Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-16 11:41 -0400 (Fri, 16 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4420 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4413 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 799/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GeneticsPed 1.67.0 (landing page) David Henderson
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the GeneticsPed package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeneticsPed.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: GeneticsPed |
Version: 1.67.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneticsPed.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GeneticsPed_1.67.0.tar.gz |
StartedAt: 2024-08-16 01:03:18 -0400 (Fri, 16 Aug 2024) |
EndedAt: 2024-08-16 01:04:17 -0400 (Fri, 16 Aug 2024) |
EllapsedTime: 59.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GeneticsPed.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneticsPed.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GeneticsPed_1.67.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/GeneticsPed.Rcheck' * using R version 4.4.1 (2024-06-14 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 * using option '--no-vignettes' * checking for file 'GeneticsPed/DESCRIPTION' ... OK * this is package 'GeneticsPed' version '1.67.0' * 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 'GeneticsPed' can be installed ... WARNING Found the following significant warnings: pedtemplate.cc:373:15: warning: format '%d' expects argument of type 'int', but argument 2 has type '__gnu_cxx::__normal_iterator<TPed*, std::vector<TPed> >::difference_type' {aka 'long long int'} [-Wformat=] See 'F:/biocbuild/bbs-3.20-bioc/meat/GeneticsPed.Rcheck/00install.out' for details. * used C compiler: 'gcc.exe (GCC) 13.2.0' * used Fortran compiler: 'GNU Fortran (GCC) 13.2.0' * used C++ compiler: 'G__~1.EXE (GCC) 13.2.0' * checking installed package size ... OK * 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 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 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 generatePedigree: no visible global function definition for 'runif' model.matrix.Pedigree: no visible global function definition for 'model.matrix' writeMendel: no visible global function definition for '?' writeMendel: no visible global function definition for 'write.csv' Undefined global functions or variables: ? model.matrix runif write.csv Consider adding importFrom("stats", "model.matrix", "runif") importFrom("utils", "?", "write.csv") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) pedigree.Rd:166-167: Lost braces in \itemize; meant \describe ? checkRd: (-1) pedigree.Rd:168-169: Lost braces in \itemize; meant \describe ? checkRd: (-1) pedigree.Rd:170-171: Lost braces in \itemize; meant \describe ? checkRd: (-1) pedigree.Rd:172: Lost braces in \itemize; meant \describe ? checkRd: (-1) pedigree.Rd:173: Lost braces in \itemize; meant \describe ? checkRd: (-1) pedigree.Rd:174: Lost braces in \itemize; meant \describe ? checkRd: (-1) pedigree.Rd:175: Lost braces in \itemize; meant \describe ? checkRd: (-1) pedigree.Rd:176: Lost braces in \itemize; meant \describe ? checkRd: (-1) pedigree.Rd:177-178: Lost braces in \itemize; meant \describe ? checkRd: (-1) pedigree.Rd:179-180: Lost braces in \itemize; meant \describe ? checkRd: (-1) pedigree.Rd:181: Lost braces in \itemize; meant \describe ? checkRd: (-1) pedigree.Rd:182: Lost braces in \itemize; meant \describe ? checkRd: (-1) pedigree.Rd:183: Lost braces in \itemize; meant \describe ? checkRd: (-1) pedigree.Rd:184: Lost braces in \itemize; meant \describe ? checkRd: (-1) pedigree.Rd:185-187: Lost braces in \itemize; meant \describe ? * 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 line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... OK * checking compiled code ... OK * checking usage of KIND in Fortran files ... OK * checking sizes of PDF files under 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'doRUnit.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: 1 WARNING, 2 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/GeneticsPed.Rcheck/00check.log' for details.
