Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (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 1417/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ngsReports 2.8.0 (landing page) Stevie Pederson
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the ngsReports package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ngsReports.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: ngsReports |
Version: 2.8.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ngsReports.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ngsReports_2.8.0.tar.gz |
StartedAt: 2024-12-20 06:55:39 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 07:02:22 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 402.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ngsReports.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ngsReports.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ngsReports_2.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ngsReports.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-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 Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ngsReports/DESCRIPTION’ ... OK * this is package ‘ngsReports’ version ‘2.8.0’ * 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 ‘ngsReports’ 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 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 ... 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 LazyData ... 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 plotSeqContent-methods 7.622 0.062 7.829 plotAdapterContent-methods 5.719 0.049 5.856 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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: OK
ngsReports.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ngsReports ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘ngsReports’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (ngsReports)
ngsReports.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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. > library(testthat) > library(ngsReports) 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, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: ggplot2 Loading required package: patchwork Loading required package: tibble > > test_check("ngsReports") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 387 ] > > proc.time() user system elapsed 101.868 2.698 106.944
ngsReports.Rcheck/ngsReports-Ex.timings
name | user | system | elapsed | |
FastqcData | 0.160 | 0.013 | 0.179 | |
FastqcDataList | 0.728 | 0.035 | 0.780 | |
TheoreticalGC-class | 0.143 | 0.006 | 0.151 | |
dot-FastqcFile-class | 0.005 | 0.002 | 0.006 | |
dot-addPercent | 0.000 | 0.000 | 0.001 | |
dot-emptyPlot | 0.289 | 0.007 | 0.299 | |
dot-makeDendro | 0.971 | 0.038 | 1.025 | |
dot-makeLabels | 0.002 | 0.000 | 0.003 | |
dot-splitByTab | 0.007 | 0.001 | 0.008 | |
estGcDistn | 0.050 | 0.002 | 0.054 | |
extract-methods | 0.721 | 0.024 | 0.756 | |
fqName-methods | 0.704 | 0.027 | 0.751 | |
fqcVersion | 0.756 | 0.025 | 0.786 | |
gcAvail | 0.040 | 0.001 | 0.041 | |
gcTheoretical | 0.068 | 0.001 | 0.070 | |
getColours-methods | 0.003 | 0.001 | 0.004 | |
getGC | 0.034 | 0.000 | 0.037 | |
getModule | 0.767 | 0.019 | 0.792 | |
getSummary | 0.726 | 0.021 | 0.758 | |
importNgsLogs | 0.048 | 0.001 | 0.050 | |
importSJ | 0.012 | 0.001 | 0.014 | |
isCompressed | 0.003 | 0.002 | 0.004 | |
mData | 0.042 | 0.001 | 0.043 | |
maxAdapterContent | 0.836 | 0.027 | 0.885 | |
overRep2Fasta-methods | 0.752 | 0.021 | 0.782 | |
path | 0.831 | 0.025 | 0.874 | |
plotAdapterContent-methods | 5.719 | 0.049 | 5.856 | |
plotAlignmentSummary | 1.062 | 0.007 | 1.087 | |
plotAssemblyStats | 1.307 | 0.102 | 1.443 | |
plotBaseQuals-methods | 3.287 | 0.096 | 3.437 | |
plotDupLevels-methods | 2.403 | 0.039 | 2.482 | |
plotFastqcPCA-methods | 1.285 | 0.024 | 1.366 | |
plotGcContent-methods | 1.908 | 0.034 | 1.989 | |
plotInsertSize-methods | 1.268 | 0.009 | 1.311 | |
plotKmers-methods | 3.194 | 0.043 | 3.280 | |
plotNContent-methods | 1.633 | 0.012 | 1.672 | |
plotOverrep-methods | 1.566 | 0.025 | 1.601 | |
plotReadTotals-methods | 1.548 | 0.031 | 1.676 | |
plotSeqContent-methods | 7.622 | 0.062 | 7.829 | |
plotSeqLengthDistn-methods | 2.424 | 0.033 | 2.516 | |
plotSeqQuals-methods | 2.729 | 0.032 | 2.890 | |
plotSummary-methods | 1.104 | 0.025 | 1.200 | |
pwf | 0.007 | 0.002 | 0.008 | |
readTotals | 0.777 | 0.021 | 0.807 | |
summariseOverrep-methods | 1.357 | 0.024 | 1.399 | |
writeHtmlReport | 0.000 | 0.001 | 0.001 | |