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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DeconvoBuddies.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DeconvoBuddies_1.3.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/DeconvoBuddies.Rcheck’
* using R version 4.6.0 alpha (2026-04-08 r89818)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-24 23:20:51 UTC
* using option ‘--no-vignettes’
* 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 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 9.458  0.328   10.15
* 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-3.23-bioc/meat/DeconvoBuddies.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DeconvoBuddies
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/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 alpha (2026-04-08 r89818)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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")
2026-04-24 19:23:47.560783 Access ExperimentHub EH9626
see ?DeconvoBuddies and browseVignettes('DeconvoBuddies') for documentation
loading from cache
2026-04-24 19:23:55.664506 Access ExperimentHub EH9626
see ?DeconvoBuddies and browseVignettes('DeconvoBuddies') for documentation
loading from cache
2026-04-24 19:23:57.755896 Access ExperimentHub EH9626
see ?DeconvoBuddies and browseVignettes('DeconvoBuddies') for documentation
loading from cache
2026-04-24 19:23:58.853899 Access ExperimentHub EH9626
see ?DeconvoBuddies and browseVignettes('DeconvoBuddies') for documentation
loading from cache
2026-04-24 19:24:01.022285 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 
 21.717   1.229  24.956