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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:macat.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings macat_1.76.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/macat.Rcheck’
* using R version 4.3.3 (2024-02-29)
* 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 Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘macat/DESCRIPTION’ ... OK
* this is package ‘macat’ version ‘1.76.0’
* 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 ‘macat’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'macat' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/macat.Rcheck/00install.out’ for details.
* 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 startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘annotate’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Biobase’ ‘annotate’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘annotate:::getTDRows’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
evalScoring : computePermSlideScores: warning in compute.sliding(permM,
  chrom = chromosome, sample = 1, kernel, kernelparams, step.width =
  step.width): partial argument match of 'chrom' to 'chromosome'
preprocessedLoader: warning in require(chip, character.only = TRUE,
  quiet = TRUE): partial argument match of 'quiet' to 'quietly'
.onAttach: no visible global function definition for ‘addVigs2WinMenu’
buildMACAT: no visible global function definition for ‘featureNames’
buildMACAT: no visible global function definition for ‘sampleNames’
buildMACAT: no visible global function definition for ‘exprs’
compare.gammas: no visible global function definition for ‘x11’
compare.gammas: no visible global function definition for ‘lines’
compare.gammas: no visible global function definition for ‘legend’
discreteKernelize: no visible binding for global variable ‘quantile’
discretize: no visible binding for global variable ‘quantile’
discretizeChromosome: no visible binding for global variable ‘quantile’
discretizeOne: no visible binding for global variable ‘quantile’
evalScoring: no visible binding for global variable ‘quantile’
getHtml: no visible global function definition for ‘browseURL’
loaddatapkg: no visible global function definition for
  ‘install.packages’
loaddatapkg: no visible global function definition for ‘contrib.url’
plot.MACATevalScoring: no visible global function definition for ‘x11’
plot.MACATevalScoring: no visible global function definition for ‘png’
plot.MACATevalScoring: no visible global function definition for ‘par’
plot.MACATevalScoring: no visible global function definition for
  ‘points’
plot.MACATevalScoring: no visible global function definition for
  ‘lines’
plot.MACATevalScoring: no visible global function definition for
  ‘title’
plot.MACATevalScoring: no visible global function definition for ‘axis’
plot.MACATevalScoring: no visible global function definition for
  ‘mtext’
plot.MACATevalScoring: no visible global function definition for
  ‘dev.off’
plotSliding: no visible global function definition for ‘lines’
preprocessedLoader: no visible global function definition for
  ‘read.delim’
preprocessedLoader: no visible global function definition for
  ‘read.table’
preprocessedLoader: no visible global function definition for
  ‘buildChromLocation’
preprocessedLoader: no visible global function definition for ‘new’
preprocessedLoader: no visible global function definition for ‘pData<-’
preprocessedLoader: no visible global function definition for
  ‘varLabels<-’
preprocessedLoader: no visible global function definition for
  ‘chromLocs’
preprocessedLoader : usedChromGenes2: no visible global function
  definition for ‘chromLocs’
preprocessedLoader : usedChromGenes2: no visible global function
  definition for ‘featureNames’
scoring : tscore: no visible global function definition for ‘median’
scoring : tscoremat: no visible binding for global variable ‘median’
scoring : pval: no visible binding for global variable ‘pt’
scoring: no visible binding for global variable ‘quantile’
Undefined global functions or variables:
  addVigs2WinMenu axis browseURL buildChromLocation chromLocs
  contrib.url dev.off exprs featureNames install.packages legend lines
  median mtext new pData<- par png points pt quantile read.delim
  read.table sampleNames title varLabels<- x11
Consider adding
  importFrom("grDevices", "dev.off", "png", "x11")
  importFrom("graphics", "axis", "legend", "lines", "mtext", "par",
             "points", "title")
  importFrom("methods", "new")
  importFrom("stats", "median", "pt", "quantile")
  importFrom("utils", "browseURL", "contrib.url", "install.packages",
             "read.delim", "read.table")
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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
discretize_tscores 13.463  0.134  13.642
get_results         6.769  0.035   6.811
* 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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/macat.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL macat
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘macat’ ...
** using staged installation
** R
** data
** demo
** 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
Warning: Package 'macat' is deprecated and will be removed from Bioconductor
  version 3.19
** testing if installed package can be loaded from final location
Warning: Package 'macat' is deprecated and will be removed from Bioconductor
  version 3.19
** testing if installed package keeps a record of temporary installation path
* DONE (macat)