############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:CoGAPS.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings CoGAPS_3.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/CoGAPS.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0 * running under: Ubuntu 22.04.3 LTS * using session charset: UTF-8 * 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:430:5: warning: enumeration value ‘GAPS_ALL_PHASES’ not handled in switch [-Wswitch] See ‘/home/biocbuild/bbs-3.17-bioc/meat/CoGAPS.Rcheck/00install.out’ for details. * used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * checking installed package size ... NOTE installed size is 25.6Mb sub-directories of 1Mb or more: extdata 19.7Mb libs 5.1Mb * 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 loading without being on the library search path ... 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 ‘/home/biocbuild/bbs-3.17-bioc/R/site-library/CoGAPS/libs/CoGAPS.so’: Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++) Found ‘__printf_chk’, possibly from ‘printf’ (C) Found ‘putchar’, possibly from ‘putchar’ (C) Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C) Found ‘stdout’, possibly from ‘stdout’ (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 ... ‘CoGAPS.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 WARNINGs, 3 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/CoGAPS.Rcheck/00check.log’ for details.