############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TPP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TPP_3.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/TPP.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * 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 ‘TPP/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘TPP’ version ‘3.35.0’ * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 24 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘TPP’ can be installed ... OK * checking installed package size ... INFO installed size is 12.8Mb sub-directories of 1Mb or more: data 1.9Mb example_data 8.0Mb test_data 1.9Mb * 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: Updated package vignette. Cannot process chunk/lines: Removed unit test that causes R CMD check to crash since the latest update of package 'testthat'. Cannot process chunk/lines: Fixed bug in plotColors for the case when no comparisons are specified * 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘broom’ All declared Imports should be used. Unexported objects imported by ':::' calls: ‘doParallel:::.options’ ‘mefa:::rep.data.frame’ 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 File ‘TPP/R/TPP.R’: .onLoad calls: packageStartupMessage(msgText, "\n") See section ‘Good practice’ in '?.onAttach'. fitSigmoidCCR: no visible global function definition for ‘capture.output’ modelSelector: no visible binding for global variable ‘testHypothesis’ modelSelector: no visible binding for global variable ‘fitMetric’ modelSelector: no visible binding for global variable ‘minMetric’ plot_fSta_distribution: no visible binding for global variable ‘density’ plot_pVal_distribution: no visible binding for global variable ‘..density..’ tpp2dCreateTPPTRreference: no visible binding for global variable ‘meltcurve_plot’ tpp2dCreateTPPTRreference: no visible binding for global variable ‘Protein_ID’ tpp2dExport: no visible binding for global variable ‘temperature’ tpp2dImport: no visible binding for global variable ‘temperature’ tpp2dNormalize: no visible binding for global variable ‘temperature’ Undefined global functions or variables: ..density.. Protein_ID capture.output density fitMetric meltcurve_plot minMetric temperature testHypothesis Consider adding importFrom("stats", "density") importFrom("utils", "capture.output") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) analyzeTPPTR.Rd:146-147: Lost braces in \itemize; meant \describe ? checkRd: (-1) analyzeTPPTR.Rd:148: Lost braces in \itemize; meant \describe ? checkRd: (-1) analyzeTPPTR.Rd:149: Lost braces in \itemize; meant \describe ? checkRd: (-1) hdacCCR_data.Rd:32: Lost braces in \itemize; meant \describe ? checkRd: (-1) hdacCCR_data.Rd:33: Lost braces in \itemize; meant \describe ? checkRd: (-1) hdacTR_data.Rd:33: Lost braces in \itemize; meant \describe ? checkRd: (-1) hdacTR_data.Rd:34: Lost braces in \itemize; meant \describe ? checkRd: (-1) hdacTR_data.Rd:35: Lost braces in \itemize; meant \describe ? checkRd: (-1) hdacTR_data.Rd:36: Lost braces in \itemize; meant \describe ? checkRd: (-1) tppccrCurveFit.Rd:42: Lost braces 42 | code{featureData(S)}. | ^ checkRd: (-1) tppccrImport.Rd:71-72: Lost braces in \itemize; meant \describe ? checkRd: (-1) tppccrImport.Rd:73: Lost braces in \itemize; meant \describe ? checkRd: (-1) tppccrPlotCurves.Rd:45: Lost braces 45 | produced plots are stored in code{featureData(S)$plot}. | ^ checkRd: (-1) tpptrImport.Rd:76-77: Lost braces in \itemize; meant \describe ? checkRd: (-1) tpptrImport.Rd:78: Lost braces in \itemize; meant \describe ? checkRd: (-1) tpptrImport.Rd:79: Lost braces in \itemize; meant \describe ? * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: analyze2DTPP.Rd: brewer.pal tpp2dCreateDRplots.Rd: brewer.pal tpptrFTest.Rd: squeezeVar tpptrFitSplines.Rd: AICc tpptrPlotSplines.Rd: AICc tpptrSplineFitAndTest.Rd: AICc Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed analyzeTPPTR 29.977 0.204 30.386 tpptrSplineFitAndTest 21.444 0.143 27.727 tppQCPlotsCorrelateExperiments 12.038 0.259 12.563 tpp2dSplineFitAndTest 11.996 0.092 12.160 tpptrPlotSplines 10.866 0.071 11.010 tpp2dCreateDRplots 10.590 0.114 10.806 tpptrFTest 10.348 0.062 10.472 tpp2dMerge2dRef 5.656 0.080 5.790 tppccrPlotCurves 5.509 0.066 5.631 analyze2DTPP 5.380 0.115 5.536 tpp2dCurveFit 5.339 0.067 5.450 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ 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: 5 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/TPP.Rcheck/00check.log’ for details.