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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:DeconvoBuddies.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings DeconvoBuddies_1.3.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/DeconvoBuddies.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-27 03:07:03 UTC
* checking for file ‘DeconvoBuddies/DESCRIPTION’ ... OK
* this is package ‘DeconvoBuddies’ version ‘1.3.3’
* 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 ‘DeconvoBuddies’ 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:
  findMarkers_1vAll.Rd: BiocParallelParam-class
  get_mean_ratio.Rd: BiocParallelParam-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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning in .local(x, ...) : 'pairwiseTTests' is deprecated.
  Warning in .local(x, ...) : 'pairwiseTTests' is deprecated.
  Warning in .local(x, ...) : 'pairwiseTTests' is deprecated.
  Warning in .local(x, ...) : 'pairwiseTTests' is deprecated.
  Warning in .local(x, ...) : 'pairwiseTTests' is deprecated.
  Warning in .local(x, ...) : 'pairwiseTTests' is deprecated.
  Warning in .local(x, ...) : 'pairwiseTTests' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
plot_marker_express_ALL  25.860  1.462  27.537
plot_gene_express        11.197  0.748  12.171
findMarkers_1vAll         8.501  0.762   9.491
fetch_deconvo_data        5.940  0.411   6.835
plot_marker_express_List  4.676  0.448   5.352
* 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 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/DeconvoBuddies.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL DeconvoBuddies
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘DeconvoBuddies’ ...
** this is package ‘DeconvoBuddies’ version ‘1.3.3’
** 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 (DeconvoBuddies)

R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 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(DeconvoBuddies)
> 
> test_check("DeconvoBuddies")
2026-04-26 23:14:19.250442 Access ExperimentHub EH9626
see ?DeconvoBuddies and browseVignettes('DeconvoBuddies') for documentation
loading from cache
2026-04-26 23:14:39.261814 Access ExperimentHub EH9626
see ?DeconvoBuddies and browseVignettes('DeconvoBuddies') for documentation
loading from cache
2026-04-26 23:14:46.013978 Access ExperimentHub EH9626
see ?DeconvoBuddies and browseVignettes('DeconvoBuddies') for documentation
loading from cache
2026-04-26 23:14:49.047582 Access ExperimentHub EH9626
see ?DeconvoBuddies and browseVignettes('DeconvoBuddies') for documentation
loading from cache
2026-04-26 23:14:53.402709 Access ExperimentHub EH9626
see ?DeconvoBuddies and browseVignettes('DeconvoBuddies') for documentation
loading from cache
[ FAIL 0 | WARN 69 | SKIP 0 | PASS 35 ]

[ FAIL 0 | WARN 69 | SKIP 0 | PASS 35 ]
> 
> proc.time()
   user  system elapsed 
 53.151   4.866  59.553