GeneticsPed.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL GeneticsPed ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'GeneticsPed' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' using Fortran compiler: 'GNU Fortran (GCC) 13.2.0' using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ainverse.cc -o ainverse.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c eibd.cc -o eibd.o gfortran -O2 -mfpmath=sse -msse2 -mstackrealign -c ggmatmult.f -o ggmatmult.o gfortran -O2 -mfpmath=sse -msse2 -mstackrealign -c gpi.f -o gpi.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c inbreed.cc -o inbreed.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c inverseAdditive.cc -o inverseAdditive.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c meuwissen.cc -o meuwissen.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pedSort.cc -o pedSort.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pedtemplate.cc -o pedtemplate.o pedtemplate.cc: In member function 'void Pedigree::ShowPed()': pedtemplate.cc:373:15: warning: format '%d' expects argument of type 'int', but argument 2 has type '__gnu_cxx::__normal_iterator<TPed*, std::vector<TPed> >::difference_type' {aka 'long long int'} [-Wformat=] 373 | Rprintf("%d\t", p - pedigree.begin()); | ~^ ~~~~~~~~~~~~~~~~~~~~ | | | | int __gnu_cxx::__normal_iterator<TPed*, std::vector<TPed> >::difference_type {aka long long int} | %lld g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c register.cc -o register.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sargolzaei.c -o sargolzaei.o sargolzaei.c: In function 'sargolzaei': sargolzaei.c:52:32: warning: '*Ped[S][0]' may be used uninitialized [-Wmaybe-uninitialized] 52 | rPed[rN][0] = Link[Ped[S][0]]; | ~~~~~~^~~ sargolzaei.c:53:34: warning: '*Ped[D][1]' may be used uninitialized [-Wmaybe-uninitialized] 53 | rPed[rN++][1] = Link[Ped[D][1]]; | ~~~~~~^~~ sargolzaei.c:58:32: warning: '*Ped[D][0]' may be used uninitialized [-Wmaybe-uninitialized] 58 | rPed[rN][0] = Link[Ped[D][0]]; | ~~~~~~^~~ sargolzaei.c:59:34: warning: '*Ped[D][1]' may be used uninitialized [-Wmaybe-uninitialized] 59 | rPed[rN++][1] = Link[Ped[D][1]]; | ~~~~~~^~~ sargolzaei.c:72:20: warning: '*Ped[<unknown>][0]' may be used uninitialized [-Wmaybe-uninitialized] 72 | if(!Ped[SId[i]][0]) | ~~~~~~~~~~~^~~ sargolzaei.c:97:26: warning: '*Ped[<unknown>][0]' may be used uninitialized [-Wmaybe-uninitialized] 97 | if(S != Ped[SId[i]][0]) break; | ~~~~~~~~~~~^~~ sargolzaei.c:98:42: warning: '*Ped[<unknown>][1]' may be used uninitialized [-Wmaybe-uninitialized] 98 | else F[SId[i]] = x[Link[Ped[SId[i]][1]]] * 0.5f; | ~~~~~~~~~~~^~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sortped.cc -o sortped.o g++ -std=gnu++17 -shared -s -static-libgcc -o GeneticsPed.dll tmp.def ainverse.o eibd.o ggmatmult.o gpi.o inbreed.o inverseAdditive.o meuwissen.o pedSort.o pedtemplate.o register.o sargolzaei.o sortped.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -lgfortran -lm -lquadmath -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-GeneticsPed/00new/GeneticsPed/libs/x64 ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GeneticsPed)
GeneticsPed.Rcheck/tests/doRUnit.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > ### doRUnit.R > ###------------------------------------------------------------------------ > ### What: Run unit tests with RUnit > ### $Id$ > ### Time-stamp: <2007-04-19 00:32:42 ggorjan> > ###------------------------------------------------------------------------ > > ## unit tests will not be done if RUnit is not available > if(require("RUnit", quietly=TRUE)) { + + ## --- Setup --- + + pkg <- "GeneticsPed" + 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) + + ## --- 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 + ## NOTE from H. Pages <hpages@fhcrc.org> from the Gentleman Lab (Oct 16, + ## 2008): I've added the test below because printHTMLProtocol() seems + ## to be broken in RUnit 0.4.19 on the OS X platform. + if (substring(R.Version()$os, 1, 6) != "darwin") + printHTMLProtocol(tests, fileName=paste(pathReport, ".html", sep="")) + + ## Return