Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:06:33 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
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 |
To the developers/maintainers of the flowFP package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/flowFP.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 661/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
flowFP 1.52.0 (landing page) Herb Holyst
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: flowFP |
Version: 1.52.0 |
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowFP.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings flowFP_1.52.0.tar.gz |
StartedAt: 2022-04-12 19:44:57 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 19:49:18 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 261.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: flowFP.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowFP.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings flowFP_1.52.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/flowFP.Rcheck' * using R version 4.1.3 (2022-03-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'flowFP/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'flowFP' version '1.52.0' * 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 'flowFP' can be installed ... OK * checking installed package size ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: data 4.3Mb * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE flowFP: no visible global function definition for 'identifier' flowFPModel: no visible global function definition for 'median' flowFPModel: no visible global function definition for 'fsApply' flowFPModel: no visible global function definition for 'identifier' initFPplot: no visible global function definition for 'legend' plotGridFP: no visible global function definition for 'legend' plotStackFP: no visible global function definition for 'legend' plotStackFP: no visible global function definition for 'axis' Undefined global functions or variables: axis fsApply identifier legend median Consider adding importFrom("graphics", "axis", "legend") importFrom("stats", "median") 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 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 include directives in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/flowFP/libs/i386/flowFP.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/flowFP/libs/x64/flowFP.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) 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. 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 ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed flowFP 0.74 0.06 6.02 ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'doRUnit.R' OK ** running tests for arch 'x64' ... Running 'doRUnit.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: 3 NOTEs See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/flowFP.Rcheck/00check.log' for details.
flowFP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/flowFP_1.52.0.tar.gz && rm -rf flowFP.buildbin-libdir && mkdir flowFP.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowFP.buildbin-libdir flowFP_1.52.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL flowFP_1.52.0.zip && rm flowFP_1.52.0.tar.gz flowFP_1.52.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 3 4457k 3 146k 0 0 638k 0 0:00:06 --:--:-- 0:00:06 640k 42 4457k 42 1908k 0 0 1532k 0 0:00:02 0:00:01 0:00:01 1533k 100 4457k 100 4457k 0 0 2050k 0 0:00:02 0:00:02 --:--:-- 2051k install for i386 * installing *source* package 'flowFP' ... ** using staged installation ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c flowFP.c -o flowFP.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c split_utils.c -o split_utils.o C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o flowFP.dll tmp.def flowFP.o init.o split_utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/flowFP.buildbin-libdir/00LOCK-flowFP/00new/flowFP/libs/i386 ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for 'append' from package 'base' in package 'flowFP' ** help *** installing help indices converting help for package 'flowFP' finding HTML links ... done append-methods html binBoundary-methods html counts-methods html flowFP-class html flowFP-package html flowFP html flowFPModel-class html flowFPModel html flowFPPlex-class html flowFPPlex html fs1 html fs2 html hasClasses-methods html index-methods html is.flowFP html is.flowFPModel html is.flowFPPlex html length-methods html nFeatures-methods html nInstances-methods html nRecursions-methods html name-methods html parameters-methods html plate html plot-methods html sampleClasses-methods html sampleNames-methods html show-methods html summary-methods html tags-methods html ** 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 install for x64 * installing *source* package 'flowFP' ... ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c flowFP.c -o flowFP.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o "C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c split_utils.c -o split_utils.o C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o flowFP.dll tmp.def flowFP.o init.o split_utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/flowFP.buildbin-libdir/flowFP/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'flowFP' as flowFP_1.52.0.zip * DONE (flowFP) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'flowFP' successfully unpacked and MD5 sums checked
