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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:autonomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings autonomics_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/autonomics.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘autonomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘autonomics’ version ‘1.2.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘autonomics’ 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 R 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 ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'normimpute'
  ‘ref’ ‘pos’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
read_rnaseq_counts           25.666  0.988  26.765
is_sig                       25.194  0.109  25.331
filter_medoid                22.796  0.840  23.660
pca                          20.096  0.265  20.411
explore_imputations          17.626  0.278  17.918
read_somascan                17.001  0.254  17.274
fit_limma                    16.647  0.195  16.853
plot_detections              14.516  0.287  14.831
read_rectangles              13.315  0.500  13.824
summarize_fit                12.413  0.295  12.716
biplot_covariates            12.431  0.256  12.701
read_metabolon               11.822  0.317  12.153
plot_venn                     9.570  0.148   9.725
plot_features                 8.959  0.162   9.188
sumexp_to_long_dt             8.524  0.334   8.942
subtract_baseline             8.375  0.215   8.602
explore_transformations       7.829  0.199   8.036
plot_violins                  7.576  0.163   7.749
log2transform                 7.584  0.119   7.715
read_proteingroups            7.510  0.108   7.626
analyze                       7.311  0.294   7.617
plot_boxplots                 6.894  0.145   7.045
biplot_corrections            6.655  0.246   6.911
biplot                        5.039  0.211   5.256
preprocess_rnaseq_counts      4.995  0.171   5.171
impute_systematic_nondetects  4.916  0.186   5.254
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-3.14-bioc/meat/autonomics.Rcheck/00check.log’
for details.