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CHECK report for RJMCMCNucleosomes on tokay1

This page was generated on 2018-04-12 13:29:12 -0400 (Thu, 12 Apr 2018).

Package 1185/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RJMCMCNucleosomes 1.2.0
Astrid Deschênes
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/RJMCMCNucleosomes
Branch: RELEASE_3_6
Last Commit: b8f3e35
Last Changed Date: 2017-10-30 12:41:24 -0400 (Mon, 30 Oct 2017)
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 [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RJMCMCNucleosomes
Version: 1.2.0
Command: rm -rf RJMCMCNucleosomes.buildbin-libdir RJMCMCNucleosomes.Rcheck && mkdir RJMCMCNucleosomes.buildbin-libdir RJMCMCNucleosomes.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RJMCMCNucleosomes.buildbin-libdir RJMCMCNucleosomes_1.2.0.tar.gz >RJMCMCNucleosomes.Rcheck\00install.out 2>&1 && cp RJMCMCNucleosomes.Rcheck\00install.out RJMCMCNucleosomes-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=RJMCMCNucleosomes.buildbin-libdir --install="check:RJMCMCNucleosomes-install.out" --force-multiarch --no-vignettes --timings RJMCMCNucleosomes_1.2.0.tar.gz
StartedAt: 2018-04-12 02:43:09 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 02:50:09 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 419.7 seconds
RetCode: 0
Status:  OK  
CheckDir: RJMCMCNucleosomes.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf RJMCMCNucleosomes.buildbin-libdir RJMCMCNucleosomes.Rcheck && mkdir RJMCMCNucleosomes.buildbin-libdir RJMCMCNucleosomes.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RJMCMCNucleosomes.buildbin-libdir RJMCMCNucleosomes_1.2.0.tar.gz >RJMCMCNucleosomes.Rcheck\00install.out 2>&1 && cp RJMCMCNucleosomes.Rcheck\00install.out RJMCMCNucleosomes-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=RJMCMCNucleosomes.buildbin-libdir --install="check:RJMCMCNucleosomes-install.out" --force-multiarch --no-vignettes --timings RJMCMCNucleosomes_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/RJMCMCNucleosomes.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RJMCMCNucleosomes/DESCRIPTION' ... OK
* this is package 'RJMCMCNucleosomes' version '1.2.0'
* package encoding: UTF-8
* 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 'RJMCMCNucleosomes' 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
** checking loading without being on the library search path ... 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 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 ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/RJMCMCNucleosomes.buildbin-libdir/RJMCMCNucleosomes/libs/i386/RJMCMCNucleosomes.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/RJMCMCNucleosomes.Rcheck/00check.log'
for details.

