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This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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

Package 1761/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RJMCMCNucleosomes 1.30.0  (landing page)
Astrid Deschênes
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/RJMCMCNucleosomes
git_branch: RELEASE_3_20
git_last_commit: 827b9c6
git_last_commit_date: 2024-10-29 10:16:24 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for RJMCMCNucleosomes on kjohnson1

To the developers/maintainers of the RJMCMCNucleosomes package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: RJMCMCNucleosomes
Version: 1.30.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RJMCMCNucleosomes.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RJMCMCNucleosomes_1.30.0.tar.gz
StartedAt: 2024-12-21 06:58:57 -0500 (Sat, 21 Dec 2024)
EndedAt: 2024-12-21 07:04:00 -0500 (Sat, 21 Dec 2024)
EllapsedTime: 303.3 seconds
RetCode: 0
Status:   OK  
CheckDir: RJMCMCNucleosomes.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RJMCMCNucleosomes.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RJMCMCNucleosomes_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/RJMCMCNucleosomes.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RJMCMCNucleosomes/DESCRIPTION’ ... OK
* this is package ‘RJMCMCNucleosomes’ version ‘1.30.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘RJMCMCNucleosomes’ can be installed ... OK
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 code 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) RJMCMCNucleosomes-package.Rd:16-17: Lost braces
    16 |     \item \code{\link{rjmcmc}} { for profiling of nucleosome positions for a
       |                                ^
checkRd: (-1) RJMCMCNucleosomes-package.Rd:18-20: Lost braces
    18 |     \item \code{\link{rjmcmcCHR}} { for profiling of nucleosome positions
       |                                   ^
checkRd: (-1) RJMCMCNucleosomes-package.Rd:21-23: Lost braces
    21 |     \item \code{\link{segmentation}} { for spliting a \code{GRanges}
       |                                      ^
checkRd: (-1) RJMCMCNucleosomes-package.Rd:24-25: Lost braces
    24 |     \item \code{\link{postTreatment}} { for merging closely positioned
       |                                       ^
checkRd: (-1) RJMCMCNucleosomes-package.Rd:26-27: Lost braces
    26 |     \item \code{\link{mergeRDSFiles}} { for merging nucleosome information
       |                                       ^
checkRd: (-1) RJMCMCNucleosomes-package.Rd:28-29: Lost braces
    28 |     \item \code{\link{plotNucleosomes}} { for generating a graph containing
       |                                         ^
checkRd: (-1) RJMCMC_result.Rd:61: Lost braces; missing escapes or markup?
    61 |     \item \code{\link{rjmcmc}} {for profiling of nucleosome positions}
       |                                ^
checkRd: (-1) RJMCMC_result.Rd:62-64: Lost braces
    62 |     \item \code{\link{rjmcmcCHR}} { for profiling of nucleosome positions
       |                                   ^
checkRd: (-1) RJMCMC_result.Rd:65-67: Lost braces
    65 |     \item \code{\link{segmentation}} { for spliting a \code{GRanges}
       |                                      ^
checkRd: (-1) RJMCMC_result.Rd:68-69: Lost braces
    68 |     \item \code{\link{postTreatment}} { for merging closely positioned
       |                                       ^
checkRd: (-1) RJMCMC_result.Rd:70-71: Lost braces
    70 |     \item \code{\link{mergeRDSFiles}} { for merging nucleosome information
       |                                       ^
checkRd: (-1) RJMCMC_result.Rd:72-73: Lost braces
    72 |     \item \code{\link{plotNucleosomes}} { for generating a graph containing
       |                                         ^
checkRd: (-1) reads_demo_01.Rd:31: Lost braces; missing escapes or markup?
    31 |     \item \code{\link{rjmcmc}} {for profiling of nucleosome positions}
       |                                ^
checkRd: (-1) reads_demo_02.Rd:33: Lost braces; missing escapes or markup?
    33 |     \item \code{\link{rjmcmc}} {for profiling of nucleosome positions}
       |                                ^
checkRd: (-1) reads_demo_02.Rd:34-36: Lost braces
    34 |     \item \code{\link{rjmcmcCHR}} { for profiling of nucleosome positions
       |                                   ^
checkRd: (-1) reads_demo_02.Rd:37-39: Lost braces
    37 |     \item \code{\link{segmentation}} { for spliting a \code{GRanges}
       |                                      ^
checkRd: (-1) reads_demo_02.Rd:40-41: Lost braces
    40 |     \item \code{\link{postTreatment}} { for merging closely positioned
       |                                       ^
checkRd: (-1) reads_demo_02.Rd:42-43: Lost braces
    42 |     \item \code{\link{mergeRDSFiles}} { for merging nucleosome information
       |                                       ^
checkRd: (-1) reads_demo_02.Rd:44-45: Lost braces
    44 |     \item \code{\link{plotNucleosomes}} { for generating a graph containing
       |                                         ^
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'runCHR.Rd':
  ‘kMax’ ‘minInterval’ ‘maxInterval’ ‘maxLength’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 is not available
File ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RJMCMCNucleosomes/libs/RJMCMCNucleosomes.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  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 nor [v]sprintf. 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/RJMCMCNucleosomes.Rcheck/00check.log’
for details.

