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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:autonomics.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings autonomics_1.14.7.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/autonomics.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'autonomics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'autonomics' version '1.14.7'
* 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 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 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 ... OK
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
read_diann_proteingroups 145.60   5.67  147.83
read_rnaseq_counts        39.31   1.94   52.70
rm_diann_contaminants     31.61   1.30   32.56
plot_exprs                32.43   0.35   32.78
plot_exprs_per_coef       31.46   0.31   31.83
default_formula           20.32   0.57   20.86
read_somascan             17.74   0.14   17.93
fit                       16.68   0.36   17.15
analyze                   16.71   0.28   17.00
read_metabolon            16.67   0.22   16.89
plot_summary              16.20   0.17   16.37
plot_volcano              13.26   0.17   13.44
plot_densities            11.41   0.18   11.61
read_fragpipe             10.48   0.28   10.62
code                       8.81   0.16    8.98
ftype                      8.27   0.28    8.61
plot_sample_nas            8.00   0.19    8.19
fcluster                   7.54   0.15    7.72
extract_coef_features      6.74   0.14    6.87
biplot_covariates          6.34   0.14    6.48
subtract_baseline          6.29   0.14    6.44
reset_fit                  5.78   0.17    6.00
fit_lmx                    5.76   0.13    5.89
dot-plot_survival          5.03   0.63    5.66
plot_subgroup_points       5.25   0.17    5.44
modelvar                   4.91   0.15    5.04
* 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 NOTE
See
  'F:/biocbuild/bbs-3.20-bioc/meat/autonomics.Rcheck/00check.log'
for details.