Stuart Lee
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/plyranges |
| git_branch: master |
| git_last_commit: 1263a98 |
| git_last_commit_date: 2021-10-26 12:43:21 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:19 -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 plyranges package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/plyranges.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 1441/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| plyranges 1.15.0 (landing page) Stuart Lee
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: plyranges |
| Version: 1.15.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:plyranges.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings plyranges_1.15.0.tar.gz |
| StartedAt: 2022-03-17 19:53:30 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:57:20 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 230.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: plyranges.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:plyranges.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings plyranges_1.15.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/plyranges.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 'plyranges/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'plyranges' version '1.15.0'
* 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 'plyranges' 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 ... WARNING
Missing link or links in documentation object 'ranges-info.Rd':
'[GenomeInfoDb:fetchExtendedChromInfoFromUCSC]{GenomeInfoDb::fetchExtendedChromInfoFromUCSC()}'
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 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: 1 WARNING
See
'D:/biocbuild/bbs-3.15-bioc/meat/plyranges.Rcheck/00check.log'
for details.
plyranges.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL plyranges
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'plyranges' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'plyranges'
finding HTML links ... done
add-nearest-distance html
as_ranges html
finding level-2 HTML links ... done
compute_coverage html
element-setops html
filter-ranges html
group_by-ranges html
io-bam-read html
io-bed-read html
io-bed-write html
io-bigwig-read html
io-bigwig-write html
io-gff-read html
io-gff-write html
io-wig-read html
io-wig-write html
mutate-ranges html
n html
n_distinct html
overlap-joins html
overscope_ranges html
plyranges-package html
ranges-anchor html
ranges-arrange html
ranges-bind html
ranges-chop html
ranges-class html
ranges-construct html
ranges-count-overlaps html
ranges-deferred html
ranges-disjoin html
ranges-expand html
ranges-filter-overlaps html
ranges-flank html
ranges-follow html
ranges-info html
ranges-interweave html
ranges-names html
ranges-nearest html
ranges-overlaps-self html
ranges-overlaps html
ranges-pairs html
ranges-precede html
ranges-reduce html
ranges-select html
ranges-setops html
ranges-setters html
ranges-shift html
ranges-summarise html
ranges-tile html
slice-ranges html
stretch html
tidyverse-reexports 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 (plyranges)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'TFBSTools' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'VarCon' is missing or broken
done
plyranges.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(plyranges)
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: IRanges
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
Attaching package: 'plyranges'
The following object is masked from 'package:IRanges':
slice
The following object is masked from 'package:stats':
filter
>
> test_check("plyranges")
[ FAIL 0 | WARN 7 | SKIP 2 | PASS 383 ]
== Skipped tests ===============================================================
* On Windows (2)
[ FAIL 0 | WARN 7 | SKIP 2 | PASS 383 ]
>
> proc.time()
user system elapsed
31.32 2.43 33.73
plyranges.Rcheck/plyranges-Ex.timings
| name | user | system | elapsed | |
| add-nearest-distance | 0.48 | 0.00 | 0.48 | |
| as_ranges | 0.08 | 0.00 | 0.08 | |
| compute_coverage | 0.02 | 0.00 | 0.02 | |
| element-setops | 0.08 | 0.00 | 0.08 | |
| filter-ranges | 0.39 | 0.08 | 0.47 | |
| group_by-ranges | 0.29 | 0.02 | 0.31 | |
| io-bam-read | 1.33 | 0.04 | 1.37 | |
| io-bed-read | 2.89 | 0.92 | 3.81 | |
| io-bed-write | 0 | 0 | 0 | |
| io-bigwig-read | 0 | 0 | 0 | |
| io-bigwig-write | 0 | 0 | 0 | |
| io-gff-read | 0.33 | 0.00 | 0.33 | |
| io-gff-write | 0 | 0 | 0 | |
| io-wig-read | 0.25 | 0.00 | 0.25 | |
| mutate-ranges | 0.60 | 0.00 | 0.61 | |
| n | 0.18 | 0.00 | 0.17 | |
| n_distinct | 0.03 | 0.00 | 0.03 | |
| overlap-joins | 0.12 | 0.00 | 0.13 | |
| ranges-anchor | 0.07 | 0.02 | 0.07 | |
| ranges-arrange | 0.03 | 0.00 | 0.04 | |
| ranges-bind | 0.11 | 0.00 | 0.11 | |
| ranges-chop | 0.26 | 0.00 | 0.26 | |
| ranges-construct | 0.08 | 0.00 | 0.08 | |
| ranges-count-overlaps | 0.05 | 0.00 | 0.05 | |
| ranges-disjoin | 0.62 | 0.00 | 0.63 | |
| ranges-expand | 0.39 | 0.00 | 0.39 | |
| ranges-filter-overlaps | 0.06 | 0.00 | 0.06 | |
| ranges-flank | 0.07 | 0.00 | 0.06 | |
| ranges-follow | 0.11 | 0.00 | 0.11 | |
| ranges-info | 0.03 | 0.00 | 0.03 | |
| ranges-interweave | 0.09 | 0.00 | 0.10 | |
| ranges-names | 0.16 | 0.00 | 0.15 | |
| ranges-nearest | 0.28 | 0.00 | 0.28 | |
| ranges-overlaps-self | 0.09 | 0.00 | 0.10 | |
| ranges-overlaps | 0.11 | 0.00 | 0.11 | |
| ranges-pairs | 0.27 | 0.00 | 0.26 | |
| ranges-precede | 0.12 | 0.00 | 0.13 | |
| ranges-reduce | 0.57 | 0.00 | 0.56 | |
| ranges-select | 0.04 | 0.00 | 0.05 | |
| ranges-setops | 0.49 | 0.00 | 0.48 | |
| ranges-shift | 0.09 | 0.00 | 0.10 | |
| ranges-summarise | 0.14 | 0.00 | 0.14 | |
| ranges-tile | 0.06 | 0.00 | 0.06 | |
| slice-ranges | 0.39 | 0.00 | 0.39 | |
| stretch | 0.16 | 0.00 | 0.16 | |