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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mia.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mia_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/mia.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mia/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mia’ version ‘1.14.0’
* 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 ‘mia’ 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘topicdoc’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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
Unknown package ‘https’ in Rd xrefs
* 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 ... NOTE
  Note: found 101 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
addNMF                  123.151 21.806 116.461
calculateDMN             99.980  0.235 101.164
hierarchy-tree           49.658  2.116  53.294
agglomerate-methods      39.256  1.055  40.756
addAlpha                 21.293  0.531  22.244
transformAssay           19.545  0.371  20.271
getCrossAssociation      14.520  0.084  14.660
getPrevalence            13.288  0.116  14.008
addLDA                   11.924  0.171  12.253
mergeSEs                 11.850  0.211  12.934
convertFromDADA2         11.348  0.446  11.964
splitOn                  10.816  0.091  11.268
runCCA                    8.822  0.187   9.335
getDissimilarity          8.034  0.636   8.664
summaries                 8.377  0.070   8.769
convertFromPhyloseq       6.723  0.160   6.897
importMetaPhlAn           5.970  0.169   7.122
getDominant               5.484  0.063   5.588
agglomerateByPrevalence   4.905  0.069   5.025
addDivergence             4.572  0.375   5.088
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’