Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:41 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 1738/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RJMCMCNucleosomes 1.29.0 (landing page) Astrid DeschĂȘnes
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | 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 | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 1.29.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RJMCMCNucleosomes.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings RJMCMCNucleosomes_1.29.0.tar.gz |
StartedAt: 2024-08-21 04:27:56 -0400 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 04:33:01 -0400 (Wed, 21 Aug 2024) |
EllapsedTime: 305.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RJMCMCNucleosomes.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RJMCMCNucleosomes.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings RJMCMCNucleosomes_1.29.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/RJMCMCNucleosomes.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'RJMCMCNucleosomes/DESCRIPTION' ... OK * this is package 'RJMCMCNucleosomes' version '1.29.0' * 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 * used C compiler: 'gcc.exe (GCC) 13.2.0' * used C++ compiler: 'G__~1.EXE (GCC) 13.2.0' * 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 for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/RJMCMCNucleosomes/libs/x64/RJMCMCNucleosomes.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) 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 'F:/biocbuild/bbs-3.20-bioc/meat/RJMCMCNucleosomes.Rcheck/00check.log' for details.
RJMCMCNucleosomes.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL RJMCMCNucleosomes ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'RJMCMCNucleosomes' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/x64/include -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c NucleoDirichlet.cpp -o NucleoDirichlet.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/x64/include -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c NucleoDirichletPA.cpp -o NucleoDirichletPA.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/x64/include -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Nucleosome.cpp -o Nucleosome.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/x64/include -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RJMCMCNucleosomes_init.c -o RJMCMCNucleosomes_init.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/x64/include -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/x64/include -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SegmentSeq.cpp -o SegmentSeq.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/x64/include -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rjmcmcNucleo.cpp -o rjmcmcNucleo.o g++ -std=gnu++17 -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:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-RJMCMCNucleosomes/00new/RJMCMCNucleosomes/libs/x64 ** 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 ** 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 version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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, 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 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 -- Wed Aug 21 04:32:50 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 25.00 1.07 50.12
RJMCMCNucleosomes.Rcheck/RJMCMCNucleosomes-Ex.timings
name | user | system | elapsed | |
RJMCMC_result | 0.55 | 0.00 | 0.56 | |
mergeAllRDSFiles | 0.08 | 0.01 | 0.09 | |
mergeAllRDSFilesFromDirectory | 0.13 | 0.01 | 0.14 | |
mergeRDSFiles | 0.11 | 0.00 | 0.11 | |
plotNucleosomes | 0.39 | 0.02 | 0.40 | |
postMerge | 0.28 | 0.04 | 0.33 | |
postTreatment | 0.39 | 0.05 | 0.44 | |
print.rjmcmcNucleosomes | 0.01 | 0.00 | 0.02 | |
print.rjmcmcNucleosomesBeforeAndAfterPostTreatment | 0.07 | 0.00 | 0.06 | |
print.rjmcmcNucleosomesMerge | 0.11 | 0.02 | 0.12 | |
reads_demo_01 | 0.06 | 0.00 | 0.07 | |
reads_demo_02 | 0.06 | 0.00 | 0.06 | |
rjmcmc | 0.12 | 0.00 | 0.13 | |
rjmcmcCHR | 0.05 | 0.01 | 0.06 | |
rjmcmcNucleo | 0.09 | 0.00 | 0.10 | |
runCHR | 0.08 | 0.00 | 0.07 | |
segmentation | 0.27 | 0.00 | 0.27 | |
validateDirectoryParameters | 0 | 0 | 0 | |
validatePlotNucleosomesParameters | 0.00 | 0.02 | 0.01 | |
validatePrepMergeParameters | 0.00 | 0.02 | 0.02 | |
validateRDSFilesParameters | 0 | 0 | 0 | |
validateRJMCMCParameters | 0.01 | 0.00 | 0.01 | |
validateSegmentationParameters | 0.02 | 0.02 | 0.03 | |