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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Harshlight.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Harshlight_1.70.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/Harshlight.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Harshlight/DESCRIPTION’ ... OK
* this is package ‘Harshlight’ version ‘1.70.0’
* 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 ‘Harshlight’ 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 ... NOTE
Calls with DUP:
   .C("cluster_defects", img <- as.integer(img), array.size <- as.integer(array.size), 
       as.integer(size.limit), as.integer(connect), as.double(simul.pval), 
       as.double(compact.pval), as.integer(type), status <- as.integer(0), 
       DUP = FALSE, PACKAGE = "Harshlight")
   .C("diffuse_defects", img <- as.double(img), as.double(diffuse.bright), 
       as.double(-diffuse.dark), as.integer(radius), diff.bright <- as.double(diff.bright), 
       diff.dark <- as.double(diff.dark), as.double(quant), as.double(thres.dark), 
       as.double(thres.bright), status <- as.integer(0), DUP = FALSE, 
       NAOK = TRUE, PACKAGE = "Harshlight")
   .C("extended_defects", as.double(img), med.obs <- as.double(med.obs), 
       as.integer(radius), status <- as.integer(0), NAOK = TRUE, 
       DUP = FALSE, PACKAGE = "Harshlight")
   .C("image_dilation", as.double(img), result <- as.double(result), 
       as.integer(radius), status <- as.integer(0), DUP = FALSE, 
       PACKAGE = "Harshlight")
   .C("image_erosion", as.double(result), img <- as.double(img), 
       as.integer(radius), status <- as.integer(0), DUP = FALSE, 
       PACKAGE = "Harshlight")
   .C("simulations", simulation.bright <- as.integer(simulation.bright), 
       as.double(compact.quant.bright), as.integer(compact.connect), 
       status <- as.integer(0), DUP = FALSE, PACKAGE = "Harshlight")
   .C("simulations", simulation.dark <- as.integer(simulation.dark), 
       as.double(compact.quant.dark), as.integer(compact.connect), 
       status <- as.integer(0), DUP = FALSE, PACKAGE = "Harshlight")
DUP is no longer supported and will be ignored.
* checking R code for possible problems ... NOTE
Harshlight: no visible binding for global variable ‘sim’
Harshlight: no visible binding for global variable ‘sim.int’
Undefined global functions or variables:
  sim sim.int
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Harshlight/libs/Harshlight.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_srand’, possibly from ‘srand’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/Harshlight.Rcheck/00check.log’
for details.