| Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-03-18 11:07:37 -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 | ||||
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To the developers/maintainers of the GenomicDistributions package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicDistributions.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 752/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenomicDistributions 1.3.5 (landing page) Kristyna Kupkova
| 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: GenomicDistributions |
| Version: 1.3.5 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomicDistributions.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings GenomicDistributions_1.3.5.tar.gz |
| StartedAt: 2022-03-17 19:10:50 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:13:15 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 144.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GenomicDistributions.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomicDistributions.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings GenomicDistributions_1.3.5.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/GenomicDistributions.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 'GenomicDistributions/DESCRIPTION' ... OK * this is package 'GenomicDistributions' version '1.3.5' * 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 'GenomicDistributions' 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
GenomicDistributions.Rcheck/00install.out
##############################################################################
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### Running command:
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### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL GenomicDistributions
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'GenomicDistributions' ...
** 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 'GenomicDistributions'
finding HTML links ... done
BSdtToGRanges html
GenomicDistributions html
TSS_hg19 html
binBSGenome html
binChroms html
binRegion html
calcChromBins html
calcChromBinsRef html
calcChromBinsRefSlow html
calcCumulativePartitions html
calcCumulativePartitionsRef html
calcDinuclFreq html
calcDinuclFreqRef html
calcExpectedPartitions html
calcExpectedPartitionsRef html
calcFeatureDist html
calcFeatureDistRefTSS html
calcGCContent html
calcGCContentRef html
calcNearestNeighbors html
calcNeighborDist html
calcPartitions html
calcPartitionsRef html
calcSummarySignal html
calcWidth html
cellTypeMetadata html
chromSizes_hg19 html
dot-requireAndReturn html
dot-validateInputs html
dtToGr html
dtToGrInternal html
exampleOpenSignalMatrix_hg19 html
geneModels_hg19 html
genomePartitionList html
getChromSizes html
getChromSizesFromFasta html
getGeneModels html
getGeneModelsFromGTF html
getGenomeBins html
getReferenceData html
getTssFromGTF html
grToDt html
labelCuts html
loadBSgenome html
loadEnsDb html
neighbordt html
nlist html
plotChromBins html
plotCumulativePartitions html
plotDinuclFreq html
plotExpectedPartitions html
plotFeatureDist html
plotGCContent html
plotNeighborDist html
plotPartitions html
plotQTHist html
plotSummarySignal html
retrieveFile html
setB_100 html
splitDataTable html
theme_blank_facet_label html
vistaEnhancers html
** 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 (GenomicDistributions)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'frenchFISH' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'treeio' is missing or broken
done
GenomicDistributions.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("GenomicDistributions")
Loading required package: IRanges
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: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
>
> test_check("GenomicDistributions")
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 48 ]
== Skipped tests ===============================================================
* empty test (1)
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 48 ]
>
> proc.time()
user system elapsed
18.07 2.26 20.28
GenomicDistributions.Rcheck/GenomicDistributions-Ex.timings
| name | user | system | elapsed | |
| binBSGenome | 0 | 0 | 0 | |
| binChroms | 0.02 | 0.00 | 0.01 | |
| binRegion | 0 | 0 | 0 | |
| calcChromBins | 1.33 | 0.02 | 1.35 | |
| calcChromBinsRef | 0.01 | 0.00 | 0.01 | |
| calcChromBinsRefSlow | 0.00 | 0.00 | 0.02 | |
| calcCumulativePartitions | 1.66 | 0.08 | 1.73 | |
| calcCumulativePartitionsRef | 1.42 | 0.17 | 1.60 | |
| calcDinuclFreq | 0 | 0 | 0 | |
| calcDinuclFreqRef | 0 | 0 | 0 | |
| calcExpectedPartitions | 1.17 | 0.14 | 1.31 | |
| calcExpectedPartitionsRef | 1.17 | 0.17 | 1.34 | |
| calcFeatureDist | 0.08 | 0.00 | 0.08 | |
| calcFeatureDistRefTSS | 0.13 | 0.02 | 0.14 | |
| calcGCContent | 0 | 0 | 0 | |
| calcGCContentRef | 0 | 0 | 0 | |
| calcNearestNeighbors | 0.03 | 0.00 | 0.03 | |
| calcNeighborDist | 0.03 | 0.00 | 0.04 | |
| calcPartitions | 0.92 | 0.17 | 1.09 | |
| calcPartitionsRef | 0.97 | 0.15 | 1.12 | |
| calcSummarySignal | 0.03 | 0.00 | 0.04 | |
| calcWidth | 0 | 0 | 0 | |
| dot-validateInputs | 0 | 0 | 0 | |
| dtToGr | 0 | 0 | 0 | |
| genomePartitionList | 1.25 | 0.22 | 1.46 | |
| getChromSizes | 0 | 0 | 0 | |
| getChromSizesFromFasta | 0.02 | 0.00 | 0.02 | |
| getGeneModels | 0.06 | 0.00 | 0.06 | |
| getGeneModelsFromGTF | 3.97 | 0.38 | 4.35 | |
| getGenomeBins | 0.73 | 0.00 | 0.73 | |
| getTssFromGTF | 0.08 | 0.00 | 0.08 | |
| loadBSgenome | 0 | 0 | 0 | |
| loadEnsDb | 0 | 0 | 0 | |
| nlist | 0 | 0 | 0 | |
| plotChromBins | 0.03 | 0.00 | 0.03 | |
| plotCumulativePartitions | 1.83 | 0.17 | 2.00 | |
| plotDinuclFreq | 0.02 | 0.00 | 0.02 | |
| plotExpectedPartitions | 1.01 | 0.06 | 1.07 | |
| plotFeatureDist | 0.14 | 0.00 | 0.14 | |
| plotGCContent | 0.02 | 0.00 | 0.02 | |
| plotNeighborDist | 0.01 | 0.00 | 0.02 | |
| plotPartitions | 1.47 | 0.16 | 1.62 | |
| plotQTHist | 0.02 | 0.00 | 0.02 | |
| plotSummarySignal | 0.06 | 0.00 | 0.06 | |
| retrieveFile | 0 | 0 | 0 | |