Installation output

RJMCMCNucleosomes.Rcheck/00install.out


install for i386

* installing *source* package 'RJMCMCNucleosomes' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I/i386/include -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c NucleoDirichlet.cpp -o NucleoDirichlet.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I/i386/include -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c NucleoDirichletPA.cpp -o NucleoDirichletPA.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I/i386/include -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c Nucleosome.cpp -o Nucleosome.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I/i386/include -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c RJMCMCNucleosomes_init.c -o RJMCMCNucleosomes_init.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I/i386/include -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I/i386/include -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c SegmentSeq.cpp -o SegmentSeq.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I/i386/include -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c rjmcmcNucleo.cpp -o rjmcmcNucleo.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o RJMCMCNucleosomes.dll tmp.def NucleoDirichlet.o NucleoDirichletPA.o Nucleosome.o RJMCMCNucleosomes_init.o RcppExports.o SegmentSeq.o rjmcmcNucleo.o -L/i386/lib -lgsl -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/RJMCMCNucleosomes.buildbin-libdir/RJMCMCNucleosomes/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'RJMCMCNucleosomes'
    finding HTML links ... done
    RJMCMCNucleosomes-package               html  
    RJMCMC_result                           html  
    mergeAllRDSFiles                        html  
    mergeAllRDSFilesFromDirectory           html  
    mergeRDSFiles                           html  
    plotNucleosomes                         html  
    postMerge                               html  
    postTreatment                           html  
    print.rjmcmcNucleosomes                 html  
    print.rjmcmcNucleosomesBeforeAndAfterPostTreatment
                                            html  
    print.rjmcmcNucleosomesMerge            html  
    reads_demo_01                           html  
    reads_demo_02                           html  
    rjmcmc                                  html  
    rjmcmcCHR                               html  
    rjmcmcNucleo                            html  
    runCHR                                  html  
    segmentation                            html  
    syntheticNucleosomeReads                html  
    validateDirectoryParameters             html  
    validatePlotNucleosomesParameters       html  
    validatePrepMergeParameters             html  
    validateRDSFilesParameters              html  
    validateRJMCMCParameters                html  
    validateSegmentationParameters          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'RJMCMCNucleosomes' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I/x64/include -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c NucleoDirichlet.cpp -o NucleoDirichlet.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I/x64/include -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c NucleoDirichletPA.cpp -o NucleoDirichletPA.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I/x64/include -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c Nucleosome.cpp -o Nucleosome.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I/x64/include -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c RJMCMCNucleosomes_init.c -o RJMCMCNucleosomes_init.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I/x64/include -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I/x64/include -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c SegmentSeq.cpp -o SegmentSeq.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I/x64/include -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include"   -I"C:/local323/include"     -O2 -Wall  -mtune=generic -c rjmcmcNucleo.cpp -o rjmcmcNucleo.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o RJMCMCNucleosomes.dll tmp.def NucleoDirichlet.o NucleoDirichletPA.o Nucleosome.o RJMCMCNucleosomes_init.o RcppExports.o SegmentSeq.o rjmcmcNucleo.o -L/x64/lib -lgsl -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/RJMCMCNucleosomes.buildbin-libdir/RJMCMCNucleosomes/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RJMCMCNucleosomes' as RJMCMCNucleosomes_1.2.0.zip
* DONE (RJMCMCNucleosomes)
In R CMD INSTALL
In R CMD INSTALL

Tests output

RJMCMCNucleosomes.Rcheck/tests_i386/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> ## Run all tests presnt in the package
> BiocGenerics:::testPackage("RJMCMCNucleosomes")

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, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min


Attaching package: 'S4Vectors'

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

    expand.grid

RJMCMCNucleosomes - Predicted nucleosomes

Call:
rjmcmc(reads = reads_demo_02, seqName = "chr_SYNTHETIC", nbrIterations = 1e+05, 
    kMax = 30, lambda = 2, minInterval = 146, maxInterval = 490, 
    minReads = 3, vSeed = 32)

