Astrid Deschênes
| Snapshot Date: 2024-11-25 13:40 -0500 (Mon, 25 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/RJMCMCNucleosomes |
| git_branch: devel |
| git_last_commit: aa06559 |
| git_last_commit_date: 2024-10-29 10:16:24 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-26 11:45 -0500 (Tue, 26 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4350 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4108 |
| 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 1745/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RJMCMCNucleosomes 1.31.0 (landing page) Astrid Deschênes
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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. |
| Package: RJMCMCNucleosomes |
| Version: 1.31.0 |
| 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_1.31.0.tar.gz |
| StartedAt: 2024-11-26 04:02:24 -0500 (Tue, 26 Nov 2024) |
| EndedAt: 2024-11-26 04:07:38 -0500 (Tue, 26 Nov 2024) |
| EllapsedTime: 314.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RJMCMCNucleosomes.Rcheck |
| Warnings: 0 |
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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_1.31.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/RJMCMCNucleosomes.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 ‘1.31.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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-1500.1.0.2.5)’
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* 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/4.5-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-3.21-bioc/meat/RJMCMCNucleosomes.Rcheck/00check.log’
for details.
RJMCMCNucleosomes.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RJMCMCNucleosomes
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘RJMCMCNucleosomes’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
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/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-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/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -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/4.5-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)
RJMCMCNucleosomes.Rcheck/tests/runTests.Rout
R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
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: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
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, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, 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"
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[1] "Done: out/results/rjmcmc_seg_14.rds"
[1] "Doing: out/results/rjmcmc_seg_15.rds"
[1] "Done: out/results/rjmcmc_seg_15.rds"
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[1] "Done: out/results/rjmcmc_seg_16.rds"
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[1] "Done: out/results/rjmcmc_seg_19.rds"
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[1] "Done: out/results/rjmcmc_seg_20.rds"
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[1] "Done: out/results/rjmcmc_seg_21.rds"
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[1] "Done: out/results/rjmcmc_seg_22.rds"
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[1] "Done: out/results/rjmcmc_seg_23.rds"
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[1] "Done: out/results/rjmcmc_seg_24.rds"
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[1] "Done: out/results/rjmcmc_seg_25.rds"
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[1] "Done: out/results/rjmcmc_seg_26.rds"
[1] "Doing: out/results/rjmcmc_seg_27.rds"
[1] "Done: out/results/rjmcmc_seg_27.rds"
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[1] "Done: out/results/rjmcmc_seg_28.rds"
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[1] "Done: out/results/rjmcmc_seg_29.rds"
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[1] "Done: out/results/rjmcmc_seg_30.rds"
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[1] "Done: out/results/rjmcmc_seg_31.rds"
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[1] "Done: out/results/rjmcmc_seg_32.rds"
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[1] "Done: out/results/rjmcmc_seg_34.rds"
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[1] "Done: out/results/rjmcmc_seg_35.rds"
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[1] "Done: out/results/rjmcmc_seg_36.rds"
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[1] "Done: out/results/rjmcmc_seg_37.rds"
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[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_1.rds"
[1] "Done: test_rjmcmcCHR_good_01/results/rjmcmc_seg_1.rds"
[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_02/results/rjmcmc_seg_1.rds"
[1] "Done: test_rjmcmcCHR_good_02/results/rjmcmc_seg_1.rds"
RUNIT TEST PROTOCOL -- Tue Nov 26 04:07:35 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
6.659 0.177 14.439
RJMCMCNucleosomes.Rcheck/RJMCMCNucleosomes-Ex.timings
| name | user | system | elapsed | |
| RJMCMC_result | 0.148 | 0.006 | 0.154 | |
| mergeAllRDSFiles | 0.028 | 0.001 | 0.029 | |
| mergeAllRDSFilesFromDirectory | 0.026 | 0.001 | 0.028 | |
| mergeRDSFiles | 0.022 | 0.001 | 0.022 | |
| plotNucleosomes | 0.091 | 0.001 | 0.092 | |
| postMerge | 0.060 | 0.002 | 0.062 | |
| postTreatment | 0.128 | 0.001 | 0.130 | |
| print.rjmcmcNucleosomes | 0.002 | 0.000 | 0.002 | |
| print.rjmcmcNucleosomesBeforeAndAfterPostTreatment | 0.020 | 0.001 | 0.021 | |
| print.rjmcmcNucleosomesMerge | 0.019 | 0.000 | 0.020 | |
| reads_demo_01 | 0.010 | 0.001 | 0.010 | |
| reads_demo_02 | 0.011 | 0.001 | 0.013 | |
| rjmcmc | 0.025 | 0.001 | 0.025 | |
| rjmcmcCHR | 0.014 | 0.001 | 0.015 | |
| rjmcmcNucleo | 0.018 | 0.001 | 0.019 | |
| runCHR | 0.023 | 0.002 | 0.024 | |
| segmentation | 0.339 | 0.002 | 0.340 | |
| validateDirectoryParameters | 0.000 | 0.000 | 0.001 | |
| validatePlotNucleosomesParameters | 0.001 | 0.002 | 0.002 | |
| validatePrepMergeParameters | 0.001 | 0.000 | 0.001 | |
| validateRDSFilesParameters | 0.000 | 0.000 | 0.001 | |
| validateRJMCMCParameters | 0.002 | 0.000 | 0.002 | |
| validateSegmentationParameters | 0.005 | 0.001 | 0.005 | |