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### Running command:
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###   /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_1.1.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/vmrseq.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.1.1’
* 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 ... 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 ... NOTE
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
* 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     43.176  7.702  14.712
vmrseqSmooth  28.852  4.647  12.915
regionSummary  4.608  0.611   4.595
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/vmrseq.Rcheck/00check.log’
for details.