Number of nucleosomes:
[1] 6

Nucleosomes positions:
GRanges object with 6 ranges and 0 metadata columns:
           seqnames         ranges strand
              <Rle>      <IRanges>  <Rle>
  [1] chr_SYNTHETIC [10072, 10072]      *
  [2] chr_SYNTHETIC [10241, 10241]      *
  [3] chr_SYNTHETIC [10574, 10574]      *
  [4] chr_SYNTHETIC [10656, 10656]      *
  [5] chr_SYNTHETIC [10669, 10669]      *
  [6] chr_SYNTHETIC [10744, 10744]      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
[1] "Doing: out/results/rjmcmc_seg_1.rds"
[1] "Done: out/results/rjmcmc_seg_1.rds"
[1] "Doing: out/results/rjmcmc_seg_2.rds"
[1] "Done: out/results/rjmcmc_seg_2.rds"
[1] "Doing: out/results/rjmcmc_seg_3.rds"
[1] "Done: out/results/rjmcmc_seg_3.rds"
[1] "Doing: out/results/rjmcmc_seg_4.rds"
[1] "Done: out/results/rjmcmc_seg_4.rds"
[1] "Doing: out/results/rjmcmc_seg_5.rds"
[1] "Done: out/results/rjmcmc_seg_5.rds"
[1] "Doing: out/results/rjmcmc_seg_6.rds"
[1] "Done: out/results/rjmcmc_seg_6.rds"
[1] "Doing: out/results/rjmcmc_seg_7.rds"
[1] "Done: out/results/rjmcmc_seg_7.rds"
[1] "Doing: out/results/rjmcmc_seg_8.rds"
[1] "Done: out/results/rjmcmc_seg_8.rds"
[1] "Doing: out/results/rjmcmc_seg_9.rds"
[1] "Done: out/results/rjmcmc_seg_9.rds"
[1] "Doing: out/results/rjmcmc_seg_10.rds"
[1] "Done: out/results/rjmcmc_seg_10.rds"
[1] "Doing: out/results/rjmcmc_seg_11.rds"
[1] "Done: out/results/rjmcmc_seg_11.rds"
[1] "Doing: out/results/rjmcmc_seg_12.rds"
[1] "Done: out/results/rjmcmc_seg_12.rds"
[1] "Doing: out/results/rjmcmc_seg_13.rds"
[1] "Done: out/results/rjmcmc_seg_13.rds"
[1] "Doing: out/results/rjmcmc_seg_14.rds"
[1] "Done: out/results/rjmcmc_seg_14.rds"
[1] "Doing: out/results/rjmcmc_seg_15.rds"
[1] "Done: out/results/rjmcmc_seg_15.rds"
[1] "Doing: out/results/rjmcmc_seg_16.rds"
[1] "Done: out/results/rjmcmc_seg_16.rds"
[1] "Doing: out/results/rjmcmc_seg_17.rds"
[1] "Done: out/results/rjmcmc_seg_17.rds"
[1] "Doing: out/results/rjmcmc_seg_18.rds"
[1] "Done: out/results/rjmcmc_seg_18.rds"
[1] "Doing: out/results/rjmcmc_seg_19.rds"
[1] "Done: out/results/rjmcmc_seg_19.rds"
[1] "Doing: out/results/rjmcmc_seg_20.rds"
[1] "Done: out/results/rjmcmc_seg_20.rds"
[1] "Doing: out/results/rjmcmc_seg_21.rds"
[1] "Done: out/results/rjmcmc_seg_21.rds"
[1] "Doing: out/results/rjmcmc_seg_22.rds"
[1] "Done: out/results/rjmcmc_seg_22.rds"
[1] "Doing: out/results/rjmcmc_seg_23.rds"
[1] "Done: out/results/rjmcmc_seg_23.rds"
[1] "Doing: out/results/rjmcmc_seg_24.rds"
[1] "Done: out/results/rjmcmc_seg_24.rds"
[1] "Doing: out/results/rjmcmc_seg_25.rds"
[1] "Done: out/results/rjmcmc_seg_25.rds"
[1] "Doing: out/results/rjmcmc_seg_26.rds"
[1] "Done: out/results/rjmcmc_seg_26.rds"
[1] "Doing: out/results/rjmcmc_seg_27.rds"
[1] "Done: out/results/rjmcmc_seg_27.rds"
[1] "Doing: out/results/rjmcmc_seg_28.rds"
[1] "Done: out/results/rjmcmc_seg_28.rds"
[1] "Doing: out/results/rjmcmc_seg_29.rds"
[1] "Done: out/results/rjmcmc_seg_29.rds"
[1] "Doing: out/results/rjmcmc_seg_30.rds"
[1] "Done: out/results/rjmcmc_seg_30.rds"
[1] "Doing: out/results/rjmcmc_seg_31.rds"
[1] "Done: out/results/rjmcmc_seg_31.rds"
[1] "Doing: out/results/rjmcmc_seg_32.rds"
[1] "Done: out/results/rjmcmc_seg_32.rds"
[1] "Doing: out/results/rjmcmc_seg_33.rds"
[1] "Done: out/results/rjmcmc_seg_33.rds"
[1] "Doing: out/results/rjmcmc_seg_34.rds"
[1] "Done: out/results/rjmcmc_seg_34.rds"
[1] "Doing: out/results/rjmcmc_seg_35.rds"
[1] "Done: out/results/rjmcmc_seg_35.rds"
[1] "Doing: out/results/rjmcmc_seg_36.rds"
[1] "Done: out/results/rjmcmc_seg_36.rds"
[1] "Doing: out/results/rjmcmc_seg_37.rds"
[1] "Done: out/results/rjmcmc_seg_37.rds"
[1] "Doing: out/results/rjmcmc_seg_38.rds"
[1] "Done: out/results/rjmcmc_seg_38.rds"
[1] "Doing: out/results/rjmcmc_seg_39.rds"
[1] "Done: out/results/rjmcmc_seg_39.rds"
[1] "Doing: out/results/rjmcmc_seg_40.rds"
[1] "Done: out/results/rjmcmc_seg_40.rds"
[1] "Doing: out/results/rjmcmc_seg_41.rds"
[1] "Done: out/results/rjmcmc_seg_41.rds"
[1] "Doing: out/results/rjmcmc_seg_42.rds"
[1] "Done: out/results/rjmcmc_seg_42.rds"
[1] "Doing: out/results/rjmcmc_seg_43.rds"
[1] "Done: out/results/rjmcmc_seg_43.rds"
[1] "Doing: out/results/rjmcmc_seg_44.rds"
[1] "Done: out/results/rjmcmc_seg_44.rds"
[1] "Doing: out/results/rjmcmc_seg_45.rds"
[1] "Done: out/results/rjmcmc_seg_45.rds"
[1] "Doing: out/results/rjmcmc_seg_46.rds"
[1] "Done: out/results/rjmcmc_seg_46.rds"
[1] "Doing: out/results/rjmcmc_seg_47.rds"
[1] "Done: out/results/rjmcmc_seg_47.rds"
[1] "Doing: out/results/rjmcmc_seg_48.rds"
[1] "Done: out/results/rjmcmc_seg_48.rds"
[1] "Doing: out/results/rjmcmc_seg_49.rds"
[1] "Done: out/results/rjmcmc_seg_49.rds"
[1] "Doing: out/results/rjmcmc_seg_50.rds"
[1] "Done: out/results/rjmcmc_seg_50.rds"
[1] "Doing: out/results/rjmcmc_seg_51.rds"
[1] "Done: out/results/rjmcmc_seg_51.rds"
[1] "Doing: out/results/rjmcmc_seg_52.rds"
[1] "Done: out/results/rjmcmc_seg_52.rds"
[1] "Doing: out/results/rjmcmc_seg_53.rds"
[1] "Done: out/results/rjmcmc_seg_53.rds"
[1] "Doing: out/results/rjmcmc_seg_54.rds"
[1] "Done: out/results/rjmcmc_seg_54.rds"
[1] "Doing: out/results/rjmcmc_seg_55.rds"
[1] "Done: out/results/rjmcmc_seg_55.rds"
[1] "Doing: out/results/rjmcmc_seg_56.rds"
[1] "Done: out/results/rjmcmc_seg_56.rds"