flowFP.Rcheck/tests_i386/doRUnit.Rout R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-bit) 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. > ## unit tests will not be done if RUnit is not available > if(require("RUnit", quietly=TRUE)) { + + ## --- Setup --- + + pkg <- "flowFP" + if(Sys.getenv("RCMDCHECK") == "") { + ## Path to unit tests for standalone running under Makefile (not R CMD check) + ## PKG/tests/unitTests + path <- file.path(getwd(), "unitTests") + cat("sourced", path, "\n") + } else { + ## Path to unit tests for R CMD check + ## PKG.Rcheck/PKG/../tests/unitTests + path <- system.file(package=pkg, "..", "tests", "unitTests") + cat("RCMDCHECK ->", path, "<-\n") + } + cat("\nRunning unit tests\n") + print(list(pkg=pkg, getwd=getwd(), pathToUnitTests=path)) + + library(package=pkg, character.only=TRUE, verbose=FALSE) + + ## 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") + } sourced C:/Users/biocbuild/bbs-3.14-bioc/meat/flowFP.Rcheck/tests_i386/unitTests Running unit tests $pkg [1] "flowFP" $getwd [1] "C:/Users/biocbuild/bbs-3.14-bioc/meat/flowFP.Rcheck/tests_i386" $pathToUnitTests [1] "C:/Users/biocbuild/bbs-3.14-bioc/meat/flowFP.Rcheck/tests_i386/unitTests" Loading required package: flowCore Loading required package: flowViz Loading required package: lattice Executing test function test.FP2 ... done successfully. Executing test function test.Reducing_model_nRecursions ... done successfully. Executing test function test.Reducing_nRecursions ... done successfully. Executing test function test.fingerprint1 ... done successfully. Executing test function test.BadParams ... Error : One or more 'parameters' don't match this flowSet or flowFrame. In addition: Warning messages: 1: In RNGkind(kind = testSuite$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$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry Error : 'parameters' is out of bounds for this flowSet or flowFrame. done successfully. Executing test function test.CheckAutoLevel ... done successfully. Executing test function test.ModelAccessors ... done successfully. Executing test function test.ModelConstruction ... done successfully. Executing test function test.NonFlowData ... done successfully. Executing test function test.plex1 ... done successfully. Executing test function test.plex2 ... done successfully. Executing test function test.plex_append ... done successfully. Executing test function test.plex_append_plex ... done successfully. Executing test function test.plex_testClasses ... done successfully. ------------------- UNIT TEST SUMMARY --------------------- RUNIT TEST PROTOCOL -- Tue Apr 12 19:48:32 2022 *********************************************** Number of test functions: 14 Number of errors: 0 Number of failures: 0 1 Test Suite : flowFP unit testing - 14 test functions, 0 errors, 0 failures Warning messages: 1: In RNGkind(kind = testSuite$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 > > proc.time() user system elapsed 14.35 0.62 14.96 |
flowFP.Rcheck/tests_x64/doRUnit.Rout R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) 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. > ## unit tests will not be done if RUnit is not available > if(require("RUnit", quietly=TRUE)) { + + ## --- Setup --- + + pkg <- "flowFP" + if(Sys.getenv("RCMDCHECK") == "") { + ## Path to unit tests for standalone running under Makefile (not R CMD check) + ## PKG/tests/unitTests + path <- file.path(getwd(), "unitTests") + cat("sourced", path, "\n") + } else { + ## Path to unit tests for R CMD check + ## PKG.Rcheck/PKG/../tests/unitTests + path <- system.file(package=pkg, "..", "tests", "unitTests") + cat("RCMDCHECK ->", path, "<-\n") + } + cat("\nRunning unit tests\n") + print(list(pkg=pkg, getwd=getwd(), pathToUnitTests=path)) + + library(package=pkg, character.only=TRUE, verbose=FALSE) + + ## 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") + } sourced C:/Users/biocbuild/bbs-3.14-bioc/meat/flowFP.Rcheck/tests_x64/unitTests Running unit tests $pkg [1] "flowFP" $getwd [1] "C:/Users/biocbuild/bbs-3.14-bioc/meat/flowFP.Rcheck/tests_x64" $pathToUnitTests [1] "C:/Users/biocbuild/bbs-3.14-bioc/meat/flowFP.Rcheck/tests_x64/unitTests" Loading required package: flowCore Loading required package: flowViz Loading required package: lattice Executing test function test.FP2 ... done successfully. Executing test function test.Reducing_model_nRecursions ... done successfully. Executing test function test.Reducing_nRecursions ... done successfully. Executing test function test.fingerprint1 ... done successfully. Executing test function test.BadParams ... Error : One or more 'parameters' don't match this flowSet or flowFrame. In addition: Warning messages: 1: In RNGkind(kind = testSuite$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$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry Error : 'parameters' is out of bounds for this flowSet or flowFrame. done successfully. Executing test function test.CheckAutoLevel ... done successfully. Executing test function test.ModelAccessors ... done successfully. Executing test function test.ModelConstruction ... done successfully. Executing test function test.NonFlowData ... done successfully. Executing test function test.plex1 ... done successfully. Executing test function test.plex2 ... done successfully. Executing test function test.plex_append ... done successfully. Executing test function test.plex_append_plex ... done successfully. Executing test function test.plex_testClasses ... done successfully. ------------------- UNIT TEST SUMMARY --------------------- RUNIT TEST PROTOCOL -- Tue Apr 12 19:48:55 2022 *********************************************** Number of test functions: 14 Number of errors: 0 Number of failures: 0 1 Test Suite : flowFP unit testing - 14 test functions, 0 errors, 0 failures Warning messages: 1: In RNGkind(kind = testSuite$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 > > proc.time() user system elapsed 13.90 1.04 21.87 |
flowFP.Rcheck/examples_i386/flowFP-Ex.timings
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flowFP.Rcheck/examples_x64/flowFP-Ex.timings
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