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CHECK report for SVM2CRM on tokay2

This page was generated on 2018-10-17 08:40:20 -0400 (Wed, 17 Oct 2018).

Package 1452/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SVM2CRM 1.12.0
Guidantonio Malagoli Tagliazucchi
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/SVM2CRM
Branch: RELEASE_3_7
Last Commit: 45c3362
Last Changed Date: 2018-04-30 10:35:36 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: SVM2CRM
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SVM2CRM.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings SVM2CRM_1.12.0.tar.gz
StartedAt: 2018-10-17 05:07:00 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 05:16:29 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 569.3 seconds
RetCode: 1
Status:  ERROR  
CheckDir: SVM2CRM.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SVM2CRM.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings SVM2CRM_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/SVM2CRM.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SVM2CRM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SVM2CRM' 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 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
* 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
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 ...
** running examples for arch 'i386' ... 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

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

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
** running examples for arch 'x64' ... WARNING
Found the following significant warnings:
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/SVM2CRMdata/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/SVM2CRMdata/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/SVM2CRMdata/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/SVM2CRMdata/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/SVM2CRMdata/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/SVM2CRMdata/data', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/SVM2CRMdata/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/SVM2CRMdata/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/SVM2CRMdata/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/SVM2CRMdata/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/SVM2CRMdata/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/SVM2CRMdata/extdata', resetting
* 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 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/SVM2CRM.Rcheck/00check.log'
for details.


Installation output

SVM2CRM.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/SVM2CRM_1.12.0.tar.gz && rm -rf SVM2CRM.buildbin-libdir && mkdir SVM2CRM.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SVM2CRM.buildbin-libdir SVM2CRM_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL SVM2CRM_1.12.0.zip && rm SVM2CRM_1.12.0.tar.gz SVM2CRM_1.12.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 30564  100 30564    0     0   415k      0 --:--:-- --:--:-- --:--:--  466k

install for i386

* installing *source* package 'SVM2CRM' ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SVM2CRM'
    finding HTML links ... done
    cisREfindbed                            html  
    createBed                               html  
    createSVMinput                          html  
    featSelectionWithKmeans                 html  
    findFeatureOverlap                      html  
    frequencyHM                             html  
    getSignal                               html  
    performanceSVM                          html  
    plotFscore                              html  
    plotROC                                 html  
    predictionGW                            html  
    smoothInputFS                           html  
    tuningParametersCombROC                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'SVM2CRM' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SVM2CRM' as SVM2CRM_1.12.0.zip
* DONE (SVM2CRM)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'SVM2CRM' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

SVM2CRM.Rcheck/examples_i386/SVM2CRM-Ex.timings

nameusersystemelapsed
cisREfindbed0.130.020.14

SVM2CRM.Rcheck/examples_x64/SVM2CRM-Ex.timings

nameusersystemelapsed
cisREfindbed0.060.030.09