RJMCMCNucleosomes - Predicted nucleosomes Before and After Post-Treatment
BEFORE POST-TREATMENT
Number of nucleosomes:
[1] 102

Nucleosomes positions:
GRanges object with 102 ranges and 0 metadata columns:
             seqnames         ranges strand
                <Rle>      <IRanges>  <Rle>
    [1] chr_SYNTHETIC   [1255, 1255]      *
    [2] chr_SYNTHETIC   [2259, 2259]      *
    [3] chr_SYNTHETIC   [3623, 3623]      *
    [4] chr_SYNTHETIC   [4259, 4259]      *
    [5] chr_SYNTHETIC   [5348, 5348]      *
    ...           ...            ...    ...
   [98] chr_SYNTHETIC [53427, 53427]      *
   [99] chr_SYNTHETIC [54220, 54220]      *
  [100] chr_SYNTHETIC [54771, 54771]      *
  [101] chr_SYNTHETIC [55358, 55358]      *
  [102] chr_SYNTHETIC [55936, 55936]      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

AFTER POST-TREATMENT
Number of nucleosomes:
[1] 89

Nucleosomes positions:
GRanges object with 89 ranges and 0 metadata columns:
            seqnames         ranges strand
               <Rle>      <IRanges>  <Rle>
   [1] chr_SYNTHETIC   [1255, 1255]      *
   [2] chr_SYNTHETIC   [2259, 2259]      *
   [3] chr_SYNTHETIC   [3623, 3623]      *
   [4] chr_SYNTHETIC   [4259, 4259]      *
   [5] chr_SYNTHETIC   [5348, 5348]      *
   ...           ...            ...    ...
  [85] chr_SYNTHETIC [53286, 53286]      *
  [86] chr_SYNTHETIC [54220, 54220]      *
  [87] chr_SYNTHETIC [54771, 54771]      *
  [88] chr_SYNTHETIC [55358, 55358]      *
  [89] chr_SYNTHETIC [55936, 55936]      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

