Stuart Lee
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/plyranges |
| Branch: RELEASE_3_12 |
| Last Commit: 5856b8c |
| Last Changed Date: 2020-10-27 11:34:01 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:32:47 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the plyranges package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1361/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| plyranges 1.10.0 (landing page) Stuart Lee
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: plyranges |
| Version: 1.10.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:plyranges.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings plyranges_1.10.0.tar.gz |
| StartedAt: 2021-05-06 05:37:09 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 05:44:52 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 462.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: plyranges.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:plyranges.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings plyranges_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/plyranges.Rcheck' * using R version 4.0.5 (2021-03-31) * 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 '1.10.0' * 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 ... WARNING Found the following significant warnings: Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUTZf9b/R.INSTALLa28161c7237/plyranges/man/as_ranges.Rd:34: file link 'AtomicList' in package 'IRanges' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUTZf9b/R.INSTALLa28161c7237/plyranges/man/io-bam-read.Rd:79: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUTZf9b/R.INSTALLa28161c7237/plyranges/man/io-bigwig-read.Rd:34: file link 'BigWigFile-class' in package 'rtracklayer' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUTZf9b/R.INSTALLa28161c7237/plyranges/man/io-bigwig-write.Rd:37: file link 'BigWigFile-class' in package 'rtracklayer' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUTZf9b/R.INSTALLa28161c7237/plyranges/man/overscope_ranges.Rd:24: file link 'new_data_mask' in package 'rlang' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUTZf9b/R.INSTALLa28161c7237/plyranges/man/tidyverse-reexports.Rd:27: file link 'group_vars' in package 'dplyr' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUTZf9b/R.INSTALLa28161c7237/plyranges/man/tidyverse-reexports.Rd:27: file link 'groups' in package 'dplyr' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUTZf9b/R.INSTALLa28161c7237/plyranges/man/tidyverse-reexports.Rd:27: file link 'summarize' in package 'dplyr' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUTZf9b/R.INSTALLa28161c7237/plyranges/man/tidyverse-reexports.Rd:27: file link 'ungroup' in package 'dplyr' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUTZf9b/R.INSTALLa28161c7237/plyranges/man/tidyverse-reexports.Rd:29: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUTZf9b/R.INSTALLa28161c7237/plyranges/man/tidyverse-reexports.Rd:31: file link '!!' in package 'rlang' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUTZf9b/R.INSTALLa28161c7237/plyranges/man/tidyverse-reexports.Rd:31: file link '!!!' in package 'rlang' does not exist and so has been treated as a topic See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/plyranges.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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... 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 'C:/Users/biocbuild/bbs-3.12-bioc/meat/plyranges.Rcheck/00check.log' for details.
plyranges.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/plyranges_1.10.0.tar.gz && rm -rf plyranges.buildbin-libdir && mkdir plyranges.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=plyranges.buildbin-libdir plyranges_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL plyranges_1.10.0.zip && rm plyranges_1.10.0.tar.gz plyranges_1.10.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 677k 100 677k 0 0 32.8M 0 --:--:-- --:--:-- --:--:-- 34.7M
install for i386
* 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
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUTZf9b/R.INSTALLa28161c7237/plyranges/man/as_ranges.Rd:34: file link 'AtomicList' in package 'IRanges' does not exist and so has been treated as a topic
compute_coverage html
element-setops html
filter-ranges html
group_by-ranges html
io-bam-read html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUTZf9b/R.INSTALLa28161c7237/plyranges/man/io-bam-read.Rd:79: file link 'BamFile' in package 'Rsamtools' does not exist and so has been treated as a topic
io-bed-read html
io-bed-write html
io-bigwig-read html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUTZf9b/R.INSTALLa28161c7237/plyranges/man/io-bigwig-read.Rd:34: file link 'BigWigFile-class' in package 'rtracklayer' does not exist and so has been treated as a topic
io-bigwig-write html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUTZf9b/R.INSTALLa28161c7237/plyranges/man/io-bigwig-write.Rd:37: file link 'BigWigFile-class' in package 'rtracklayer' does not exist and so has been treated as a topic
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
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUTZf9b/R.INSTALLa28161c7237/plyranges/man/overscope_ranges.Rd:24: file link 'new_data_mask' in package 'rlang' does not exist and so has been treated as a topic
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
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUTZf9b/R.INSTALLa28161c7237/plyranges/man/tidyverse-reexports.Rd:27: file link 'group_vars' in package 'dplyr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUTZf9b/R.INSTALLa28161c7237/plyranges/man/tidyverse-reexports.Rd:27: file link 'groups' in package 'dplyr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUTZf9b/R.INSTALLa28161c7237/plyranges/man/tidyverse-reexports.Rd:27: file link 'summarize' in package 'dplyr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUTZf9b/R.INSTALLa28161c7237/plyranges/man/tidyverse-reexports.Rd:27: file link 'ungroup' in package 'dplyr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUTZf9b/R.INSTALLa28161c7237/plyranges/man/tidyverse-reexports.Rd:29: file link '%>%' in package 'magrittr' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUTZf9b/R.INSTALLa28161c7237/plyranges/man/tidyverse-reexports.Rd:31: file link '!!' in package 'rlang' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpUTZf9b/R.INSTALLa28161c7237/plyranges/man/tidyverse-reexports.Rd:31: file link '!!!' in package 'rlang' does not exist and so has been treated as a topic
*** 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
install for x64
* installing *source* package 'plyranges' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'plyranges' as plyranges_1.10.0.zip
* DONE (plyranges)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'plyranges' successfully unpacked and MD5 sums checked
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plyranges.Rcheck/tests_i386/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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 object is masked from 'package:base':
expand.grid
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")
== Skipped tests ===============================================================
* On Windows (1)
[ FAIL 0 | WARN 7 | SKIP 1 | PASS 385 ]
>
> proc.time()
user system elapsed
62.84 2.59 67.12
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plyranges.Rcheck/tests_x64/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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 object is masked from 'package:base':
expand.grid
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")
== Skipped tests ===============================================================
* On Windows (1)
[ FAIL 0 | WARN 7 | SKIP 1 | PASS 385 ]
>
> proc.time()
user system elapsed
46.21 1.32 49.18
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plyranges.Rcheck/examples_i386/plyranges-Ex.timings
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plyranges.Rcheck/examples_x64/plyranges-Ex.timings
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