stop() to cause R CMD check stop in case of + ## - failures i.e. FALSE to unit tests or + ## - errors i.e. R errors + tmp <- getErrors(tests) + if(tmp$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] "GeneticsPed" $getwd [1] "F:/biocbuild/bbs-3.20-bioc/meat/GeneticsPed.Rcheck/tests" $pathToUnitTests [1] "F:/biocbuild/bbs-3.20-bioc/tmpdir/RtmpqMwHeC/RLIBS_821432924a86/GeneticsPed/unitTests" Loading required package: MASS Attaching package: 'GeneticsPed' The following object is masked from 'package:stats': family Executing test function test.extend ... done successfully. Executing test function test.A ... done successfully. Executing test function test.F ... done successfully. Executing test function test.Z ... done successfully. Executing test function test.gpLong2Wide ... Loading required package: genetics Loading required package: combinat Attaching package: 'combinat' The following object is masked from 'package:utils': combn Loading required package: gdata Attaching package: 'gdata' The following object is masked from 'package:stats': nobs The following object is masked from 'package:utils': object.size The following object is masked from 'package:base': startsWith Loading required package: gtools Loading required package: mvtnorm NOTE: THIS PACKAGE IS NOW OBSOLETE. The R-Genetics project has developed an set of enhanced genetics packages to replace 'genetics'. Please visit the project homepage at http://rgenetics.org for informtion. Attaching package: 'genetics' The following objects are masked from 'package:base': %in%, as.factor, order done successfully. Executing test function test.gpi ... done successfully. Executing test function test.hwp ... Error in hwp(x = "A/A") : 'x' must be of a genotype class In addition: Warning messages: 1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties 2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry 3: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties 4: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry 5: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties 6: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry done successfully. Executing test function test.Pedigree ... Error in Pedigree(x = Mrode3.1, subject = "calf", ascendant = c("sire", : values of 'ascendantSex' must accord with values of 'sex' column In addition: Warning messages: 1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties 2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry done successfully. Executing test function test.prune ... done successfully. Executing test function test.TODO ... done successfully. ------------------- UNIT TEST SUMMARY --------------------- RUNIT TEST PROTOCOL -- Fri Aug 16 01:04:06 2024 *********************************************** Number of test functions: 10 Number of errors: 0 Number of failures: 0 1 Test Suite : GeneticsPed unit testing - 10 test functions, 0 errors, 0 failures Warning messages: 1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties 2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry 3: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties 4: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry > > ###------------------------------------------------------------------------ > ### doRUnit.R ends here > > proc.time() user system elapsed 0.42 0.25 0.79
GeneticsPed.Rcheck/GeneticsPed-Ex.timings
name | user | system | elapsed | |
TDT | 0.02 | 0.03 | 0.04 | |
check | 0.03 | 0.00 | 0.03 | |
datasets | 0.01 | 0.02 | 0.03 | |
extend | 0.05 | 0.00 | 0.05 | |
family | 0.02 | 0.00 | 0.02 | |
founder | 0 | 0 | 0 | |
geneContribution | 0.03 | 0.00 | 0.03 | |
generatePedigree | 0.08 | 0.00 | 0.08 | |
generation | 0.01 | 0.02 | 0.03 | |
gpi | 0 | 0 | 0 | |
gpiUtil | 0.03 | 0.02 | 0.14 | |
inbreeding | 0.11 | 0.00 | 0.11 | |
model.matrix | 0.01 | 0.01 | 0.03 | |
nIndividual | 0 | 0 | 0 | |
pedigree | 0 | 0 | 0 | |
prune | 0.03 | 0.00 | 0.03 | |
relationshipAdditive | 0.11 | 0.00 | 0.11 | |
removeIndividual | 0.02 | 0.00 | 0.02 | |
sort.pedigree | 0.03 | 0.00 | 0.03 | |
summary.pedigree | 0 | 0 | 0 | |