* using log directory 'd:/RCompile/CRANincoming/R-devel/gMCP.Rcheck' * using R Under development (unstable) (2024-03-22 r86169 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'gMCP/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'gMCP' version '0.8-17' * package encoding: UTF-8 * checking CRAN incoming feasibility ... [10s] Note_to_CRAN_maintainers Maintainer: 'Kornelius Rohmeyer ' * 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 serialization versions ... OK * checking whether package 'gMCP' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 13.2.0' * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... 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 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking use of S3 registration ... 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 ... [15s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... 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 pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking sizes of PDF files under 'inst/doc' ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [65s] ERROR Running 'doRUnit.R' [65s] Running the tests in 'tests/doRUnit.R' failed. Complete output: > ## File from http://rwiki.sciviews.org/doku.php?id=developers:runit > ## Unit tests will not be done if RUnit is not available > if(require("RUnit", quietly=TRUE)) { + ## --- Setup --- + pkg <- "gMCP" + if(Sys.getenv("RCMDCHECK") == "FALSE") { + ## Path to unit tests for standalone running under Makefile (not R CMD check) + ## PKG/tests/../inst/unitTests + path <- file.path(getwd(), "..", "inst", "unitTests") + } else { + ## Path to unit tests for R CMD check + ## PKG.Rcheck/tests/../PKG/unitTests + path <- system.file(package=pkg, "unitTests") + } + cat("\nRunning unit tests\n") + print(list(pkg=pkg, getwd=getwd(), pathToUnitTests=path)) + + library(package=pkg, character.only=TRUE) + + ## If desired, load the name space to allow testing of private functions + ## if (is.element(pkg, loadedNamespaces())) + ## attach(loadNamespace(pkg), name=paste("namespace", pkg, sep=":"), pos=3) + ## + ## or simply call PKG:::myPrivateFunction() in tests + + ## --- Testing --- + + ## Define tests + testSuite <- defineTestSuite(name=paste(pkg, "unit testing"), + dirs=path) + ## Run + tests <- runTestSuite(testSuite) + + ## Default report name + ## pathReport <- file.path(path, "report") + + ## Report to stdout and text files + cat("------------------- UNIT TEST SUMMARY ---------------------\n\n") + printTextProtocol(tests, showDetails=FALSE) + ##printTextProtocol(tests, showDetails=FALSE, fileName=paste(pathReport, "Summary.txt", sep="")) + ##printTextProtocol(tests, showDetails=TRUE, fileName=paste(pathReport, ".txt", sep="")) + + ## Report to HTML file + ##printHTMLProtocol(tests, fileName=paste(pathReport, ".html", sep="")) + + ## Return stop() to cause R CMD check stop in case of + ## - failures i.e. FALSE to unit tests or + ## - errors i.e. R errors + tmp <- getErrors(tests) + if(tmp$nFail > 0 | tmp$nErr > 0) { + stop(paste("\n\nunit testing failed (#test failures: ", tmp$nFail, + ", #R errors: ", tmp$nErr, ")\n\n", sep="")) + } + } else { + warning("cannot run unit tests -- package RUnit is not available") + } Running unit tests $pkg [1] "gMCP" $getwd [1] "d:/RCompile/CRANincoming/R-devel/gMCP.Rcheck/tests" $pathToUnitTests [1] "D:/temp/RtmpKm353x/RLIBS_16af038d45a47/gMCP/unitTests" Executing test function test.LaTeX ... Skipping interactive control of LaTeX output. done successfully. Executing test function test.fractionStrings ... done successfully. Executing test function test.adjPValues ... done successfully. Executing test function test.gMCP.correlation ... done successfully. Executing test function test.gMCP.correlation.Alpha.Simulation ... Skipping alpha level simulation. done successfully. Executing test function test.everything.analysis ... Graph contains variables (or unparsable terms). No analysis possible. done successfully. Executing test function test.everything.calcPower ... done successfully. Executing test function test.bonferroni ... done successfully. Executing test function test.graphTest ... done successfully. Executing test function test.parametric ... done successfully. Executing test function test.power ... done successfully. Executing test function test.simes ... done successfully. Executing test function test.FastgMCP ... done successfully. Executing test function test.Simes ... done successfully. Executing test function test.checkWeights ... done successfully. Executing test function test.upscale ... done successfully. Executing test function test.gMCP.ext ... Info: Subset {4}: rejected (adj-p: 0.02) Subset {3}: rejected (adj-p: 0.03) Subset {3,4}: rejected (adj-p: 0.04) Subset {2}: rejected (adj-p: 0.05) Subset {2,4}: rejected (adj-p: 0.04) Subset {2,3}: not rejected (adj-p: 0.06) Subset {2,3,4}: not rejected (adj-p: 0.06) Subset {1}: rejected (adj-p: 0.01) Subset {1,4}: rejected (adj-p: 0.02) Subset {1,3}: rejected (adj-p: 0.02) Subset {1,3,4}: rejected (adj-p: 0.03) Subset {1,2}: rejected (adj-p: 0.02) Subset {1,2,4}: rejected (adj-p: 0.03) Subset {1,2,3}: rejected (adj-p: 0.03) Subset {1,2,3,4}: rejected (adj-p: 0.04) Info: Subset {4}: rejected (adj-p: 0.02) Subset {3}: rejected (adj-p: 0.03) Subset {3,4}: rejected (adj-p: 0.03) Subset {2}: rejected (adj-p: 0.05) Subset {2,4}: rejected (adj-p: 0.04) Subset {2,3}: rejected (adj-p: 0.05) Subset {2,3,4}: rejected (adj-p: 0.045) Subset {1}: rejected (adj-p: 0.01) Subset {1,4}: rejected (adj-p: 0.02) Subset {1,3}: rejected (adj-p: 0.02) Subset {1,3,4}: rejected (adj-p: 0.03) Subset {1,2}: rejected (adj-p: 0.02) Subset {1,2,4}: rejected (adj-p: 0.03) Subset {1,2,3}: rejected (adj-p: 0.03) Subset {1,2,3,4}: rejected (adj-p: 0.04) Remaining hypotheses (new numbering): 1: H1 2: H2 3: H3 4: H4 Subset {4} (padj: 0.02): p_4=0.02<=a*(w_4) =0.05*(1)=0.05 Subset {3} (padj: 0.03): p_3=0.03<=a*(w_3) =0.05*(1)=0.05 Subset {3,4} (padj: 0.03): p_4=0.02<=a*(w_4) =0.05*(0.5)=0.025 Subset {2} (padj: 0.05): p_2=0.05<=a*(w_2) =0.05*(1)=0.05 Subset {2,4} (padj: 0.04): p_4=0.02<=a*(w_4) =0.05*(0.5)=0.025 Subset {2,3} (padj: 0.05): p_2=0.05<=a*(w_2+w_3) =0.05*(0.5+0.5)=0.05 Subset {2,3,4} (padj: 0.045): p_3=0.03<=a*(w_3+w_4) =0.05*(0.333333333333333+0.333333333333333)=0.0333333333333333 Subset {1} (padj: 0.01): p_1=0.01<=a*(w_1) =0.05*(1)=0.05 Subset {1,4} (padj: 0.02): p_4=0.02<=a*(w_1+w_4) =0.05*(0.5+0.5)=0.05 Subset {1,3} (padj: 0.02): p_3=0.03<=a*(w_1+w_3) =0.05*(0.5+0.5)=0.05 Subset {1,3,4} (padj: 0.03): p_4=0.02<=a*(w_1+w_4) =0.05*(0.333333333333333+0.333333333333333)=0.0333333333333333 