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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ISAnalytics.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ISAnalytics_1.6.2.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/ISAnalytics.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'ISAnalytics/DESCRIPTION' ... OK
* this is package 'ISAnalytics' version '1.6.2'
* 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 whether package 'ISAnalytics' 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 ... NOTE
.sh_row_permut: no visible global function definition for '.'
.sharing_multdf_mult_key: no visible binding for global variable '.'
.sharing_multdf_single_key: no visible binding for global variable '.'
.sharing_singledf_mult_key: no visible binding for global variable '.'
.sharing_singledf_single_key: no visible binding for global variable
  '.'
cumulative_is: no visible binding for global variable 'is'
gene_frequency_fisher: no visible binding for global variable '.'
sharing_heatmap : plot_rel_heat: no visible binding for global variable
  '..fill..'
Undefined global functions or variables:
  . ..fill.. is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* 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
sharing_venn                   33.81   0.98   34.88
import_parallel_Vispa2Matrices  2.70   0.50   17.02
import_Vispa2_stats             2.43   0.33    9.23
HSC_population_plot             1.06   0.03    5.83
iss_source                      1.00   0.03    7.14
realign_after_collisions        0.94   0.04    5.19
remove_collisions               0.83   0.09    5.18
HSC_population_size_estimate    0.86   0.05    5.78
compute_near_integrations       0.43   0.03    6.51
* 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 NOTE
See
  'F:/biocbuild/bbs-3.15-bioc/meat/ISAnalytics.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL ISAnalytics
###
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* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'ISAnalytics' ...
** 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 (ISAnalytics)

R version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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(ISAnalytics)
Loading required package: magrittr

Attaching package: 'magrittr'

The following objects are masked from 'package:testthat':

    equals, is_less_than, not

> 
> test_check("ISAnalytics")
Loading required namespace: plotly
Loading required namespace: rmarkdown
Report correctly saved
i Report saved to: F:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpMhphAt/file2d5c7648665/2022-10-19_collision_removal_report.html
Report correctly saved
i Report saved to: F:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpMhphAt/file2d5c66386a3a/2022-10-19_outlier_test_pool_fragments_report.html
[ FAIL 0 | WARN 926 | SKIP 0 | PASS 801 ]

[ FAIL 0 | WARN 926 | SKIP 0 | PASS 801 ]
Warning messages:
1: Using an external vector in selections was deprecated in tidyselect 1.1.0.
ℹ Please use `all_of()` or `any_of()` instead.
  # Was:
  data %>% select(key)

  # Now:
  data %>% select(all_of(key))

See <https://tidyselect.r-lib.org/reference/faq-external-vector.html>. 
2: Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
ℹ Please use `all_of(var)` (or `any_of(var)`) instead of `.data[[var]]` 
3: Use of .data in tidyselect expressions was deprecated in tidyselect 1.2.0.
ℹ Please use `"Found"` instead of `.data$Found` 
> 
> proc.time()
   user  system elapsed 
 164.42    7.09  395.36