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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:lisaClust.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings lisaClust_1.8.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/lisaClust.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘lisaClust/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘lisaClust’ version ‘1.8.2’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘lisaClust’ 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
getK: no visible binding for global variable ‘j’
getK: no visible binding for global variable ‘cellTypeI’
getK: no visible binding for global variable ‘i’
getK: no visible binding for global variable ‘d’
getK: no visible binding for global variable ‘cellTypeJ’
getK: no visible binding for global variable ‘value’
getK: no visible global function definition for ‘.’
getK: no visible binding for global variable ‘wt’
getL: no visible binding for global variable ‘j’
getL: no visible binding for global variable ‘cellTypeI’
getL: no visible binding for global variable ‘i’
getL: no visible binding for global variable ‘d’
getL: no visible binding for global variable ‘cellTypeJ’
getL: no visible binding for global variable ‘value’
getL: no visible global function definition for ‘.’
getL: no visible binding for global variable ‘wt’
inhomLocalK: no visible binding for global variable ‘i’
regionMap: no visible binding for global variable ‘Var1’
regionMap: no visible binding for global variable ‘Var2’
regionMap: no visible binding for global variable ‘Freq’
regionMap: no visible binding for global variable ‘Freq2’
Undefined global functions or variables:
  . Freq Freq2 Var1 Var2 cellTypeI cellTypeJ d i j value wt
* 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
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
hatchingPlot 10.407  0.386  16.721
lisa         10.484  0.227  16.362
lisaClust    10.076  0.187  15.080
scale_region  6.932  0.111   9.743
regionMap     5.555  0.085   7.140
* 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
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/lisaClust.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL lisaClust
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘lisaClust’ ...
** 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 (lisaClust)