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### Running command:
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###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:autonomics.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings autonomics_1.12.1.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/autonomics.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* 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 '1.12.1'
* 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 ... NOTE
checkRd: (-1) dequantify.Rd:24: Lost braces; missing escapes or markup?
    24 | Encode {channel} as suffix.
       |        ^
* 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 147.13   5.70  150.34
read_rnaseq_counts        36.30   2.05   43.64
rm_diann_contaminants     27.65   1.16   28.55
plot_exprs                26.19   0.39   26.67
plot_exprs_per_coef       22.42   0.41   22.95
default_formula           18.60   0.72   19.36
read_metabolon            17.04   0.28   17.40
read_somascan             16.61   0.20   16.80
fit                       15.47   0.36   16.00
plot_summary              14.25   0.25   14.57
analyze                   13.80   0.34   14.33
plot_volcano              11.31   0.36   11.80
read_fragpipe             11.19   0.21   11.31
plot_densities            10.97   0.32   11.41
plot_sample_nas            6.64   0.10    6.76
extract_coef_features      5.83   0.11    5.99
dot-plot_survival          5.28   0.58    5.86
subtract_baseline          5.66   0.16    5.84
biplot_covariates          5.59   0.11    5.81
explore_transformations    5.34   0.22    5.58
plot_subgroup_points       5.31   0.14    5.58
fit_lmx                    5.22   0.14    5.48
biplot                     5.11   0.24    5.45
reset_fit                  5.05   0.20    5.31
code                       5.13   0.10    5.31
log2transform              4.99   0.12    5.16
plot_violins               4.56   0.27    5.03
* 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: 2 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/autonomics.Rcheck/00check.log'
for details.