Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:43 -0500 (Mon, 02 Jan 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
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 |
To the developers/maintainers of the periodicDNA package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1450/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
periodicDNA 1.9.0 (landing page) Jacques Serizay
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ||||||||
Package: periodicDNA |
Version: 1.9.0 |
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:periodicDNA.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings periodicDNA_1.9.0.tar.gz |
StartedAt: 2022-12-29 02:14:48 -0500 (Thu, 29 Dec 2022) |
EndedAt: 2022-12-29 02:19:51 -0500 (Thu, 29 Dec 2022) |
EllapsedTime: 303.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: periodicDNA.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:periodicDNA.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings periodicDNA_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/periodicDNA.Rcheck' * using R Under development (unstable) (2022-12-25 r83502 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 10.4.0 GNU Fortran (GCC) 10.4.0 * running under: Windows Server x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'periodicDNA/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'periodicDNA' version '1.9.0' * 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 'periodicDNA' can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import 'GenomicRanges::subtract' by 'magrittr::subtract' when loading 'periodicDNA' See 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/periodicDNA.Rcheck/00install.out' for details. * 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 * 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 files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed getPeriodicity 23.86 1.28 31.44 getPeriodicityWithIterations 8.19 0.01 8.20 getPeriodicityTrack 7.19 0.13 7.31 plotPeriodicityResults 6.67 0.06 6.74 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'testthat.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 WARNING See 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/periodicDNA.Rcheck/00check.log' for details.
periodicDNA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL periodicDNA ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'periodicDNA' ... ** using staged installation ** R ** data ** byte-compile and prepare package for lazy loading Warning: replacing previous import 'GenomicRanges::subtract' by 'magrittr::subtract' when loading 'periodicDNA' ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import 'GenomicRanges::subtract' by 'magrittr::subtract' when loading 'periodicDNA' ** testing if installed package can be loaded from final location Warning: replacing previous import 'GenomicRanges::subtract' by 'magrittr::subtract' when loading 'periodicDNA' ** testing if installed package keeps a record of temporary installation path * DONE (periodicDNA)
periodicDNA.Rcheck/tests/testthat.Rout
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" Copyright (C) 2022 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. > library(testthat) > library(periodicDNA) Loading required package: Biostrings Loading required package: BiocGenerics 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, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: XVector Loading required package: GenomeInfoDb Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: GenomicRanges Loading required package: BSgenome Loading required package: rtracklayer Loading required package: BiocParallel Warning message: replacing previous import 'GenomicRanges::subtract' by 'magrittr::subtract' when loading 'periodicDNA' > library(BiocParallel) > register(setUpBPPARAM(1), default = TRUE) > > test_check("periodicDNA") [ FAIL 0 | WARN 4 | SKIP 0 | PASS 6 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 6 ] > > proc.time() user system elapsed 60.34 2.09 62.45
periodicDNA.Rcheck/periodicDNA-Ex.timings
name | user | system | elapsed | |
ce11_ATACseq | 0.06 | 0.00 | 0.06 | |
ce11_TSSs | 0.05 | 0.02 | 0.07 | |
ce11_WW_10bp | 0.03 | 0.00 | 0.03 | |
ce11_all_REs | 0.17 | 0.00 | 0.18 | |
ce11_proms | 0.05 | 0.00 | 0.04 | |
ce11_proms_seqs | 0.03 | 0.02 | 0.05 | |
getPeriodicity | 23.86 | 1.28 | 31.44 | |
getPeriodicityTrack | 7.19 | 0.13 | 7.31 | |
getPeriodicityWithIterations | 8.19 | 0.01 | 8.20 | |
plotAggregateCoverage | 2.17 | 0.05 | 2.22 | |
plotPeriodicityResults | 6.67 | 0.06 | 6.74 | |
setUpBPPARAM | 0.64 | 0.00 | 0.64 | |
theme_ggplot2 | 0.11 | 0.00 | 0.11 | |