Installation output

RJMCMCNucleosomes.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RJMCMCNucleosomes
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘RJMCMCNucleosomes’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `gsl-config --cflags` -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c NucleoDirichlet.cpp -o NucleoDirichlet.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `gsl-config --cflags` -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c NucleoDirichletPA.cpp -o NucleoDirichletPA.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `gsl-config --cflags` -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c Nucleosome.cpp -o Nucleosome.o
Nucleosome.cpp:149:9: warning: variable 'pv' set but not used [-Wunused-but-set-variable]
    int pv = 0;
        ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `gsl-config --cflags` -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RJMCMCNucleosomes_init.c -o RJMCMCNucleosomes_init.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `gsl-config --cflags` -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `gsl-config --cflags` -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c SegmentSeq.cpp -o SegmentSeq.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `gsl-config --cflags` -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c rjmcmcNucleo.cpp -o rjmcmcNucleo.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o RJMCMCNucleosomes.so NucleoDirichlet.o NucleoDirichletPA.o Nucleosome.o RJMCMCNucleosomes_init.o RcppExports.o SegmentSeq.o rjmcmcNucleo.o -L/opt/R/arm64/lib -lgsl -lgslcblas -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-RJMCMCNucleosomes/00new/RJMCMCNucleosomes/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RJMCMCNucleosomes)

Tests output

RJMCMCNucleosomes.Rcheck/tests/runTests.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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, aperm, 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, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

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 -- Sat Dec 21 07:03:50 2024 
*********************************************** 
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 
 25.420   0.816  53.559

Example timings

RJMCMCNucleosomes.Rcheck/RJMCMCNucleosomes-Ex.timings

nameusersystemelapsed
RJMCMC_result0.4130.0380.454
mergeAllRDSFiles0.0620.0090.073
mergeAllRDSFilesFromDirectory0.0490.0070.059
mergeRDSFiles0.0640.0080.073
plotNucleosomes0.2180.0080.229
postMerge0.1150.0030.120
postTreatment0.1550.0030.162
print.rjmcmcNucleosomes0.0030.0020.005
print.rjmcmcNucleosomesBeforeAndAfterPostTreatment0.0450.0030.048
print.rjmcmcNucleosomesMerge0.0880.0020.090
reads_demo_010.0350.0020.038
reads_demo_020.0410.0020.043
rjmcmc0.0810.0030.088
rjmcmcCHR0.0470.0040.052
rjmcmcNucleo0.0630.0030.066
runCHR0.0990.0060.105
segmentation0.1050.0050.110
validateDirectoryParameters0.0010.0000.002
validatePlotNucleosomesParameters0.0030.0040.008
validatePrepMergeParameters0.0030.0020.007
validateRDSFilesParameters0.0020.0010.003
validateRJMCMCParameters0.0110.0000.012
validateSegmentationParameters0.0200.0030.024