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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:tidyomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings tidyomics_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/tidyomics.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tidyomics/DESCRIPTION’ ... OK
* this is package ‘tidyomics’ version ‘1.3.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘tidyomics’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 whether startup messages can be suppressed ... 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 ... WARNING
Undocumented code objects:
  ‘tidyomics’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/tidyomics.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL tidyomics
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘tidyomics’ ...
** using staged installation
** R
** 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 (tidyomics)

R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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.

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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/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(tidyomics)
── Attaching core tidyomics packages ──────────────────────── tidyomics 1.3.0 ──
✔ dplyr                    1.1.4      ✔ tidySummarizedExperiment 1.17.0
✔ ggplot2                  3.5.1      ✔ tidybulk                 1.19.0
✔ nullranges               1.13.0     ✔ tidyr                    1.3.1 
✔ plyranges                1.27.0     ✔ tidyseurat               0.8.0 
✔ tidySingleCellExperiment 1.17.0     
── Conflicts ────────────────────────────────────────── tidyomics_conflicts() ──
✖ plyranges::between()     masks dplyr::between()
✖ tidybulk::bind_cols()    masks ttservice::bind_cols(), dplyr::bind_cols()
✖ plyranges::filter()      masks tidybulk::filter(), dplyr::filter(), stats::filter()
✖ S4Vectors::findMatches() masks utils::findMatches()
✖ S4Vectors::head()        masks utils::head()
✖ plyranges::n()           masks dplyr::n()
✖ plyranges::n_distinct()  masks dplyr::n_distinct()
✖ IRanges::relist()        masks BiocGenerics::relist(), utils::relist()
✖ tidybulk::rename()       masks S4Vectors::rename(), dplyr::rename()
✖ plyranges::slice()       masks IRanges::slice(), dplyr::slice()
✖ IRanges::stack()         masks S4Vectors::stack(), utils::stack()
✖ S4Vectors::tail()        masks utils::tail()
✖ tidyseurat::tidy()       masks tidySingleCellExperiment::tidy(), tidySummarizedExperiment::tidy(), generics::tidy()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
> 
> test_check("tidyomics")
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 0 ]

══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On CRAN (3): 'test-attach.R:2:3', 'test-attach.R:7:3', 'test-attach.R:13:3'

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
  6.047   0.245   6.293