Subset {1,2} (padj: 0.02): p_2=0.05<=a*(w_1+w_2) =0.05*(0.5+0.5)=0.05 Subset {1,2,4} (padj: 0.03): p_4=0.02<=a*(w_1+w_4) =0.05*(0.333333333333333+0.333333333333333)=0.0333333333333333 Subset {1,2,3} (padj: 0.03): p_3=0.03<=a*(w_1+w_3) =0.05*(0.333333333333333+0.333333333333333)=0.0333333333333333 Subset {1,2,3,4} (padj: 0.04): p_4=0.02<=a*(w_1+w_4) =0.05*(0.25+0.25)=0.025 Info: Subset {4}: rejected (adj-p: 0.02) Subset {3}: rejected (adj-p: 0.03) Subset {3,4}: rejected (adj-p: 0.0284) Subset {2}: rejected (adj-p: 0.05) Subset {2,4}: rejected (adj-p: 0.04) Subset {2,3}: not rejected (adj-p: 0.06) Subset {2,3,4}: rejected (adj-p: 0.0484) Subset {1}: rejected (adj-p: 0.01) Subset {1,4}: rejected (adj-p: 0.02) Subset {1,3}: rejected (adj-p: 0.02) Subset {1,3,4}: rejected (adj-p: 0.02458) Subset {1,2}: rejected (adj-p: 0.02) Subset {1,2,4}: rejected (adj-p: 0.03) Subset {1,2,3}: rejected (adj-p: 0.03) Subset {1,2,3,4}: rejected (adj-p: 0.03458) Info: Subset {4}: rejected [pvalues=0.02, weights=1] Subset {3}: rejected [pvalues=0.03, weights=1] Subset {3,4}: rejected [pvalues=c(0.03, 0.02), weights=c(0.5, 0.5)] Subset {2}: rejected [pvalues=0.05, weights=1] Subset {2,4}: rejected [pvalues=c(0.05, 0.02), weights=c(0.5, 0.5)] Subset {2,3}: rejected [pvalues=c(0.05, 0.03), weights=c(0.5, 0.5)] Subset {2,3,4}: not rejected [pvalues=c(0.05, 0.03, 0.02), weights=c(0.3333, 0.3333, 0.3333)] Subset {1}: rejected [pvalues=0.01, weights=1] Subset {1,4}: rejected [pvalues=c(0.01, 0.02), weights=c(0.5, 0.5)] Subset {1,3}: rejected [pvalues=c(0.01, 0.03), weights=c(0.5, 0.5)] Subset {1,3,4}: rejected [pvalues=c(0.01, 0.03, 0.02), weights=c(0.3333, 0.3333, 0.3333)] Subset {1,2}: rejected [pvalues=c(0.01, 0.05), weights=c(0.5, 0.5)] Subset {1,2,4}: rejected [pvalues=c(0.01, 0.05, 0.02), weights=c(0.3333, 0.3333, 0.3333)] Subset {1,2,3}: rejected [pvalues=c(0.01, 0.05, 0.03), weights=c(0.3333, 0.3333, 0.3333)] Subset {1,2,3,4}: rejected [pvalues=c(0.01, 0.05, 0.03, 0.02), weights=c(0.25, 0.25, 0.25, 0.25)] Info: Subset {4}: rejected (adj-p: 0.02) Subset {3}: rejected (adj-p: 0.03) Subset {3,4}: rejected (adj-p: 0.04) Subset {2}: rejected (adj-p: 0.05) Subset {2,4}: rejected (adj-p: 0.04) Subset {2,3}: not rejected (adj-p: 0.06) Subset {2,3,4}: not rejected (adj-p: 0.06) Subset {1}: rejected (adj-p: 0.01) Subset {1,4}: rejected (adj-p: 0.02) Subset {1,3}: rejected (adj-p: 0.02) Subset {1,3,4}: rejected (adj-p: 0.03) Subset {1,2}: rejected (adj-p: 0.02) Subset {1,2,4}: rejected (adj-p: 0.03) Subset {1,2,3}: rejected (adj-p: 0.03) Subset {1,2,3,4}: rejected (adj-p: 0.04) Subset: 4 -> Bonferroni Subset: 3 -> Bonferroni Subset: 3 4 -> Bonferroni Subset: 2 -> Bonferroni Subset: 2 4 -> Bonferroni Subset: 2 3 -> Bonferroni Subset: 2 3 4 -> Bonferroni Subset: 1 -> Bonferroni Subset: 1 4 -> Bonferroni Subset: 1 3 -> Bonferroni Subset: 1 3 4 -> Bonferroni Subset: 1 2 -> Bonferroni Subset: 1 2 4 -> Bonferroni Subset: 1 2 3 -> Bonferroni Subset: 1 2 3 4 -> Bonferroni Info: Subset {4}: rejected (adj-p: 0.02) Subset {3}: rejected (adj-p: 0.03) Subset {3,4}: rejected (adj-p: 0.04) Subset {2}: rejected (adj-p: 0.05) Subset {2,4}: rejected (adj-p: 0.04) Subset {2,3}: not rejected (adj-p: 0.06) Subset {2,3,4}: not rejected (adj-p: 0.06) Subset {1}: rejected (adj-p: 0.01) Subset {1,4}: rejected (adj-p: 0.02) Subset {1,3}: rejected (adj-p: 0.02) Subset {1,3,4}: rejected (adj-p: 0.03) Subset {1,2}: rejected (adj-p: 0.02) Subset {1,2,4}: rejected (adj-p: 0.03) Subset {1,2,3}: rejected (adj-p: 0.03) Subset {1,2,3,4}: rejected (adj-p: 0.04) Info: Subset {4}: rejected (adj-p: 0.02) Subset {3}: rejected (adj-p: 0.03) Subset {3,4}: rejected (adj-p: 0.04) Subset {2}: rejected (adj-p: 0.05) Subset {2,4}: rejected (adj-p: 0.04) Subset {2,3}: not rejected (adj-p: 0.06) Subset {2,3,4}: not rejected (adj-p: 0.06) Subset {1}: rejected (adj-p: 0.01) Subset {1,4}: rejected (adj-p: 0.02) Subset {1,3}: rejected (adj-p: 0.02) Subset {1,3,4}: rejected (adj-p: 0.03) Subset {1,2}: rejected (adj-p: 0.02) Subset {1,2,4}: rejected (adj-p: 0.03) Subset {1,2,3}: rejected (adj-p: 0.03) Subset {1,2,3,4}: rejected (adj-p: 0.04) done successfully. Executing test function test.gMCP.ext.warnings.and.errors ... Error in gMCP.extended(graph = graph, pvalues = pvalues, test = bonferroni.test, : (converted from warning) Parameter 'subsets' will not be used by this test. In addition: There were 19 warnings (use warnings() to see them) Error in gMCP.extended(graph = graph, pvalues = pvalues, test = bonferroni.test, : (converted from warning) Parameter 'correlation' will not be used by this test. Error in gMCP.extended(graph = graph, pvalues = pvalues, test = simes.on.subsets.test, : Specified test requires parameter 'subsets', which is missing. Error in gMCP.extended(graph = graph, pvalues = pvalues, test = parametric.test, : Specified test requires parameter 'correlation', which is missing. done successfully. Executing test function test.adjPValues ... done successfully. Executing test function test.bonferroniHolm ... done successfully. Executing test function test.gMCP ... Error in gMCP(bhG3, 0, alpha = 0.6) : Length of pvalues must equal number of nodes. In addition: Warning messages: 1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties 2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry Error in gMCP(bhG3, rep(0, 6), alpha = 0.6) : Length of pvalues must equal number of nodes. done successfully. Executing test function test.gMCPBretzEtAl ... done successfully. Executing test function test.gMCPParallelGatekeeping ... done successfully. Executing test function test.graph2matrix ... done successfully. Executing test function test.graphMCP ... done successfully. Executing test function test.only.no.error ... \documentclass[11pt]{article} \usepackage{tikz} \usetikzlibrary{decorations,arrows,shapes} \begin{document} \subsection*{Graph for SRMTP} \begin{tikzpicture} \node (H1) at (125bp,-225bp)[draw,circle split,fill=green!80] {$H1$ \nodepart{lower} $\frac{1}{3}$}; \node (H2) at (325bp,-225bp)[draw,circle split,fill=green!80] {$H2$ \nodepart{lower} $\frac{1}{3}$}; \node (H3) at (525bp,-225bp)[draw,circle split,fill=green!80] {$H3$ \nodepart{lower} $\frac{1}{3}$}; \draw [->,line width=1pt] (H1.42) arc(132:90:125bp) node[fill=blue!20] {$\frac{1}{2}$} arc(90:50:125bp) to (H2); \draw [->,line width=1pt] (H1.47) arc(137:90:250bp) node[fill=blue!20] {$\frac{1}{2}$} arc(90:45:250bp) to (H3); \draw [->,line width=1pt] (H2.222) arc(312:270:125bp) node[fill=blue!20] {$\frac{1}{2}$} arc(270:230:125bp) to (H1); \draw [->,line