############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TPP.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings TPP_3.20.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/TPP.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'TPP/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'TPP' version '3.20.1' * 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 whether package 'TPP' can be installed ... OK * checking installed package size ... NOTE installed size is 13.2Mb 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 ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 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 fitMetric meltcurve_plot minMetric temperature testHypothesis Consider adding importFrom("utils", "capture.output") to your NAMESPACE file. * 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed analyzeTPPTR 28.77 0.01 28.78 tppQCPlotsCorrelateExperiments 12.92 0.01 12.94 tpptrSplineFitAndTest 10.72 0.01 24.14 tpp2dCreateDRplots 8.92 0.00 8.93 tpp2dSplineFitAndTest 8.73 0.05 14.16 tpp2dMerge2dRef 5.76 0.01 5.78 tpp2dCurveFit 5.55 0.05 5.59 analyze2DTPP 5.38 0.08 5.45 tppccrPlotCurves 5.40 0.02 5.42 tpptrPlotSplines 5.20 0.02 13.50 tpptrFTest 5.03 0.00 13.94 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed analyzeTPPTR 33.04 0.02 33.06 tppQCPlotsCorrelateExperiments 11.25 0.03 11.29 tpptrSplineFitAndTest 10.05 0.02 26.53 tpp2dCreateDRplots 9.23 0.02 9.25 tpp2dSplineFitAndTest 8.36 0.03 15.31 analyze2DTPP 6.14 0.07 6.22 tpp2dCurveFit 5.53 0.00 5.53 tpp2dMerge2dRef 5.42 0.00 5.43 tpptrPlotSplines 5.33 0.03 13.97 tpptrFTest 5.20 0.00 14.61 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' ERROR Running the tests in 'tests/testthat.R' failed. Last 13 lines of output: 3. | \-TPP::tpptrSplineFitAndTest(...) 4. | \-TPP::tpptrFitSplines(...) 5. | \-`%dopar%`(...) 6. | \-e$fun(obj, substitute(ex), parent.frame(), e$data) 7. | \-parallel::clusterCall(...) 8. | \-parallel:::sendCall(cl[[i]], fun, list(...)) 9. | \-parallel:::postNode(...) 10. | +-parallel:::sendData(con, list(type = type, data = value, tag = tag)) 11. | \-parallel:::sendData.SOCKnode(...) 12. | \-base::serialize(data, node$con) 13. \-dplyr::mutate(., Protein_ID = as.character(Protein_ID)) [ FAIL 1 | WARN 1 | SKIP 0 | PASS 299 ] Error: Test failures Execution halted ** running tests for arch 'x64' ... 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: 1 ERROR, 3 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/TPP.Rcheck/00check.log' for details.