Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-07-12 17:42 -0400 (Fri, 12 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4741
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4483
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4512
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4461
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

Package 740/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowFP 1.62.0  (landing page)
Herb Holyst , Wade Rogers
Snapshot Date: 2024-07-10 14:00 -0400 (Wed, 10 Jul 2024)
git_url: https://git.bioconductor.org/packages/flowFP
git_branch: RELEASE_3_19
git_last_commit: c7ea156
git_last_commit_date: 2024-04-30 10:20:11 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for flowFP on kjohnson1

To the developers/maintainers of the flowFP package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: flowFP
Version: 1.62.0
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_1.62.0.tar.gz
StartedAt: 2024-07-11 19:47:22 -0400 (Thu, 11 Jul 2024)
EndedAt: 2024-07-11 19:49:23 -0400 (Thu, 11 Jul 2024)
EllapsedTime: 120.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: flowFP.Rcheck
Warnings: 1

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_1.62.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/flowFP.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowFP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowFP’ version ‘1.62.0’
* 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 ... WARNING
Found the following significant warnings:
  flowFP.c:189:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
See ‘/Users/biocbuild/bbs-3.19-bioc/meat/flowFP.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 code 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) flowFPPlex.Rd:41: Escaped LaTeX specials: \_
checkRd: (-1) flowFPPlex.Rd:42: Escaped LaTeX specials: \_
* 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-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/4.4-arm64/Resources/library’
* installing *source* package ‘flowFP’ ...
** using staged installation
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c flowFP.c -o flowFP.o
flowFP.c:189:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
        if(((!isReal(rmatrix)) & !isInteger(rmatrix)) | isNull(dim) | (LENGTH(dim)!=2))
           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                               &&
flowFP.c:189:6: note: cast one or both operands to int to silence this warning
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c init.c -o init.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c split_utils.c -o split_utils.o
split_utils.c:22:6: warning: variable 'num_low' set but not used [-Wunused-but-set-variable]
        int num_low = 0;
            ^
split_utils.c:23:6: warning: variable 'num_hi' set but not used [-Wunused-but-set-variable]
        int num_hi = 0;
            ^
2 warnings generated.
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/4.4-arm64/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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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-3.19-bioc/meat/flowFP.Rcheck/tests/unitTests 

Running unit tests
$pkg
[1] "flowFP"

$getwd
[1] "/Users/biocbuild/bbs-3.19-bioc/meat/flowFP.Rcheck/tests"

$pathToUnitTests
[1] "/Users/biocbuild/bbs-3.19-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 -- Thu Jul 11 19:49:10 2024 
*********************************************** 
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 
 18.498   0.812  20.271 

Example timings

flowFP.Rcheck/flowFP-Ex.timings

nameusersystemelapsed
append-methods2.8340.1483.090
flowFP-class0.9740.0811.081
flowFP-package0.0000.0010.000
flowFP1.0270.0651.161
flowFPModel-class1.4980.0731.578
flowFPModel1.2470.0561.316
flowFPPlex-class0.0010.0000.002
flowFPPlex2.5240.1262.697
fs10.2890.0080.298
fs20.2790.0090.291
is.flowFP1.3820.0731.496
is.flowFPModel1.2970.0851.398
is.flowFPPlex1.3720.0731.532
plate0.3850.0100.402