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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpeCond.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpeCond_1.60.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SpeCond.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpeCond/DESCRIPTION’ ... OK
* this is package ‘SpeCond’ version ‘1.60.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘SpeCond’ 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 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘fields’ ‘hwriter’ ‘mclust’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
SpeCond: warning in getSpecificOutliersStep1(expressionMatrix, fit =
  fit1, param.detection = param.detection, multitest.correction.method
  = "BY", prefix.file = prefix.file, print.hist.pv = FALSE): partial
  argument match of 'fit' to 'fit1'
SpeCond: warning in getSpecificResult(expressionMatrix, fit = fit2,
  specificOutlierStep1 = specificOutlierStep1, param.detection =
  param.detection, multitest.correction.method =
  multitest.correction.method, prefix.file = prefix.file, print.hist.pv
  = print.hist.pv): partial argument match of 'fit' to 'fit2'
createSingleGeneHtmlPage: warning in matrix(c("color:#000DFE", NA), nr
  = 1, nc = 2): partial argument match of 'nr' to 'nrow'
createSingleGeneHtmlPage: warning in matrix(c("color:#000DFE", NA), nr
  = 1, nc = 2): partial argument match of 'nc' to 'ncol'
getExpressionpatternLegend: warning in matrix(" ", nr = 2, nc =
  1): partial argument match of 'nr' to 'nrow'
getExpressionpatternLegend: warning in matrix(" ", nr = 2, nc =
  1): partial argument match of 'nc' to 'ncol'
SpeCond: no visible global function definition for ‘is’
SpeCond: no visible global function definition for ‘new’
callMclustInStep2: no visible global function definition for ‘Mclust’
callMclustInStep2: no visible global function definition for
  ‘priorControl’
createSingleGeneHtmlPage: no visible global function definition for
  ‘openPage’
createSingleGeneHtmlPage: no visible global function definition for
  ‘hwrite’
createSingleGeneHtmlPage: no visible global function definition for
  ‘sessionInfo’
createSingleGeneHtmlPage: no visible global function definition for
  ‘closePage’
fitNoPriorWithExclusion : <anonymous>: no visible global function
  definition for ‘Mclust’
fitPrior : <anonymous>: no visible global function definition for
  ‘Mclust’
fitPrior : <anonymous>: no visible global function definition for
  ‘priorControl’
getDifferenceMedian: no visible global function definition for ‘median’
getExpressionpatternLegend: no visible global function definition for
  ‘hwrite’
getFullHtmlSpeCondResult: no visible global function definition for
  ‘openPage’
getFullHtmlSpeCondResult: no visible global function definition for
  ‘is’
getFullHtmlSpeCondResult: no visible global function definition for
  ‘hwrite’
getFullHtmlSpeCondResult: no visible global function definition for
  ‘png’
getFullHtmlSpeCondResult: no visible global function definition for
  ‘barplot’
getFullHtmlSpeCondResult: no visible global function definition for
  ‘dev.off’
getFullHtmlSpeCondResult: no visible global function definition for
  ‘par’
getFullHtmlSpeCondResult: no visible global function definition for
  ‘axis’
getFullHtmlSpeCondResult: no visible global function definition for
  ‘points’
getFullHtmlSpeCondResult: no visible global function definition for
  ‘legend’
getFullHtmlSpeCondResult: no visible global function definition for
  ‘mtext’
getFullHtmlSpeCondResult: no visible global function definition for
  ‘hwriteImage’
getFullHtmlSpeCondResult: no visible global function definition for
  ‘colorRampPalette’
getFullHtmlSpeCondResult: no visible global function definition for
  ‘sessionInfo’
getFullHtmlSpeCondResult: no visible global function definition for
  ‘closePage’
getFullHtmlSpeCondResult: no visible global function definition for
  ‘write.table’
getGeneHtmlPage: no visible global function definition for ‘is’
getGeneHtmlPage: no visible global function definition for ‘openPage’
getGeneHtmlPage: no visible global function definition for ‘hwrite’
getGeneHtmlPage: no visible global function definition for
  ‘sessionInfo’
getGeneHtmlPage: no visible global function definition for ‘closePage’
getHeatmap: no visible global function definition for ‘png’
getHeatmap: no visible global function definition for ‘heatmap’
getHeatmap: no visible global function definition for ‘colorbar.plot’
getHeatmap: no visible global function definition for ‘dev.off’
getHeatmap: no visible global function definition for ‘pdf’
getMatrixFromExpressionSet: no visible global function definition for
  ‘is’
getMatrixFromExpressionSet: no visible global function definition for
  ‘exprs’
getMinLoglikelihoodNull: no visible global function definition for
  ‘dnorm’
getPValueMean : <anonymous>: no visible global function definition for
  ‘pnorm’
getProfileHeatmap: no visible global function definition for ‘png’
getProfileHeatmap: no visible global function definition for ‘heatmap’
getProfileHeatmap: no visible global function definition for ‘dev.off’
getProfileHeatmap: no visible global function definition for ‘pdf’
getScaleMAD: no visible global function definition for ‘mad’
getSpecific: no visible global function definition for ‘pdf’
getSpecific: no visible global function definition for ‘hist’
getSpecific: no visible global function definition for ‘dev.off’
getSpecific: no visible global function definition for ‘p.adjust’
getSpecific: no visible global function definition for ‘new’
plotNormalMixture: no visible global function definition for ‘png’
plotNormalMixture: no visible global function definition for ‘points’
plotNormalMixture: no visible global function definition for
  ‘hwriteImage’
plotNormalMixture: no visible global function definition for ‘dev.off’
plotNormalMixture: no visible global function definition for ‘hist’
plotNormalMixture : f1: no visible global function definition for
  ‘dnorm’
plotNormalMixture : f2: no visible global function definition for
  ‘dnorm’
plotNormalMixture : f3: no visible global function definition for
  ‘dnorm’
plotNormalMixture : f4: no visible global function definition for
  ‘dnorm’
plotNormalMixture : f5: no visible global function definition for
  ‘dnorm’
plotNormalMixture: no visible global function definition for ‘lines’
plotNormalMixture: no visible global function definition for ‘legend’
plotNormalMixture : f_null : <anonymous>: no visible global function
  definition for ‘dnorm’
show.sp_list: no visible global function definition for ‘is’
writeGeneResult: no visible global function definition for
  ‘write.table’
writeSpeCondResult: no visible global function definition for
  ‘write.table’
writeUniqueProfileSpecificResult: no visible global function definition
  for ‘write.table’
Undefined global functions or variables:
  Mclust axis barplot closePage colorRampPalette colorbar.plot dev.off
  dnorm exprs heatmap hist hwrite hwriteImage is legend lines mad
  median mtext new openPage p.adjust par pdf png pnorm points
  priorControl sessionInfo write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf", "png")
  importFrom("graphics", "axis", "barplot", "hist", "legend", "lines",
             "mtext", "par", "points")
  importFrom("methods", "is", "new")
  importFrom("stats", "dnorm", "heatmap", "mad", "median", "p.adjust",
             "pnorm")
  importFrom("utils", "sessionInfo", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) getFullHtmlSpeCondResult.Rd:19: Escaped LaTeX specials: \_
checkRd: (-1) getProfile.Rd:12: Escaped LaTeX specials: \$ \$ \$
* 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 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 ... 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-3.20-bioc/meat/SpeCond.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SpeCond
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘SpeCond’ ...
** using staged installation
** R
** data
** 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 (SpeCond)