Back to Multiple platform build/check report for BioC 3.14
ABCDE[F]GHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-04-13 12:08:00 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (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

CHECK results for flowFP on machv2


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? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 661/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowFP 1.52.0  (landing page)
Herb Holyst
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/flowFP
git_branch: RELEASE_3_14
git_last_commit: 5e0174a
git_last_commit_date: 2021-10-26 11:54:08 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: flowFP
Version: 1.52.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowFP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowFP_1.52.0.tar.gz
StartedAt: 2022-04-12 13:22:29 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 13:24:43 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 133.7 seconds
RetCode: 0
Status:   OK  
CheckDir: flowFP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowFP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowFP_1.52.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/flowFP.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.52.0’
* 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 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/flowFP.Rcheck/00check.log’
for details.



Installation output

flowFP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/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)

Tests output

flowFP.Rcheck/tests/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-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-3.14-bioc/meat/flowFP.Rcheck/tests/unitTests 

Running unit tests
$pkg
[1] "flowFP"

$getwd
[1] "/Users/biocbuild/bbs-3.14-bioc/meat/flowFP.Rcheck/tests"

$pathToUnitTests
[1] "/Users/biocbuild/bbs-3.14-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.

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 13:24:31 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 
 17.515   0.740  18.250 

Example timings

flowFP.Rcheck/flowFP-Ex.timings

nameusersystemelapsed
append-methods2.4320.0932.531
flowFP-class0.9380.0390.977
flowFP-package0.0000.0000.001
flowFP0.9520.0340.989
flowFPModel-class1.2060.0351.243
flowFPModel0.7490.0280.780
flowFPPlex-class0.0010.0000.002
flowFPPlex2.3060.0652.376
fs10.3240.0090.333
fs20.3040.0090.314
is.flowFP1.2500.0421.295
is.flowFPModel1.0620.0271.090
is.flowFPPlex1.3130.0321.346
plate0.2050.0110.217