| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-01 11:36:03 -0400 (Wed, 01 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4518 |
| 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 1584/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| plyinteractions 1.2.0 (landing page) Jacques Serizay
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the plyinteractions package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/plyinteractions.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: plyinteractions |
| Version: 1.2.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:plyinteractions.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings plyinteractions_1.2.0.tar.gz |
| StartedAt: 2024-05-01 08:42:31 -0400 (Wed, 01 May 2024) |
| EndedAt: 2024-05-01 08:58:57 -0400 (Wed, 01 May 2024) |
| EllapsedTime: 985.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: plyinteractions.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:plyinteractions.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings plyinteractions_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/plyinteractions.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘plyinteractions/DESCRIPTION’ ... OK
* this is package ‘plyinteractions’ version ‘1.2.0’
* 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 ‘plyinteractions’ 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 loading without being on the library search path ... 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 ... NOTE
count.GInteractions: no visible binding for global variable ‘group’
Undefined global functions or variables:
group
* 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 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.19-bioc/meat/plyinteractions.Rcheck/00check.log’
for details.
plyinteractions.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL plyinteractions ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘plyinteractions’ ... ** using staged installation ** R ** data ** 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 (plyinteractions)
plyinteractions.Rcheck/tests/testthat.Rout
R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(plyinteractions)
Attaching package: 'plyinteractions'
The following object is masked from 'package:stats':
filter
>
> gi <- read.table(text = "
+ chr1 11 20 chr1 21 30 + +
+ chr1 11 20 chr1 51 55 + +
+ chr1 11 30 chr1 51 55 - -
+ chr1 11 30 chr2 51 60 - -",
+ col.names = c(
+ "seqnames1", "start1", "end1",
+ "seqnames2", "start2", "end2", "strand1", "strand2")
+ ) |>
+ as_ginteractions() |>
+ mutate(score = runif(4), type = c('cis', 'cis', 'cis', 'trans'))
>
> test_check("plyinteractions")
GInteractions object with 4 interactions and 2 metadata columns:
seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | score
<Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <numeric>
[1] chr1 11-20 + --- chr1 21-30 + | 0.86091538
[2] chr1 11-20 + --- chr1 51-55 + | 0.64031061
[3] chr1 11-30 - --- chr1 51-55 - | 0.00949576
[4] chr1 11-30 - --- chr2 51-60 - | 0.23255051
type
<character>
[1] cis
[2] cis
[3] cis
[4] trans
-------
regions: 6 ranges and 0 metadata columns
seqinfo: 2 sequences from an unspecified genome; no seqlengths
PinnedGInteractions object with 4 interactions and 2 metadata columns:
Pinned on: anchors2
seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | score
<Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <numeric>
[1] chr1 11-20 + --- chr1 21-30 + | 0.86091538
[2] chr1 11-20 + --- chr1 51-55 + | 0.64031061
[3] chr1 11-30 - --- chr1 51-55 - | 0.00949576
[4] chr1 11-30 - --- chr2 51-60 - | 0.23255051
type
<character>
[1] cis
[2] cis
[3] cis
[4] trans
-------
regions: 6 ranges and 0 metadata columns
seqinfo: 2 sequences from an unspecified genome; no seqlengths
AnchoredPinnedGInteractions object with 4 interactions and 2 metadata columns:
Pinned on: anchors2 | Anchored by: 5p
seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | score
<Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <numeric>
[1] chr1 11-20 + --- chr1 21-30 + | 0.86091538
[2] chr1 11-20 + --- chr1 51-55 + | 0.64031061
[3] chr1 11-30 - --- chr1 51-55 - | 0.00949576
[4] chr1 11-30 - --- chr2 51-60 - | 0.23255051
type
<character>
[1] cis
[2] cis
[3] cis
[4] trans
-------
regions: 6 ranges and 0 metadata columns
seqinfo: 2 sequences from an unspecified genome; no seqlengths
GroupedGInteractions object with 4 interactions and 3 metadata columns:
Groups: group [2]
seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | score
<Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <numeric>
[1] chr1 11-20 + --- chr1 21-30 + | 0.86091538
[2] chr1 11-20 + --- chr1 51-55 + | 0.64031061
[3] chr1 11-30 - --- chr1 51-55 - | 0.00949576
[4] chr1 11-30 - --- chr2 51-60 - | 0.23255051
type group
<character> <numeric>
[1] cis 1
[2] cis 1
[3] cis 2
[4] trans 2
-------
regions: 6 ranges and 0 metadata columns
seqinfo: 2 sequences from an unspecified genome; no seqlengths
AnchoredPinnedGInteractions object with 4 interactions and 2 metadata columns:
Pinned on: anchors2 | Anchored by: 5p
seqnames1 ranges1 strand1 seqnames2 ranges2 strand2 | score
<Rle> <IRanges> <Rle> <Rle> <IRanges> <Rle> | <numeric>
[1] chr1 11-20 + --- chr1 21-30 + | 0.86091538
[2] chr1 11-20 + --- chr1 51-55 + | 0.64031061
[3] chr1 11-30 - --- chr1 51-55 - | 0.00949576
[4] chr1 11-30 - --- chr2 51-60 - | 0.23255051
type
<character>
[1] cis
[2] cis
[3] cis
[4] trans
-------
regions: 6 ranges and 0 metadata columns
seqinfo: 2 sequences from an unspecified genome; no seqlengths
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 177 ]
>
> proc.time()
user system elapsed
24.004 1.239 25.234
plyinteractions.Rcheck/plyinteractions-Ex.timings
| name | user | system | elapsed | |
| dplyr-arrange | 0.758 | 0.012 | 0.770 | |
| dplyr-count | 1.411 | 0.069 | 1.479 | |
| dplyr-filter | 0.500 | 0.092 | 0.592 | |
| dplyr-group_by | 0.668 | 0.028 | 0.696 | |
| dplyr-mutate | 1.308 | 0.016 | 1.324 | |
| dplyr-rename | 0.150 | 0.000 | 0.151 | |
| dplyr-select | 0.293 | 0.008 | 0.300 | |
| dplyr-slice | 0.093 | 0.004 | 0.097 | |
| dplyr-summarize | 0.618 | 0.011 | 0.629 | |
| ginteractions-anchor | 0.167 | 0.004 | 0.171 | |
| ginteractions-annotate | 2.764 | 0.176 | 2.941 | |
| ginteractions-construct | 0.696 | 0.036 | 0.734 | |
| ginteractions-count-overlaps | 0.340 | 0.000 | 0.341 | |
| ginteractions-filter-overlaps | 0.448 | 0.012 | 0.460 | |
| ginteractions-find-overlaps | 0.524 | 0.040 | 0.564 | |
| ginteractions-getters | 0.148 | 0.001 | 0.149 | |
| ginteractions-join-overlap-left | 0.641 | 0.014 | 0.655 | |
| ginteractions-pin | 0.228 | 0.004 | 0.232 | |
| group-group_data | 0.213 | 0.020 | 0.233 | |
| plyranges-flank | 0.391 | 0.000 | 0.392 | |
| plyranges-shift | 0.515 | 0.016 | 0.531 | |
| plyranges-stretch | 0.586 | 0.000 | 0.586 | |
| reexports | 0.001 | 0.000 | 0.000 | |
| replace_anchors | 0.625 | 0.012 | 0.636 | |