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This page was generated on 2025-09-27 12:05 -0400 (Sat, 27 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4832
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4620
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4565
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4563
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 1598/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
plyxp 1.3.9  (landing page)
Justin Landis
Snapshot Date: 2025-09-26 13:45 -0400 (Fri, 26 Sep 2025)
git_url: https://git.bioconductor.org/packages/plyxp
git_branch: devel
git_last_commit: eda1814
git_last_commit_date: 2025-09-25 13:42:38 -0400 (Thu, 25 Sep 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    ERROR    OK  
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for plyxp on lconway

To the developers/maintainers of the plyxp package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/plyxp.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.

raw results


Summary

Package: plyxp
Version: 1.3.9
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:plyxp.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings plyxp_1.3.9.tar.gz
StartedAt: 2025-09-26 23:19:01 -0400 (Fri, 26 Sep 2025)
EndedAt: 2025-09-26 23:22:18 -0400 (Fri, 26 Sep 2025)
EllapsedTime: 197.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: plyxp.Rcheck
Warnings: NA

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:plyxp.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings plyxp_1.3.9.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/plyxp.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘plyxp/DESCRIPTION’ ... OK
* this is package ‘plyxp’ version ‘1.3.9’
* 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 ‘plyxp’ 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 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 ... ERROR
Running examples in ‘plyxp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: vectors
> ### Title: S7 classes for vctrs and S4 Vectors
> ### Aliases: vectors class_vctrs class_s4_vctrs class_DF
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # used for defining methods on S7 generics
> 
> S7::method(vec_slice, class_vctrs)
Error in as_dispatch(generic, class = class, object = object) : 
  Can't dispatch on unions; must be a concrete type
Calls: <Anonymous> -> as_dispatch
Execution halted
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/plyxp.Rcheck/00check.log’
for details.


Installation output

plyxp.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL plyxp
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘plyxp’ ...
** this is package ‘plyxp’ version ‘1.3.9’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘rownames’ from package ‘base’ in package ‘plyxp’
Creating a generic function for ‘colnames’ from package ‘base’ in package ‘plyxp’
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘plyxp’
Creating a generic function for ‘ncol’ from package ‘base’ in package ‘plyxp’
** 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 (plyxp)

Tests output

plyxp.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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("plyxp")

Attaching package: 'plyxp'

The following object is masked from 'package:stats':

    filter

> 
> test_check("plyxp")
[ FAIL 0 | WARN 0 | SKIP 6 | PASS 172 ]

══ Skipped tests (6) ═══════════════════════════════════════════════════════════
• On CRAN (6): 'test_printing.R:2:3', 'test_printing.R:6:3',
  'test_printing.R:13:3', 'test_printing.R:20:3', 'test_printing.R:24:3',
  'test_printing.R:28:3'

[ FAIL 0 | WARN 0 | SKIP 6 | PASS 172 ]
> 
> proc.time()
   user  system elapsed 
 15.732   0.795  16.662 

Example timings

plyxp.Rcheck/plyxp-Ex.timings

nameusersystemelapsed
PlySummarizedExperiment-methods0.0440.0060.049
arrange0.5570.0160.575
as.data.frame0.0070.0010.008
dot-pronouns0.1420.0090.152
filter0.5080.0130.523
group_by0.2140.0030.217
group_data0.1610.0020.163
group_vars0.0740.0000.075
mutate0.1770.0010.178
new_plyxp0.0910.0010.093
plyxp-context0.1350.0010.137
plyxp-printing0.2920.0090.303
plyxp0.1040.0010.106
pull0.0710.0020.073
reexports0.2660.0030.270
se_simple0.0080.0010.009
select0.5160.0050.524
slice0.3210.0020.324
summarize0.6170.0050.623
vctrs-vec_recycle0.0110.0000.012
vctrs-vec_rep0.0290.0000.030
vctrs_slice0.0070.0000.007