RJMCMCNucleosomes - Predicted nucleosomes

Number of nucleosomes:
[1] 11

Nucleosomes positions:
GRanges object with 11 ranges and 0 metadata columns:
            seqnames         ranges strand
               <Rle>      <IRanges>  <Rle>
   [1] chr_SYNTHETIC [10077, 10077]      *
   [2] chr_SYNTHETIC [10236, 10236]      *
   [3] chr_SYNTHETIC [10406, 10406]      *
   [4] chr_SYNTHETIC [10571, 10571]      *
   [5] chr_SYNTHETIC [10744, 10744]      *
   [6] chr_SYNTHETIC [10842, 10842]      *
   [7] chr_SYNTHETIC [10846, 10846]      *
   [8] chr_SYNTHETIC [10896, 10896]      *
   [9] chr_SYNTHETIC [10906, 10906]      *
  [10] chr_SYNTHETIC [11410, 11410]      *
  [11] chr_SYNTHETIC [11580, 11580]      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
[1] "Doing: test_rjmcmcCHR_good_01/results/rjmcmc_seg_2.rds"
[1] "Done: test_rjmcmcCHR_good_01/results/rjmcmc_seg_2.rds"
[1] "Doing: test_rjmcmcCHR_good_01/results/rjmcmc_seg_1.rds"
[1] "Done: test_rjmcmcCHR_good_01/results/rjmcmc_seg_1.rds"
[1] "Doing: test_rjmcmcCHR_good_02/results/rjmcmc_seg_1.rds"
[1] "Done: test_rjmcmcCHR_good_02/results/rjmcmc_seg_1.rds"


RUNIT TEST PROTOCOL -- Thu Apr 12 02:48:48 2018 
*********************************************** 
Number of test functions: 86 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
RJMCMCNucleosomes RUnit Tests - 86 test functions, 0 errors, 0 failures
Number of test functions: 86 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  42.89    0.42   52.43

RJMCMCNucleosomes.Rcheck/tests_x64/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> ## Run all tests presnt in the package
> BiocGenerics:::testPackage("RJMCMCNucleosomes")

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, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min


Attaching package: 'S4Vectors'

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

    expand.grid

RJMCMCNucleosomes - Predicted nucleosomes

Call:
rjmcmc(reads = reads_demo_02, seqName = "chr_SYNTHETIC", nbrIterations = 1e+05, 
    kMax = 30, lambda = 2, minInterval = 146, maxInterval = 490, 
    minReads = 3, vSeed = 32)

