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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:HCATonsilData.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings HCATonsilData_1.5.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/HCATonsilData.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘HCATonsilData/DESCRIPTION’ ... OK
* this is package ‘HCATonsilData’ version ‘1.5.0’
* 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 ‘HCATonsilData’ 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  HCATonsilData.Rd: SingleCellExperiment-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... INFO
  Note: found 5 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
HCATonsilData 8.049  0.978   9.716
* 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-3.21-data-experiment/meat/HCATonsilData.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL HCATonsilData
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘HCATonsilData’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (HCATonsilData)

R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
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.

> library(testthat)
> library(HCATonsilData)
> 
> test_check("HCATonsilData")
see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation
loading from cache
require("rhdf5")
see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation
loading from cache
require("S4Vectors")
see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation
loading from cache
see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation
loading from cache
see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation
loading from cache
see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation
loading from cache
see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation
loading from cache
see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation
loading from cache
see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation
loading from cache
see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation
loading from cache
see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation
loading from cache
see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation
loading from cache
see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation
loading from cache
see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation
loading from cache
see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation
loading from cache
see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation
loading from cache
see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation
loading from cache
see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation
loading from cache
see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation
loading from cache
see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation
loading from cache
see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation
loading from cache
see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation
loading from cache
see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation
loading from cache
see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation
loading from cache
see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation
loading from cache
see ?HCATonsilData and browseVignettes('HCATonsilData') for documentation
loading from cache
/usr/bin/pandoc +RTS -K512m -RTS file3dbe4e42239d9 --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output file3dbe4e42239d9.html --lua-filter /home/biocbuild/bbs-3.21-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.21-bioc/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --variable bs3=TRUE --section-divs --template /home/biocbuild/bbs-3.21-bioc/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=bootstrap --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/RtmpUCIAVB/rmarkdown-str3dbe4e4e8a5411.html 
[WARNING] This document format requires a nonempty <title> element.
  Defaulting to 'file3dbe4e42239d9' as the title.
  To specify a title, use 'title' in metadata or --metadata title="...".

Output created: file3dbe4e42239d9.html
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 33 ]
> 
> proc.time()
   user  system elapsed 
 40.089   2.410  45.244 
xdg-open: file '/tmp/RtmpUCIAVB/file3dbe4e42239d9.html' does not exist