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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CoGAPS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CoGAPS_3.20.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/CoGAPS.Rcheck’
* using R version 4.3.1 (2023-06-16)
* 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 Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CoGAPS/DESCRIPTION’ ... OK
* this is package ‘CoGAPS’ version ‘3.20.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘CoGAPS’ can be installed ... WARNING
Found the following significant warnings:
  GapsRunner.cpp:430:13: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/CoGAPS.Rcheck/00install.out’ for details.
* 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 21.4Mb
  sub-directories of 1Mb or more:
    extdata  19.9Mb
* 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
plot.CogapsResult: no visible global function definition for ‘axis’
plot.CogapsResult: no visible global function definition for ‘text’
plot.CogapsResult: no visible global function definition for ‘par’
MANOVA,matrix-CogapsResult: no visible global function definition for
  ‘manova’
fromCSV,character: no visible global function definition for ‘read.csv’
getPatternHallmarks,CogapsResult: no visible binding for global
  variable ‘.’
getPatternHallmarks,CogapsResult: no visible binding for global
  variable ‘MsigDB_Hallmark’
getPatternHallmarks,CogapsResult: no visible binding for global
  variable ‘padj’
plotPatternHallmarks,CogapsResult-list-numeric: no visible binding for
  global variable ‘overlapGenes’
plotPatternHallmarks,CogapsResult-list-numeric: no visible binding for
  global variable ‘padj’
show,CogapsParams: no visible binding for global variable
  ‘checkpointFile’
toCSV,CogapsResult-character: no visible global function definition for
  ‘write.csv’
Undefined global functions or variables:
  . MsigDB_Hallmark axis checkpointFile manova overlapGenes padj par
  read.csv text write.csv
Consider adding
  importFrom("graphics", "axis", "par", "text")
  importFrom("stats", "manova")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘MANOVA’ ‘fromCSV’ ‘getPatternHallmarks’ ‘plotPatternHallmarks’
  ‘toCSV’
Undocumented data sets:
  ‘ModSimBases’ ‘ModSimData’
Undocumented S4 methods:
  generic 'MANOVA' and siglist 'matrix,CogapsResult'
  generic 'fromCSV' and siglist 'character'
  generic 'getPatternHallmarks' and siglist 'CogapsResult'
  generic 'plotPatternHallmarks' and siglist
    'CogapsResult,list,numeric'
  generic 'toCSV' and siglist 'CogapsResult,character'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'CoGAPS':
CoGAPS
  Code: function(data, params = new("CogapsParams"), nThreads = 1,
                 messages = TRUE, outputFrequency = 1000, uncertainty =
                 NULL, useCheckPoint = FALSE, checkpointOutFile =
                 "gaps_checkpoint.out", checkpointInterval = 0,
                 checkpointFile = NULL, transposeData = FALSE, BPPARAM
                 = NULL, workerID = 1, asynchronousUpdates = TRUE,
                 nSnapshots = 0, snapshotPhase = "sampling", ...)
  Docs: function(data, params = new("CogapsParams"), nThreads = 1,
                 messages = TRUE, outputFrequency = 1000, uncertainty =
                 NULL, checkpointOutFile = "gaps_checkpoint.out",
                 checkpointInterval = 0, checkpointInFile = NULL,
                 transposeData = FALSE, BPPARAM = NULL, workerID = 1,
                 asynchronousUpdates = TRUE, nSnapshots = 0,
                 snapshotPhase = "sampling", ...)
  Argument names in code not in docs:
    useCheckPoint checkpointFile
  Argument names in docs not in code:
    checkpointInFile
  Mismatches in argument names (first 3):
    Position: 7 Code: useCheckPoint Docs: checkpointOutFile
    Position: 8 Code: checkpointOutFile Docs: checkpointInterval
    Position: 9 Code: checkpointInterval Docs: checkpointInFile