Number of nucleosomes:
[1] 6

Nucleosomes positions:
GRanges object with 6 ranges and 0 metadata columns:
           seqnames         ranges strand
              <Rle>      <IRanges>  <Rle>
  [1] chr_SYNTHETIC [10072, 10072]      *
  [2] chr_SYNTHETIC [10241, 10241]      *
  [3] chr_SYNTHETIC [10574, 10574]      *
  [4] chr_SYNTHETIC [10656, 10656]      *
  [5] chr_SYNTHETIC [10669, 10669]      *
  [6] chr_SYNTHETIC [10744, 10744]      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
[1] "Doing: out/results/rjmcmc_seg_1.rds"
[1] "Done: out/results/rjmcmc_seg_1.rds"
[1] "Doing: out/results/rjmcmc_seg_2.rds"
[1] "Done: out/results/rjmcmc_seg_2.rds"
[1] "Doing: out/results/rjmcmc_seg_3.rds"
[1] "Done: out/results/rjmcmc_seg_3.rds"
[1] "Doing: out/results/rjmcmc_seg_4.rds"
[1] "Done: out/results/rjmcmc_seg_4.rds"
[1] "Doing: out/results/rjmcmc_seg_5.rds"
[1] "Done: out/results/rjmcmc_seg_5.rds"
[1] "Doing: out/results/rjmcmc_seg_6.rds"
[1] "Done: out/results/rjmcmc_seg_6.rds"
[1] "Doing: out/results/rjmcmc_seg_7.rds"
[1] "Done: out/results/rjmcmc_seg_7.rds"
[1] "Doing: out/results/rjmcmc_seg_8.rds"
[1] "Done: out/results/rjmcmc_seg_8.rds"
[1] "Doing: out/results/rjmcmc_seg_9.rds"
[1] "Done: out/results/rjmcmc_seg_9.rds"
[1] "Doing: out/results/rjmcmc_seg_10.rds"
[1] "Done: out/results/rjmcmc_seg_10.rds"
[1] "Doing: out/results/rjmcmc_seg_11.rds"
[1] "Done: out/results/rjmcmc_seg_11.rds"
[1] "Doing: out/results/rjmcmc_seg_12.rds"
[1] "Done: out/results/rjmcmc_seg_12.rds"
[1] "Doing: out/results/rjmcmc_seg_13.rds"
[1] "Done: out/results/rjmcmc_seg_13.rds"
[1] "Doing: out/results/rjmcmc_seg_14.rds"
[1] "Done: out/results/rjmcmc_seg_14.rds"
[1] "Doing: out/results/rjmcmc_seg_15.rds"
[1] "Done: out/results/rjmcmc_seg_15.rds"
[1] "Doing: out/results/rjmcmc_seg_16.rds"
[1] "Done: out/results/rjmcmc_seg_16.rds"
[1] "Doing: out/results/rjmcmc_seg_17.rds"
[1] "Done: out/results/rjmcmc_seg_17.rds"
[1] "Doing: out/results/rjmcmc_seg_18.rds"
[1] "Done: out/results/rjmcmc_seg_18.rds"
[1] "Doing: out/results/rjmcmc_seg_19.rds"
[1] "Done: out/results/rjmcmc_seg_19.rds"
[1] "Doing: out/results/rjmcmc_seg_20.rds"
[1] "Done: out/results/rjmcmc_seg_20.rds"
[1] "Doing: out/results/rjmcmc_seg_21.rds"
[1] "Done: out/results/rjmcmc_seg_21.rds"
[1] "Doing: out/results/rjmcmc_seg_22.rds"
[1] "Done: out/results/rjmcmc_seg_22.rds"
[1] "Doing: out/results/rjmcmc_seg_23.rds"
[1] "Done: out/results/rjmcmc_seg_23.rds"
[1] "Doing: out/results/rjmcmc_seg_24.rds"
[1] "Done: out/results/rjmcmc_seg_24.rds"
[1] "Doing: out/results/rjmcmc_seg_25.rds"
[1] "Done: out/results/rjmcmc_seg_25.rds"
[1] "Doing: out/results/rjmcmc_seg_26.rds"
[1] "Done: out/results/rjmcmc_seg_26.rds"
[1] "Doing: out/results/rjmcmc_seg_27.rds"
[1] "Done: out/results/rjmcmc_seg_27.rds"
[1] "Doing: out/results/rjmcmc_seg_28.rds"
[1] "Done: out/results/rjmcmc_seg_28.rds"
[1] "Doing: out/results/rjmcmc_seg_29.rds"
[1] "Done: out/results/rjmcmc_seg_29.rds"
[1] "Doing: out/results/rjmcmc_seg_30.rds"
[1] "Done: out/results/rjmcmc_seg_30.rds"
[1] "Doing: out/results/rjmcmc_seg_31.rds"
[1] "Done: out/results/rjmcmc_seg_31.rds"
[1] "Doing: out/results/rjmcmc_seg_32.rds"
[1] "Done: out/results/rjmcmc_seg_32.rds"
[1] "Doing: out/results/rjmcmc_seg_33.rds"
[1] "Done: out/results/rjmcmc_seg_33.rds"
[1] "Doing: out/results/rjmcmc_seg_34.rds"
[1] "Done: out/results/rjmcmc_seg_34.rds"
[1] "Doing: out/results/rjmcmc_seg_35.rds"
[1] "Done: out/results/rjmcmc_seg_35.rds"
[1] "Doing: out/results/rjmcmc_seg_36.rds"
[1] "Done: out/results/rjmcmc_seg_36.rds"
[1] "Doing: out/results/rjmcmc_seg_37.rds"
[1] "Done: out/results/rjmcmc_seg_37.rds"
[1] "Doing: out/results/rjmcmc_seg_38.rds"
[1] "Done: out/results/rjmcmc_seg_38.rds"
[1] "Doing: out/results/rjmcmc_seg_39.rds"
[1] "Done: out/results/rjmcmc_seg_39.rds"
[1] "Doing: out/results/rjmcmc_seg_40.rds"
[1] "Done: out/results/rjmcmc_seg_40.rds"
[1] "Doing: out/results/rjmcmc_seg_41.rds"
[1] "Done: out/results/rjmcmc_seg_41.rds"
[1] "Doing: out/results/rjmcmc_seg_42.rds"
[1] "Done: out/results/rjmcmc_seg_42.rds"
[1] "Doing: out/results/rjmcmc_seg_43.rds"
[1] "Done: out/results/rjmcmc_seg_43.rds"
[1] "Doing: out/results/rjmcmc_seg_44.rds"
[1] "Done: out/results/rjmcmc_seg_44.rds"
[1] "Doing: out/results/rjmcmc_seg_45.rds"
[1] "Done: out/results/rjmcmc_seg_45.rds"
[1] "Doing: out/results/rjmcmc_seg_46.rds"
[1] "Done: out/results/rjmcmc_seg_46.rds"
[1] "Doing: out/results/rjmcmc_seg_47.rds"
[1] "Done: out/results/rjmcmc_seg_47.rds"
[1] "Doing: out/results/rjmcmc_seg_48.rds"
[1] "Done: out/results/rjmcmc_seg_48.rds"
[1] "Doing: out/results/rjmcmc_seg_49.rds"
[1] "Done: out/results/rjmcmc_seg_49.rds"
[1] "Doing: out/results/rjmcmc_seg_50.rds"
[1] "Done: out/results/rjmcmc_seg_50.rds"
[1] "Doing: out/results/rjmcmc_seg_51.rds"
[1] "Done: out/results/rjmcmc_seg_51.rds"
[1] "Doing: out/results/rjmcmc_seg_52.rds"
[1] "Done: out/results/rjmcmc_seg_52.rds"
[1] "Doing: out/results/rjmcmc_seg_53.rds"
[1] "Done: out/results/rjmcmc_seg_53.rds"
[1] "Doing: out/results/rjmcmc_seg_54.rds"
[1] "Done: out/results/rjmcmc_seg_54.rds"
[1] "Doing: out/results/rjmcmc_seg_55.rds"
[1] "Done: out/results/rjmcmc_seg_55.rds"
[1] "Doing: out/results/rjmcmc_seg_56.rds"
[1] "Done: out/results/rjmcmc_seg_56.rds"

