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This page was generated on 2022-01-21 13:06:59 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for RJMCMCNucleosomes on tokay2


To the developers/maintainers of the RJMCMCNucleosomes package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RJMCMCNucleosomes.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1616/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RJMCMCNucleosomes 1.18.0  (landing page)
Astrid DeschĂȘnes
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/RJMCMCNucleosomes
git_branch: RELEASE_3_14
git_last_commit: 0d6b941
git_last_commit_date: 2021-10-26 12:32:18 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: RJMCMCNucleosomes
Version: 1.18.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RJMCMCNucleosomes.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RJMCMCNucleosomes_1.18.0.tar.gz
StartedAt: 2022-01-21 01:44:29 -0500 (Fri, 21 Jan 2022)
EndedAt: 2022-01-21 01:50:35 -0500 (Fri, 21 Jan 2022)
EllapsedTime: 365.8 seconds
RetCode: 0
Status:   OK  
CheckDir: RJMCMCNucleosomes.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RJMCMCNucleosomes.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RJMCMCNucleosomes_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/RJMCMCNucleosomes.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '1.18.0'
* 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
* 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 ... 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 use of PKG_*FLAGS in Makefiles ... 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-3.14-bioc/R/library/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)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RJMCMCNucleosomes/libs/x64/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 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-3.14-bioc/meat/RJMCMCNucleosomes.Rcheck/00check.log'
for details.



Installation output

RJMCMCNucleosomes.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/RJMCMCNucleosomes_1.18.0.tar.gz && rm -rf RJMCMCNucleosomes.buildbin-libdir && mkdir RJMCMCNucleosomes.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RJMCMCNucleosomes.buildbin-libdir RJMCMCNucleosomes_1.18.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL RJMCMCNucleosomes_1.18.0.zip && rm RJMCMCNucleosomes_1.18.0.tar.gz RJMCMCNucleosomes_1.18.0.zip
###
##############################################################################
##############################################################################


  % 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  289k  100  289k    0     0  1271k      0 --:--:-- --:--:-- --:--:-- 1280k

install for i386

* installing *source* package 'RJMCMCNucleosomes' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/i386/include -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c NucleoDirichlet.cpp -o NucleoDirichlet.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/i386/include -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c NucleoDirichletPA.cpp -o NucleoDirichletPA.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/i386/include -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Nucleosome.cpp -o Nucleosome.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/i386/include -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c RJMCMCNucleosomes_init.c -o RJMCMCNucleosomes_init.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/i386/include -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/i386/include -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c SegmentSeq.cpp -o SegmentSeq.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/i386/include -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rjmcmcNucleo.cpp -o rjmcmcNucleo.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -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:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/RJMCMCNucleosomes.buildbin-libdir/00LOCK-RJMCMCNucleosomes/00new/RJMCMCNucleosomes/libs/i386
** R
** data
** inst
** byte-compile and prepare 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'RJMCMCNucleosomes' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/x64/include -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c NucleoDirichlet.cpp -o NucleoDirichlet.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/x64/include -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c NucleoDirichletPA.cpp -o NucleoDirichletPA.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/x64/include -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Nucleosome.cpp -o Nucleosome.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/x64/include -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c RJMCMCNucleosomes_init.c -o RJMCMCNucleosomes_init.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/x64/include -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/x64/include -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c SegmentSeq.cpp -o SegmentSeq.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I/x64/include -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rjmcmcNucleo.cpp -o rjmcmcNucleo.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -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:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/RJMCMCNucleosomes.buildbin-libdir/RJMCMCNucleosomes/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RJMCMCNucleosomes' as RJMCMCNucleosomes_1.18.0.zip
* DONE (RJMCMCNucleosomes)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'RJMCMCNucleosomes' successfully unpacked and MD5 sums checked

Tests output

RJMCMCNucleosomes.Rcheck/tests_i386/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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: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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'IRanges'

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

    windows

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      *
  [2] chr_SYNTHETIC     10241      *
  [3] chr_SYNTHETIC     10574      *
  [4] chr_SYNTHETIC     10656      *
  [5] chr_SYNTHETIC     10669      *
  [6] chr_SYNTHETIC     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      *
    [2] chr_SYNTHETIC      2259      *
    [3] chr_SYNTHETIC      3623      *
    [4] chr_SYNTHETIC      4259      *
    [5] chr_SYNTHETIC      5348      *
    ...           ...       ...    ...
   [98] chr_SYNTHETIC     53427      *
   [99] chr_SYNTHETIC     54220      *
  [100] chr_SYNTHETIC     54771      *
  [101] chr_SYNTHETIC     55358      *
  [102] chr_SYNTHETIC     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      *
   [2] chr_SYNTHETIC      2259      *
   [3] chr_SYNTHETIC      3623      *
   [4] chr_SYNTHETIC      4259      *
   [5] chr_SYNTHETIC      5348      *
   ...           ...       ...    ...
  [85] chr_SYNTHETIC     53286      *
  [86] chr_SYNTHETIC     54220      *
  [87] chr_SYNTHETIC     54771      *
  [88] chr_SYNTHETIC     55358      *
  [89] chr_SYNTHETIC     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      *
   [2] chr_SYNTHETIC     10236      *
   [3] chr_SYNTHETIC     10406      *
   [4] chr_SYNTHETIC     10571      *
   [5] chr_SYNTHETIC     10744      *
   [6] chr_SYNTHETIC     10842      *
   [7] chr_SYNTHETIC     10846      *
   [8] chr_SYNTHETIC     10896      *
   [9] chr_SYNTHETIC     10906      *
  [10] chr_SYNTHETIC     11410      *
  [11] chr_SYNTHETIC     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 -- Fri Jan 21 01:49:39 2022 
*********************************************** 
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 
  24.60    1.62   44.84 

