Back to Multiple platform build/check report for BioC 3.8
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

CHECK report for SVM2CRM on malbec1

This page was generated on 2019-04-16 11:51:14 -0400 (Tue, 16 Apr 2019).

Package 1531/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SVM2CRM 1.14.0
Guidantonio Malagoli Tagliazucchi
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/SVM2CRM
Branch: RELEASE_3_8
Last Commit: e1e185a
Last Changed Date: 2018-10-30 11:41:57 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ ERROR ]
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: SVM2CRM
Version: 1.14.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:SVM2CRM.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings SVM2CRM_1.14.0.tar.gz
StartedAt: 2019-04-16 03:20:17 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 03:24:04 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 227.2 seconds
RetCode: 1
Status:  ERROR 
CheckDir: SVM2CRM.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:SVM2CRM.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings SVM2CRM_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/SVM2CRM.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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 ‘1.14.0’
* 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 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 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: createBed
> ### Title: Create bed file of predictions using svm.
> ### Aliases: createBed createBed
> ### Keywords: create bed, save output, results
> 
> ### ** 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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, 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,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

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"
[1] "H3K4me1.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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/SVM2CRM.Rcheck/00check.log’
for details.


Installation output

SVM2CRM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL SVM2CRM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘SVM2CRM’ ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SVM2CRM)

Tests output


Example timings

SVM2CRM.Rcheck/SVM2CRM-Ex.timings

nameusersystemelapsed
cisREfindbed0.160.000.16