RJMCMCNucleosomes - Predicted nucleosomes Before and After Post-Treatment
BEFORE POST-TREATMENT
Number of nucleosomes:
[1] 102

Nucleosomes positions:
GRanges object with 102 ranges and 0 metadata columns:
             seqnames         ranges strand
                <Rle>      <IRanges>  <Rle>
    [1] chr_SYNTHETIC   [1255, 1255]      *
    [2] chr_SYNTHETIC   [2259, 2259]      *
    [3] chr_SYNTHETIC   [3623, 3623]      *
    [4] chr_SYNTHETIC   [4259, 4259]      *
    [5] chr_SYNTHETIC   [5348, 5348]      *
    ...           ...            ...    ...
   [98] chr_SYNTHETIC [53427, 53427]      *
   [99] chr_SYNTHETIC [54220, 54220]      *
  [100] chr_SYNTHETIC [54771, 54771]      *
  [101] chr_SYNTHETIC [55358, 55358]      *
  [102] chr_SYNTHETIC [55936, 55936]      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

AFTER POST-TREATMENT
Number of nucleosomes:
[1] 89

Nucleosomes positions:
GRanges object with 89 ranges and 0 metadata columns:
            seqnames         ranges strand
               <Rle>      <IRanges>  <Rle>
   [1] chr_SYNTHETIC   [1255, 1255]      *
   [2] chr_SYNTHETIC   [2259, 2259]      *
   [3] chr_SYNTHETIC   [3623, 3623]      *
   [4] chr_SYNTHETIC   [4259, 4259]      *
   [5] chr_SYNTHETIC   [5348, 5348]      *
   ...           ...            ...    ...
  [85] chr_SYNTHETIC [53286, 53286]      *
  [86] chr_SYNTHETIC [54220, 54220]      *
  [87] chr_SYNTHETIC [54771, 54771]      *
  [88] chr_SYNTHETIC [55358, 55358]      *
  [89] chr_SYNTHETIC [55936, 55936]      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

