Herb Holyst
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/flowFP |
| Branch: RELEASE_3_7 |
| Last Commit: f9ec8df |
| Last Changed Date: 2018-04-30 10:35:11 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:22:46 -0400 (Wed, 17 Oct 2018).
| Package 506/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| flowFP 1.38.0 Herb Holyst
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: flowFP |
| Version: 1.38.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:flowFP.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings flowFP_1.38.0.tar.gz |
| StartedAt: 2018-10-16 00:25:47 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 00:26:54 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 67.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: flowFP.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:flowFP.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings flowFP_1.38.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/flowFP.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (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 ‘1.38.0’
* 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 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 include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* 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: 2 NOTEs
See
‘/home/biocbuild/bbs-3.7-bioc/meat/flowFP.Rcheck/00check.log’
for details.
flowFP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL flowFP ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘flowFP’ ... configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c flowFP.c -o flowFP.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c split_utils.c -o split_utils.o gcc -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o flowFP.so flowFP.o init.o split_utils.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.7-bioc/R/library/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 * DONE (flowFP)
flowFP.Rcheck/tests/doRUnit.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 /home/biocbuild/bbs-3.7-bioc/meat/flowFP.Rcheck/tests/unitTests
Running unit tests
$pkg
[1] "flowFP"
$getwd
[1] "/home/biocbuild/bbs-3.7-bioc/meat/flowFP.Rcheck/tests"
$pathToUnitTests
[1] "/home/biocbuild/bbs-3.7-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 -- Tue Oct 16 00:26:51 2018
***********************************************
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
11.544 0.312 11.864
flowFP.Rcheck/flowFP-Ex.timings
| name | user | system | elapsed | |
| append-methods | 2.008 | 0.040 | 2.047 | |
| flowFP-class | 0.628 | 0.012 | 0.641 | |
| flowFP-package | 0.004 | 0.000 | 0.000 | |
| flowFP | 0.680 | 0.012 | 0.692 | |
| flowFPModel-class | 0.852 | 0.008 | 0.861 | |
| flowFPModel | 0.616 | 0.016 | 0.634 | |
| flowFPPlex-class | 0.004 | 0.000 | 0.001 | |
| flowFPPlex | 1.680 | 0.032 | 1.716 | |
| fs1 | 0.212 | 0.000 | 0.209 | |
| fs2 | 0.192 | 0.004 | 0.197 | |
| is.flowFP | 0.916 | 0.016 | 0.933 | |
| is.flowFPModel | 0.840 | 0.012 | 0.854 | |
| is.flowFPPlex | 0.812 | 0.016 | 0.825 | |
| plate | 0.108 | 0.004 | 0.113 | |