RJMCMCNucleosomes.Rcheck/tests_x64/runTests.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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: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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'IRanges'

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

    windows

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      *
  [2] chr_SYNTHETIC     10241      *
  [3] chr_SYNTHETIC     10574      *
  [4] chr_SYNTHETIC     10656      *
  [5] chr_SYNTHETIC     10669      *
  [6] chr_SYNTHETIC     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      *
    [2] chr_SYNTHETIC      2259      *
    [3] chr_SYNTHETIC      3623      *
    [4] chr_SYNTHETIC      4259      *
    [5] chr_SYNTHETIC      5348      *
    ...           ...       ...    ...
   [98] chr_SYNTHETIC     53427      *
   [99] chr_SYNTHETIC     54220      *
  [100] chr_SYNTHETIC     54771      *
  [101] chr_SYNTHETIC     55358      *
  [102] chr_SYNTHETIC     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      *
   [2] chr_SYNTHETIC      2259      *
   [3] chr_SYNTHETIC      3623      *
   [4] chr_SYNTHETIC      4259      *
   [5] chr_SYNTHETIC      5348      *
   ...           ...       ...    ...
  [85] chr_SYNTHETIC     53286      *
  [86] chr_SYNTHETIC     54220      *
  [87] chr_SYNTHETIC     54771      *
  [88] chr_SYNTHETIC     55358      *
  [89] chr_SYNTHETIC     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      *
   [2] chr_SYNTHETIC     10236      *
   [3] chr_SYNTHETIC     10406      *
   [4] chr_SYNTHETIC     10571      *
   [5] chr_SYNTHETIC     10744      *
   [6] chr_SYNTHETIC     10842      *
   [7] chr_SYNTHETIC     10846      *
   [8] chr_SYNTHETIC     10896      *
   [9] chr_SYNTHETIC     10906      *
  [10] chr_SYNTHETIC     11410      *
  [11] chr_SYNTHETIC     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 -- Fri Jan 21 01:50:27 2022 
*********************************************** 
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 
  26.65    0.48   47.71 

Example timings

RJMCMCNucleosomes.Rcheck/examples_i386/RJMCMCNucleosomes-Ex.timings

nameusersystemelapsed
RJMCMC_result1.170.091.27
mergeAllRDSFiles0.110.000.11
mergeAllRDSFilesFromDirectory0.100.080.17
mergeRDSFiles0.140.040.19
plotNucleosomes0.680.080.78
postMerge0.430.110.53
postTreatment0.460.190.66
print.rjmcmcNucleosomes0.000.010.01
print.rjmcmcNucleosomesBeforeAndAfterPostTreatment0.140.040.17
print.rjmcmcNucleosomesMerge0.130.140.27
reads_demo_010.070.010.09
reads_demo_020.080.000.08
rjmcmc0.160.020.17
rjmcmcCHR0.080.000.08
rjmcmcNucleo0.120.000.12
runCHR0.080.010.10
segmentation0.090.030.12
validateDirectoryParameters0.000.020.02
validatePlotNucleosomesParameters000
validatePrepMergeParameters0.000.020.01
validateRDSFilesParameters000
validateRJMCMCParameters0.020.000.02
validateSegmentationParameters0.030.000.03

RJMCMCNucleosomes.Rcheck/examples_x64/RJMCMCNucleosomes-Ex.timings

nameusersystemelapsed
RJMCMC_result0.510.070.58
mergeAllRDSFiles0.130.000.12
mergeAllRDSFilesFromDirectory0.110.010.12
mergeRDSFiles0.110.020.13
plotNucleosomes0.720.000.72
postMerge0.410.010.42
postTreatment0.510.000.51
print.rjmcmcNucleosomes0.020.000.02
print.rjmcmcNucleosomesBeforeAndAfterPostTreatment0.140.020.16
print.rjmcmcNucleosomesMerge0.170.000.17
reads_demo_010.080.000.08
reads_demo_020.080.010.09
rjmcmc0.170.000.17
rjmcmcCHR0.080.000.08
rjmcmcNucleo0.120.020.14
runCHR0.100.000.09
segmentation0.110.010.13
validateDirectoryParameters000
validatePlotNucleosomesParameters0.010.000.02
validatePrepMergeParameters000
validateRDSFilesParameters000
validateRJMCMCParameters0.030.000.03
validateSegmentationParameters0.030.000.03