utils", "combn", "read.table", "setTxtProgressBar",
             "txtProgressBar", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ‘SVM2CRM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: perfomanceSVM
> ### Title: Estimate the performance of prediction.
> ### Aliases: performanceSVM performanceSVM
> ### Keywords: perfomanceSVM
> 
> ### ** Examples
> 
> 
>     library("GenomicRanges")
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
>     library("SVM2CRMdata")
> 
>     setwd(system.file("data",package="SVM2CRMdata"))
>     load("CD4_matrixInputSVMbin100window1000.rda")
>     completeTABLE<-CD4_matrixInputSVMbin100window1000
> 
>     new.strings<-gsub(x=colnames(completeTABLE[,c(6:ncol(completeTABLE))]),pattern="CD4.",replacement="")
>     new.strings<-gsub(new.strings,pattern=".norm.w100.bed",replacement="")
>     colnames(completeTABLE)[c(6:ncol(completeTABLE))]<-new.strings
> 
>     #list_file<-grep(dir(),pattern=".sort.txt",value=TRUE)
> 
>     #train_positive<-getSignal(list_file,chr="chr1",reference="p300.distal.fromTSS.txt",win.size=500,bin.size=100,label1="enhancers")
>     #train_negative<-getSignal(list_file,chr="chr1",reference="random.region.hg18.nop300.txt",win.size=500,bin.size=100,label1="not_enhancers")
>     setwd(system.file("data",package="SVM2CRMdata"))
>     load("train_positive.rda")
>     load("train_negative.rda")
> 
>     training_set<-rbind(train_positive,train_negative)
>     #the colnames of the training set should be the same of data_enhancer_svm
>     colnames(training_set)[c(5:ncol(training_set))]<-gsub(x=gsub(x=colnames(training_set[,c(5:ncol(training_set))]),pattern="sort.txt.",replacement=""),pattern="CD4.",replacement="")
> 
> 
>     setwd(system.file("extdata", package = "SVM2CRMdata"))
>     data_level2 <- read.table(file = "GSM393946.distal.p300fromTSS.txt",sep = "\t", stringsAsFactors = FALSE)
>     data_level2<-data_level2[data_level2[,1]=="chr1",]
> 
>     DB <- data_level2[, c(1:3)]
>     colnames(DB)<-c("chromosome","start","end")
> 
>     label <- "p300"
> 
>     table.final.overlap<-findFeatureOverlap(query=completeTABLE,subject=DB,select="all")
> 
>     data_enhancer_svm<-createSVMinput(inputpos=table.final.overlap,inputfull=completeTABLE,label1="enhancers",label2="not_enhancers")
>     colnames(data_enhancer_svm)[c(5:ncol(data_enhancer_svm))]<-gsub(gsub(x=colnames(data_enhancer_svm[,c(5:ncol(data_enhancer_svm))]),pattern="CD4.",replacement=""),pattern=".norm.w100.bed",replacement="")
> 
>     listcolnames<-c("H2AK5ac","H2AK9ac","H3K23ac","H3K27ac","H3K27me3","H3K4me1","H3K4me3")
> 
>     dftotann<-smoothInputFS(train_positive[,c(6:ncol(train_positive))],listcolnames,k=20)
[1] "H2AK5ac"
[1] "rename"
[1] "H2AK9ac"
[1] "rename"
[1] "H3K23ac"
[1] "rename"
[1] "H3K27ac"
[1] "rename"
[1] "H3K27me3"
[1] "rename"
[1] "H3K4me1"
[1] "rename"
[1] "H3K4me3"
[1] "rename"
> 
> 
>     results<-featSelectionWithKmeans(dftotann,5)
[1] "H2AK5ac_1"
[1] "H2AK9ac_1"
[1] "H3K23ac_1"
[1] "H3K27ac_1"
[1] "H3K27me3_1"
[1] "H3K4me1_1"
[1] "H3K4me3_1"
[1] "H2AK5ac_1"
[1] "H2AK9ac_1"
[1] "H3K23ac_1"
[1] "H3K27ac_1"
[1] "H3K27me3_1"
[1] "H3K4me1_1"
[1] "H3K4me3_1"
> 
>     resultsFS<-results[[7]]
> 
>     resultsFSfilter<-resultsFS[which(resultsFS[,2]>median(resultsFS[,2])),]
> 
>     resultsFSfilterICRR<-resultsFSfilter[which(resultsFSfilter[,3]<0.50),]
> 
>     listHM<-resultsFSfilterICRR[,1]
>     listHM<-gsub(gsub(listHM,pattern="_.",replacement=""),pattern="CD4.",replacement="")
> 
>     selectFeature<-grep(x=colnames(training_set[,c(6:ncol(training_set))]),pattern=paste(listHM,collapse="|"),value=TRUE)
> 
>     colSelect<-c("chromosome","start","end","label",selectFeature)
>     training_set<-training_set[,colSelect]
> 
>     vecS <- c(2:length(listHM))
>     typeSVM <- c(0, 6, 7)[1]
>     costV <- c(0.001, 0.01, 0.1, 1, 10, 100, 1000)[6]
>     wlabel <- c("not_enhancer", "enhancer")
>     infofile<-data.frame(a=c(paste(listHM,"signal",sep=".")))
>     infofile[,1]<-gsub(gsub(x=infofile[,1],pattern="CD4.",replacement=""),pattern=".sort.bed",replacement="")
> 
>     tuningTAB <- tuningParametersCombROC(training_set = training_set, typeSVM = typeSVM, costV = costV,different.weight="TRUE", vecS = vecS[1],pcClass=100,ncClass=400,infofile)
[1] "last comparison"
[1] 3 2
[1] 3 2
[1] "k-fold-validation in all combination"
[1] "H3K27ac.signal" "H3K4me1.signal"
[1] "H3K27ac.signal" "H3K4me3.signal"
Error in wilcox.test.default(pred[obs == 1], pred[obs == 0], alternative = "great") : 
  not enough (finite) 'x' observations
Calls: tuningParametersCombROC ... plotROC -> roc.area -> wilcox.test -> wilcox.test.default
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-3.4-bioc/meat/SVM2CRM.Rcheck/00check.log’
for details.

SVM2CRM.Rcheck/00install.out:

* installing *source* package ‘SVM2CRM’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SVM2CRM)

SVM2CRM.Rcheck/SVM2CRM-Ex.timings:

nameusersystemelapsed
cisREfindbed0.1060.0030.110