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CHECK report for flowFP on malbec2

This page was generated on 2018-10-17 08:22:46 -0400 (Wed, 17 Oct 2018).

Package 506/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowFP 1.38.0
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)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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###
### 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
###
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* 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.



Installation output

flowFP.Rcheck/00install.out

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###
### 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)

Tests output

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 

Example timings

flowFP.Rcheck/flowFP-Ex.timings

nameusersystemelapsed
append-methods2.0080.0402.047
flowFP-class0.6280.0120.641
flowFP-package0.0040.0000.000
flowFP0.6800.0120.692
flowFPModel-class0.8520.0080.861
flowFPModel0.6160.0160.634
flowFPPlex-class0.0040.0000.001
flowFPPlex1.6800.0321.716
fs10.2120.0000.209
fs20.1920.0040.197
is.flowFP0.9160.0160.933
is.flowFPModel0.8400.0120.854
is.flowFPPlex0.8120.0160.825
plate0.1080.0040.113