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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:tripr.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings tripr_1.14.0.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/tripr.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'tripr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'tripr' version '1.14.0'
* 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 whether package 'tripr' can be installed ... OK
* checking installed package size ... INFO
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R         1.2Mb
    app       1.4Mb
    extdata   4.1Mb
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' imports not declared from:
  'purrr' 'tidyr'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
alignment : <anonymous>: no visible binding for global variable
  'V.gene'
alignment : <anonymous>: no visible binding for global variable 'AA
  Junction'
alignment : <anonymous>: no visible binding for global variable
  'prev_cluster'
alignment : one_run: no visible global function definition for
  'na.omit'
alignment: no visible global function definition for 'na.omit'
clonotypes: no visible binding for global variable 'Clonotype ID'
clonotypes: no visible binding for global variable 'V Gene and allele'
clonotypes: no visible binding for global variable 'D Gene and allele'
clonotypes: no visible binding for global variable 'J Gene and allele'
clonotypes: no visible binding for global variable 'AA Junction'
clonotypes: no visible binding for global variable 'AA Junction length'
clonotypes: no visible binding for global variable 'V.REGION.identity'
clonotypes: no visible binding for global variable 'pI'
clonotypes : one_run: no visible binding for global variable 'V-Region
  identity'
clonotypes : one_run: no visible binding for global variable 'No. of
  sequences'
clonotypes : one_run : modify_dfs: no visible global function
  definition for 'tail'
clonotypes : one_run : modify_dfs: no visible global function
  definition for 'head'
clonotypes : one_run: no visible binding for global variable 'Clonotype
  ID'
clonotypes : one_run: no visible binding for global variable 'V Gene
  and allele'
clonotypes : one_run: no visible binding for global variable 'D Gene
  and allele'
clonotypes : one_run: no visible binding for global variable 'J Gene
  and allele'
clonotypes : one_run: no visible binding for global variable 'AA
  Junction'
clonotypes : one_run: no visible binding for global variable 'AA
  Junction length'
clonotypes : one_run: no visible binding for global variable
  'V.REGION.identity'
clonotypes : one_run: no visible binding for global variable 'pI'
meta_clonotypes : modify_dfs: no visible global function definition for
  'tail'
meta_clonotypes : modify_dfs: no visible global function definition for
  'head'
Undefined global functions or variables:
  AA Junction AA Junction length Clonotype ID D Gene and allele J Gene
  and allele No. of sequences V Gene and allele V-Region identity
  V.REGION.identity V.gene head na.omit pI prev_cluster tail
Consider adding
  importFrom("base", "identity", "length")
  importFrom("stats", "D", "na.omit")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
* 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
* 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 WARNING, 2 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/tripr.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL tripr
###
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'tripr' ...
** this is package 'tripr' version '1.14.0'
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (tripr)

R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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(tripr)
Loading required package: shiny
Loading required package: shinyBS
Welcome to tripr!
> library(fs)
> 
> test_check("tripr")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
> 
> proc.time()
   user  system elapsed 
   4.03    0.51    4.53