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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:vmrseq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings vmrseq_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/vmrseq.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘vmrseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘vmrseq’ version ‘1.0.0’
* 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 ‘vmrseq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 ... NOTE
.computeProb1Unit : .computeLag: no visible binding for global variable
  ‘chr’
.computeProb1Unit : .computeLag: no visible binding for global variable
  ‘state’
.computeProb1Unit : .computeLag: no visible binding for global variable
  ‘state_lag’
.computeProb1Unit : .computeLag: no visible binding for global variable
  ‘dist_bp’
.computeProb1Unit: no visible binding for global variable ‘dist_bp’
.computeProb1Unit: no visible binding for global variable ‘N_00’
.computeProb1Unit: no visible binding for global variable ‘N_10’
.computeProb1Unit: no visible binding for global variable ‘N_01’
.computeProb1Unit: no visible binding for global variable ‘N_11’
.computeProb1Unit: no visible binding for global variable ‘p_00’
.computeProb1Unit: no visible binding for global variable ‘p_01’
.estimTransitProbsFromSummary: no visible binding for global variable
  ‘dist_bp’
.estimTransitProbsFromSummary: no visible binding for global variable
  ‘p_00’
.estimTransitProbsFromSummary: no visible binding for global variable
  ‘p_01’
.estimTransitProbsFromSummary: no visible binding for global variable
  ‘p_10’
.estimTransitProbsFromSummary: no visible binding for global variable
  ‘p_11’
.estimTransitProbsFromSummary : .selectCols: no visible binding for
  global variable ‘dist_bp’
HDF5NAdrop2matrix: no visible global function definition for ‘as’
computeVar : varByCluster: no visible global function definition for
  ‘as’
computeVarCutoff: no visible global function definition for ‘quantile’
extractInfo: no visible binding for global variable ‘meth’
extractInfo: no visible binding for global variable ‘total’
extractInfo: no visible binding for global variable ‘bool’
tpPlot: no visible binding for global variable ‘dist_bp’
tpPlot: no visible binding for global variable ‘pbar’
tpPlot: no visible binding for global variable ‘phat’
vmrseqFit: no visible binding for global variable ‘bpWindow’
Undefined global functions or variables:
  N_00 N_01 N_10 N_11 as bool bpWindow chr dist_bp meth p_00 p_01 p_10
  p_11 pbar phat quantile state state_lag total
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "quantile")
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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
vmrseqFit     43.247  7.879  14.786
vmrseqSmooth  28.520  4.552  12.900
regionSummary  4.514  0.601   4.473
* 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
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/vmrseq.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL vmrseq
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘vmrseq’ ...
** this is package ‘vmrseq’ version ‘1.0.0’
** 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 (vmrseq)

R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(vmrseq)
> 
> test_check("vmrseq")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 23 ]
> 
> proc.time()
   user  system elapsed 
 14.706   0.770  15.556