Herb Holyst
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/flowFP |
| Branch: RELEASE_3_11 |
| Last Commit: c405979 |
| Last Changed Date: 2020-04-27 14:19:37 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:35 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE flowFP PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 614/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| flowFP 1.46.0 Herb Holyst
| malbec2 | Linux (Ubuntu 18.04.4 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: 1.46.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowFP.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings flowFP_1.46.0.tar.gz |
| StartedAt: 2020-10-17 04:07:04 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 04:10:11 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 187.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: flowFP.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:flowFP.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings flowFP_1.46.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/flowFP.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.46.0'
* 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 5.1Mb
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-3.11-bioc/R/library/flowFP/libs/i386/flowFP.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.11-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
** 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-3.11-bioc/meat/flowFP.Rcheck/00check.log'
for details.
flowFP.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/flowFP_1.46.0.tar.gz && rm -rf flowFP.buildbin-libdir && mkdir flowFP.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=flowFP.buildbin-libdir flowFP_1.46.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL flowFP_1.46.0.zip && rm flowFP_1.46.0.tar.gz flowFP_1.46.0.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
100 4456k 100 4456k 0 0 51.0M 0 --:--:-- --:--:-- --:--:-- 55.0M
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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-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-3~1.11-/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-3~1.11-/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-3~1.11-/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-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/flowFP.buildbin-libdir/flowFP/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'flowFP' as flowFP_1.46.0.zip
* DONE (flowFP)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'flowFP' successfully unpacked and MD5 sums checked
|
flowFP.Rcheck/tests_i386/doRUnit.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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-3.11-bioc/meat/flowFP.Rcheck/tests_i386/unitTests
Running unit tests
$pkg
[1] "flowFP"
$getwd
[1] "C:/Users/biocbuild/bbs-3.11-bioc/meat/flowFP.Rcheck/tests_i386"
$pathToUnitTests
[1] "C:/Users/biocbuild/bbs-3.11-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: There were 50 or more warnings (use warnings() to see the first 50)
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 -- Sat Oct 17 04:09:46 2020
***********************************************
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
There were 50 or more warnings (use warnings() to see the first 50)
>
> proc.time()
user system elapsed
15.15 0.71 15.86
|
flowFP.Rcheck/tests_x64/doRUnit.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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-3.11-bioc/meat/flowFP.Rcheck/tests_x64/unitTests
Running unit tests
$pkg
[1] "flowFP"
$getwd
[1] "C:/Users/biocbuild/bbs-3.11-bioc/meat/flowFP.Rcheck/tests_x64"
$pathToUnitTests
[1] "C:/Users/biocbuild/bbs-3.11-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: There were 50 or more warnings (use warnings() to see the first 50)
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 -- Sat Oct 17 04:10:02 2020
***********************************************
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
There were 50 or more warnings (use warnings() to see the first 50)
>
> proc.time()
user system elapsed
14.68 0.67 15.34
|
|
flowFP.Rcheck/examples_i386/flowFP-Ex.timings
|
flowFP.Rcheck/examples_x64/flowFP-Ex.timings
|