Steve Pederson
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/ngsReports |
| git_branch: master |
| git_last_commit: 384bcb5 |
| git_last_commit_date: 2021-10-26 12:50:47 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:10 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 ngsReports package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1302/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ngsReports 1.11.0 (landing page) Steve Pederson
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ngsReports |
| Version: 1.11.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ngsReports.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ngsReports_1.11.0.tar.gz |
| StartedAt: 2022-03-17 19:44:37 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:46:52 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 135.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ngsReports.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ngsReports.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ngsReports_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/ngsReports.Rcheck' * using R Under development (unstable) (2021-11-21 r81221) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'ngsReports/DESCRIPTION' ... OK * this is package 'ngsReports' version '1.11.0' * 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 '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 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in 'vignettes' ... OK * checking examples ... OK * 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: OK
ngsReports.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL ngsReports
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/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
converting help for package 'ngsReports'
finding HTML links ... done
FastqcData html
FastqcDataList html
PwfCols-class html
TheoreticalGC-class html
dot-FastqcFile-class html
dot-addPercent html
dot-emptyPlot html
dot-getToolName html
dot-hidePWFRects html
dot-isValidAdapterRemovalLog html
dot-isValidBowtieLog html
dot-isValidBuscoLog html
dot-isValidCutadaptLog html
dot-isValidDuplicationMetricsLog html
dot-isValidFeatureCountsLog html
dot-isValidFlagstatLog html
dot-isValidHisat2Log html
dot-isValidMacs2CallpeakLog html
dot-isValidQuastLog html
dot-isValidStarLog html
dot-isValidTrimmomaticLog html
dot-makeDendro html
dot-makeLabels html
dot-makeSidebar html
dot-parseAdapterRemovalLogs html
dot-parseBowtieLogs html
dot-parseBuscoLogs html
dot-parseCutadaptLogs html
dot-parseDuplicationMetricsLogs html
dot-parseFeatureCountsLogs html
dot-parseFlagstatLogs html
dot-parseHisat2Logs html
dot-parseMacs2CallpeakLogs html
dot-parseQuastLogs html
dot-parseStarLogs html
dot-parseTrimmomaticLogs html
dot-renderDendro html
dot-scale_fill_pwf html
dot-splitByTab html
estGcDistn html
extract-methods html
fqName-methods html
fqcVersion html
gcAvail html
gcTheoretical html
getColours-methods html
getGC html
getModule html
getSummary html
importNgsLogs html
importSJ html
isCompressed html
mData html
maxAdapterContent html
overRep2Fasta-methods html
path html
plotAdapterContent-methods html
plotAlignmentSummary html
plotAssemblyStats html
plotBaseQuals-methods html
plotDupLevels-methods html
plotFastqcPCA-methods html
plotGcContent-methods html
plotKmers-methods html
plotNContent-methods html
plotOverrep-methods html
plotReadTotals-methods html
plotSeqContent-methods html
plotSeqLengthDistn-methods html
plotSeqQuals-methods html
plotSummary-methods html
pwf html
readTotals html
runFastQC-methods html
writeHtmlReport html
*** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'MSstatsSampleSize' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'timeOmics' is missing or broken
done
ngsReports.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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(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, 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: ggplot2
Loading required package: tibble
>
> test_check("ngsReports")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 205 ]
>
> proc.time()
user system elapsed
12.95 1.31 15.46
ngsReports.Rcheck/ngsReports-Ex.timings
| name | user | system | elapsed | |
| FastqcData | 0.03 | 0.01 | 0.04 | |
| FastqcDataList | 0.25 | 0.00 | 0.25 | |
| TheoreticalGC-class | 0.06 | 0.00 | 0.07 | |
| dot-FastqcFile-class | 0 | 0 | 0 | |
| dot-addPercent | 0 | 0 | 0 | |
| dot-emptyPlot | 0.09 | 0.00 | 0.09 | |
| dot-makeDendro | 0.25 | 0.00 | 0.25 | |
| dot-makeLabels | 0 | 0 | 0 | |
| dot-splitByTab | 0 | 0 | 0 | |
| estGcDistn | 0.02 | 0.00 | 0.01 | |
| extract-methods | 0.22 | 0.02 | 0.24 | |
| fqName-methods | 0.20 | 0.03 | 0.23 | |
| fqcVersion | 0.27 | 0.00 | 0.27 | |
| gcAvail | 0.01 | 0.00 | 0.01 | |
| gcTheoretical | 0.00 | 0.01 | 0.02 | |
| getColours-methods | 0 | 0 | 0 | |
| getGC | 0.02 | 0.00 | 0.02 | |
| getModule | 0.25 | 0.02 | 0.26 | |
| getSummary | 0.26 | 0.02 | 0.28 | |
| importNgsLogs | 0.02 | 0.00 | 0.02 | |
| importSJ | 0.03 | 0.00 | 0.03 | |
| isCompressed | 0 | 0 | 0 | |
| mData | 0.02 | 0.00 | 0.02 | |
| maxAdapterContent | 0.28 | 0.01 | 0.29 | |
| overRep2Fasta-methods | 0.51 | 0.00 | 0.52 | |
| path | 0.22 | 0.00 | 0.22 | |
| plotAdapterContent-methods | 1.02 | 0.10 | 1.11 | |
| plotAlignmentSummary | 0.19 | 0.00 | 0.18 | |
| plotAssemblyStats | 0.43 | 0.01 | 0.46 | |
| plotBaseQuals-methods | 0.63 | 0.02 | 0.64 | |
| plotDupLevels-methods | 0.62 | 0.04 | 0.67 | |
| plotFastqcPCA-methods | 0.32 | 0.03 | 0.34 | |
| plotGcContent-methods | 0.45 | 0.00 | 0.46 | |
| plotKmers-methods | 0.39 | 0.02 | 0.40 | |
| plotNContent-methods | 0.23 | 0.02 | 0.25 | |
| plotOverrep-methods | 0.35 | 0.03 | 0.38 | |
| plotReadTotals-methods | 0.45 | 0.00 | 0.45 | |
| plotSeqContent-methods | 0.33 | 0.00 | 0.33 | |
| plotSeqLengthDistn-methods | 0.84 | 0.01 | 0.86 | |
| plotSeqQuals-methods | 0.52 | 0.03 | 0.54 | |
| plotSummary-methods | 0.36 | 0.00 | 0.36 | |
| pwf | 0 | 0 | 0 | |
| readTotals | 0.24 | 0.00 | 0.23 | |
| writeHtmlReport | 0 | 0 | 0 | |