width=1pt] (H2.42) arc(132:90:125bp) node[fill=blue!20] {$\frac{1}{2}$} arc(90:50:125bp) to (H3); \draw [->,line width=1pt] (H3.227) arc(317:270:250bp) node[fill=blue!20] {$\frac{1}{2}$} arc(270:225:250bp) to (H1); \draw [->,line width=1pt] (H3.222) arc(312:270:125bp) node[fill=blue!20] {$\frac{1}{2}$} arc(270:230:125bp) to (H2); \end{tikzpicture} \end{document}\documentclass[11pt]{article} \usepackage{tikz} \usetikzlibrary{decorations,arrows,shapes} \begin{document} \subsection*{Initial graph} \begin{tikzpicture} \node (H1) at (125bp,-225bp)[draw,circle split,fill=green!80] {$H1$ \nodepart{lower} $\frac{1}{3}$}; \node (H2) at (325bp,-225bp)[draw,circle split,fill=green!80] {$H2$ \nodepart{lower} $\frac{1}{3}$}; \node (H3) at (525bp,-225bp)[draw,circle split,fill=green!80] {$H3$ \nodepart{lower} $\frac{1}{3}$}; \draw [->,line width=1pt] (H1.42) arc(132:90:125bp) node[fill=blue!20] {$\frac{1}{2}$} arc(90:50:125bp) to (H2); \draw [->,line width=1pt] (H1.47) arc(137:90:250bp) node[fill=blue!20] {$\frac{1}{2}$} arc(90:45:250bp) to (H3); \draw [->,line width=1pt] (H2.222) arc(312:270:125bp) node[fill=blue!20] {$\frac{1}{2}$} arc(270:230:125bp) to (H1); \draw [->,line width=1pt] (H2.42) arc(132:90:125bp) node[fill=blue!20] {$\frac{1}{2}$} arc(90:50:125bp) to (H3); \draw [->,line width=1pt] (H3.227) arc(317:270:250bp) node[fill=blue!20] {$\frac{1}{2}$} arc(270:225:250bp) to (H1); \draw [->,line width=1pt] (H3.222) arc(312:270:125bp) node[fill=blue!20] {$\frac{1}{2}$} arc(270:230:125bp) to (H2); \end{tikzpicture} \subsection*{P-Values} \begin{table}[ht] \begin{center} \begin{tabular}{rrr} \hline H1&H2&H3 \\ \hline 0.10000&0.20000&0.30000\\ \hline \end{tabular} \end{center} \end{table} \subsection*{Adjusted p-values} \begin{table}[ht] \begin{center} \begin{tabular}{rrr} \hline H1&H2&H3 \\ \hline 0.30000&0.40000&0.40000\\ \hline \end{tabular} \end{center} \end{table} \subsection*{Rejected Hypotheses with $\alpha=0.05$} \begin{table}[ht] \begin{center} \begin{tabular}{rrr} \hline H1&H2&H3 \\ \hline FALSE&FALSE&FALSE\\ \hline \end{tabular} \end{center} \end{table} \end{document} done successfully. Executing test function test.makeEpsilonString ... done successfully. Executing test function test.matrix2graph ... done successfully. Executing test function test.parseEpsPolynom ... done successfully. Executing test function test.replaceVariables ... done successfully. Executing test function test.api.compatibility ... done successfully. Executing test function test.calcpower ... done successfully. Executing test function test.rqmvnorm ... Skipping checks for rqmvnorm. done successfully. Executing test function test.sampSize ... lower limit for sample size is decreased done successfully. ------------------- UNIT TEST SUMMARY --------------------- RUNIT TEST PROTOCOL -- Sun Mar 24 19:42:33 2024 *********************************************** Number of test functions: 34 Number of errors: 0 Number of failures: 0 1 Test Suite : gMCP unit testing - 34 test functions, 0 errors, 0 failures There were 14 warnings (use warnings() to see them) > > proc.time() user system elapsed 7.95 0.18 8.12 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [55s] OK * checking PDF version of manual ... [14s] OK * checking HTML version of manual ... OK * DONE Status: 1 ERROR