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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DECIPHER.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DECIPHER_2.31.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/DECIPHER.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DECIPHER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DECIPHER’ version ‘2.31.3’
* 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 ‘DECIPHER’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... NOTE
  installed size is 12.3Mb
  sub-directories of 1Mb or more:
    R         1.5Mb
    data      7.5Mb
    extdata   2.3Mb
* 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
AlignSeqs: no visible binding for global variable ‘deltaGrulesRNA’
DesignSignatures: no visible binding for global variable ‘deltaHrules’
FindGenes: no visible binding for global variable ‘deltaHrulesRNA’
FindNonCoding: no visible binding for global variable ‘deltaHrulesRNA’
LearnNonCoding: no visible binding for global variable ‘deltaHrulesRNA’
PredictDBN: no visible binding for global variable ‘deltaGrulesRNA’
TreeLine: multiple local function definitions for ‘.minimize’ with
  different formal arguments
Undefined global functions or variables:
  deltaGrulesRNA deltaHrules deltaHrulesRNA
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* 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
AlignSeqs          450.716  7.902 593.645
LearnNonCoding     171.686  6.263 206.505
MapCharacters      143.010  1.816 178.610
FindNonCoding       83.889  5.762 109.141
FindGenes           55.341  1.275  67.807
BrowseSeqs          55.499  0.999  76.527
WriteGenes          54.669  1.826  67.948
Genes-class         54.438  1.718  67.243
ExtractGenes        54.583  1.346  67.068
DetectRepeats       38.119  0.353  46.715
CorrectFrameshifts  35.994  1.857  47.727
StaggerAlignment    27.729  1.250  34.985
AlignTranslation    25.099  0.423  32.828
TreeLine            18.405  0.508  22.561
Taxa-class          17.203  0.693  24.003
IdTaxa              15.162  0.543  18.236
Clusterize          11.070  0.861  15.528
LearnTaxa            9.573  2.210  13.588
ScoreAlignment      11.065  0.335  13.544
Array2Matrix         9.409  0.141  11.983
DesignArray          9.165  0.076  11.407
TileSeqs             8.314  0.084  14.100
AlignPairs           7.847  0.232   9.703
AlignSynteny         5.874  0.096   7.831
TrainingSet_16S      4.842  0.088   6.624
Synteny-class        4.672  0.153   8.913
* 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-3.19-bioc/meat/DECIPHER.Rcheck/00check.log’
for details.