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### Running command:
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###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:lisaClust.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings lisaClust_1.7.1.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/lisaClust.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'lisaClust/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'lisaClust' version '1.7.1'
* 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 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 ... WARNING
Codoc mismatches from documentation object 'hatchingPlot':
hatchingPlot
  Code: function(data, useImages = NULL, region = "region", imageID =
                 "imageID", cellType = "cellType", spatialCoords =
                 c("x", "y"), window = "concave", line.spacing = 21,
                 hatching.colour = 1, nbp = 50, window.length = NULL)
  Docs: function(data, imageID = NULL, regionName = "region", window =
                 "concave", line.spacing = 21, hatching.colour = 1, nbp
                 = 50, window.length = NULL)
  Argument names in code not in docs:
    useImages region cellType spatialCoords
  Argument names in docs not in code:
    regionName
  Mismatches in argument names (first 3):
    Position: 2 Code: useImages Docs: imageID
    Position: 3 Code: region Docs: regionName
    Position: 4 Code: imageID Docs: window
  Mismatches in argument default values:
    Name: 'imageID' Code: "imageID" Docs: NULL

* 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
lisa         7.09   0.37    7.25
hatchingPlot 6.27   0.35    6.61
lisaClust    5.63   0.13    5.58
* 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 WARNING, 1 NOTE
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/lisaClust.Rcheck/00check.log'
for details.

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### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL lisaClust
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/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)