Codoc mismatches from documentation object 'GWCoGAPS':
GWCoGAPS
  Code: function(data, params = new("CogapsParams"), nThreads = 1,
                 messages = TRUE, outputFrequency = 500, uncertainty =
                 NULL, checkpointOutFile = "gaps_checkpoint.out",
                 checkpointInterval = 1000, checkpointFile = NULL,
                 transposeData = FALSE, BPPARAM = NULL, workerID = 1,
                 asynchronousUpdates = FALSE, ...)
  Docs: function(data, params = new("CogapsParams"), nThreads = 1,
                 messages = TRUE, outputFrequency = 500, uncertainty =
                 NULL, checkpointOutFile = "gaps_checkpoint.out",
                 checkpointInterval = 1000, checkpointInFile = NULL,
                 transposeData = FALSE, BPPARAM = NULL, workerID = 1,
                 asynchronousUpdates = FALSE, ...)
  Argument names in code not in docs:
    checkpointFile
  Argument names in docs not in code:
    checkpointInFile
  Mismatches in argument names:
    Position: 9 Code: checkpointFile Docs: checkpointInFile

Codoc mismatches from documentation object 'plotPatternMarkers':
plotPatternMarkers
  Code: function(object, data, patternMarkers, patternPalette,
                 sampleNames, samplePalette = NULL, heatmapCol =
                 bluered, colDendrogram = TRUE, scale = "row", ...)
  Docs: function(object, data, patternPalette, sampleNames,
                 samplePalette = NULL, heatmapCol = bluered,
                 colDenogram = TRUE, scale = "row", ...)
  Argument names in code not in docs:
    patternMarkers colDendrogram
  Argument names in docs not in code:
    colDenogram
  Mismatches in argument names (first 3):
    Position: 3 Code: patternMarkers Docs: patternPalette
    Position: 4 Code: patternPalette Docs: sampleNames
    Position: 5 Code: sampleNames Docs: samplePalette

Codoc mismatches from documentation object 'scCoGAPS':
scCoGAPS
  Code: function(data, params = new("CogapsParams"), nThreads = 1,
                 messages = TRUE, outputFrequency = 500, uncertainty =
                 NULL, checkpointOutFile = "gaps_checkpoint.out",
                 checkpointInterval = 1000, checkpointFile = NULL,
                 transposeData = FALSE, BPPARAM = NULL, workerID = 1,
                 asynchronousUpdates = FALSE, ...)
  Docs: function(data, params = new("CogapsParams"), nThreads = 1,
                 messages = TRUE, outputFrequency = 500, uncertainty =
                 NULL, checkpointOutFile = "gaps_checkpoint.out",
                 checkpointInterval = 1000, checkpointInFile = NULL,
                 transposeData = FALSE, BPPARAM = NULL, workerID = 1,
                 asynchronousUpdates = FALSE, ...)
  Argument names in code not in docs:
    checkpointFile
  Argument names in docs not in code:
    checkpointInFile
  Mismatches in argument names:
    Position: 9 Code: checkpointFile Docs: checkpointInFile

S4 class codoc mismatches from documentation object 'CogapsParams-class':
Slots for class 'CogapsParams'
  Code: alphaA alphaP checkpointFile checkpointInterval
        checkpointOutFile cut distributed explicitSets fixedPatterns
        geneNames maxGibbsMassA maxGibbsMassP maxNS minNS nIterations
        nPatterns nSets sampleNames samplingAnnotation samplingWeight
        seed sparseOptimization subsetDim subsetIndices takePumpSamples
        whichMatrixFixed
  Docs: alphaA alphaP cut distributed explicitSets fixedPatterns
        geneNames maxGibbsMassA maxGibbsMassP maxNS minNS nIterations
        nPatterns nSets sampleNames samplingAnnotation samplingWeight
        seed sparseOptimization subsetDim subsetIndices takePumpSamples
        whichMatrixFixed

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... WARNING
Files not of a type allowed in a ‘data’ directory:
  ‘ModSimResult.Rds’ ‘ModSimResult.h5ad’
Please use e.g. ‘inst/extdata’ for non-R data files

* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... 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
File ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CoGAPS/libs/CoGAPS.so’:
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_printf’, possibly from ‘printf’ (C)
  Found ‘_putchar’, possibly from ‘putchar’ (C)
  Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (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 nor [v]sprintf. 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 4 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/CoGAPS.Rcheck/00check.log’
for details.