Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:35 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the flowFP package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowFP.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 651/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
flowFP 1.50.0 (landing page) Herb Holyst
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: 1.50.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowFP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowFP_1.50.0.tar.gz |
StartedAt: 2021-10-14 19:07:04 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 19:09:01 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 116.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: flowFP.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowFP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowFP_1.50.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/flowFP.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘flowFP/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘flowFP’ version ‘1.50.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘flowFP’ can be installed ... OK * 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 R 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 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 is not available * 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 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 ‘/Users/biocbuild/bbs-3.13-bioc/meat/flowFP.Rcheck/00check.log’ for details.
flowFP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL flowFP ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘flowFP’ ... ** using staged installation configure: creating ./config.status config.status: creating src/Makevars ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c flowFP.c -o flowFP.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c split_utils.c -o split_utils.o clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o flowFP.so flowFP.o init.o split_utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-flowFP/00new/flowFP/libs ** 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 ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (flowFP)
flowFP.Rcheck/tests/doRUnit.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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 /Users/biocbuild/bbs-3.13-bioc/meat/flowFP.Rcheck/tests/unitTests Running unit tests $pkg [1] "flowFP" $getwd [1] "/Users/biocbuild/bbs-3.13-bioc/meat/flowFP.Rcheck/tests" $pathToUnitTests [1] "/Users/biocbuild/bbs-3.13-bioc/meat/flowFP.Rcheck/tests/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. 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 -- Thu Oct 14 19:08:51 2021 *********************************************** 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 > > proc.time() user system elapsed 14.987 0.631 15.609
flowFP.Rcheck/flowFP-Ex.timings
name | user | system | elapsed | |
append-methods | 2.031 | 0.068 | 2.100 | |
flowFP-class | 0.863 | 0.040 | 0.905 | |
flowFP-package | 0.001 | 0.001 | 0.000 | |
flowFP | 0.844 | 0.032 | 0.876 | |
flowFPModel-class | 1.073 | 0.034 | 1.108 | |
flowFPModel | 0.719 | 0.034 | 0.755 | |
flowFPPlex-class | 0.001 | 0.000 | 0.002 | |
flowFPPlex | 2.100 | 0.059 | 2.164 | |
fs1 | 0.283 | 0.010 | 0.293 | |
fs2 | 0.213 | 0.012 | 0.226 | |
is.flowFP | 1.008 | 0.023 | 1.032 | |
is.flowFPModel | 0.901 | 0.029 | 0.935 | |
is.flowFPPlex | 1.097 | 0.036 | 1.137 | |
plate | 0.146 | 0.009 | 0.155 | |