RJMCMCNucleosomes - Predicted nucleosomes

Number of nucleosomes:
[1] 11

Nucleosomes positions:
GRanges object with 11 ranges and 0 metadata columns:
            seqnames         ranges strand
               <Rle>      <IRanges>  <Rle>
   [1] chr_SYNTHETIC [10077, 10077]      *
   [2] chr_SYNTHETIC [10236, 10236]      *
   [3] chr_SYNTHETIC [10406, 10406]      *
   [4] chr_SYNTHETIC [10571, 10571]      *
   [5] chr_SYNTHETIC [10744, 10744]      *
   [6] chr_SYNTHETIC [10842, 10842]      *
   [7] chr_SYNTHETIC [10846, 10846]      *
   [8] chr_SYNTHETIC [10896, 10896]      *
   [9] chr_SYNTHETIC [10906, 10906]      *
  [10] chr_SYNTHETIC [11410, 11410]      *
  [11] chr_SYNTHETIC [11580, 11580]      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths
[1] "Doing: test_rjmcmcCHR_good_01/results/rjmcmc_seg_2.rds"
[1] "Done: test_rjmcmcCHR_good_01/results/rjmcmc_seg_2.rds"
[1] "Doing: test_rjmcmcCHR_good_01/results/rjmcmc_seg_1.rds"
[1] "Done: test_rjmcmcCHR_good_01/results/rjmcmc_seg_1.rds"
[1] "Doing: test_rjmcmcCHR_good_02/results/rjmcmc_seg_1.rds"
[1] "Done: test_rjmcmcCHR_good_02/results/rjmcmc_seg_1.rds"


RUNIT TEST PROTOCOL -- Thu Apr 12 02:50:04 2018 
*********************************************** 
Number of test functions: 86 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
RJMCMCNucleosomes RUnit Tests - 86 test functions, 0 errors, 0 failures
Number of test functions: 86 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  67.98    0.35   76.39

Example timings

RJMCMCNucleosomes.Rcheck/examples_i386/RJMCMCNucleosomes-Ex.timings

nameusersystemelapsed
RJMCMC_result1.240.031.27
mergeAllRDSFiles0.250.000.25
mergeAllRDSFilesFromDirectory0.060.000.06
mergeRDSFiles0.030.000.03
plotNucleosomes0.550.000.55
postMerge0.430.020.45
postTreatment0.430.000.42
print.rjmcmcNucleosomes0.000.010.02
print.rjmcmcNucleosomesBeforeAndAfterPostTreatment0.180.000.19
print.rjmcmcNucleosomesMerge0.050.000.04
reads_demo_010.030.000.04
reads_demo_020.050.000.04
rjmcmc0.140.000.14
rjmcmcCHR0.270.000.27
rjmcmcNucleo0.090.020.11
runCHR0.350.000.35
segmentation0.080.010.09
validateDirectoryParameters000
validatePlotNucleosomesParameters0.030.020.05
validatePrepMergeParameters000
validateRDSFilesParameters0.010.000.01
validateRJMCMCParameters000
validateSegmentationParameters0.020.000.02

RJMCMCNucleosomes.Rcheck/examples_x64/RJMCMCNucleosomes-Ex.timings

nameusersystemelapsed
RJMCMC_result2.020.032.04
mergeAllRDSFiles0.550.000.55
mergeAllRDSFilesFromDirectory0.120.000.13
mergeRDSFiles0.080.010.09
plotNucleosomes0.580.020.60
postMerge1.070.001.08
postTreatment0.730.000.74
print.rjmcmcNucleosomes0.020.000.01
print.rjmcmcNucleosomesBeforeAndAfterPostTreatment0.390.000.39
print.rjmcmcNucleosomesMerge0.110.000.11
reads_demo_010.060.010.08
reads_demo_020.080.020.09
rjmcmc0.190.010.21
rjmcmcCHR0.420.020.43
rjmcmcNucleo0.110.000.11
runCHR0.060.050.11
segmentation0.090.000.10
validateDirectoryParameters0.020.000.01
validatePlotNucleosomesParameters0.030.000.03
validatePrepMergeParameters0.000.010.02
validateRDSFilesParameters000
validateRJMCMCParameters0.020.000.02
validateSegmentationParameters0.010.000.01