| Back to Rapid builds (Linux only) of a subset of BioC 3.24 Report updated every 4 hours |
This page was generated on 2026-05-21 14:26 -0400 (Thu, 21 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 (2026-04-24) -- "Because it was There" | 918 |
| 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 89/229 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BIOCCHECK | |||||||
| flowCore 2.25.0 (landing page) Mike Jiang
| teran2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | WARNINGS | ERRORS | |||||||
|
To the developers/maintainers of the flowCore package: - 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. |
| Package: flowCore |
| Version: 2.25.0 |
| Command: /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/R CMD check --install=check:flowCore.install-out.txt --library=/home/rapidbuild/bbs-3.24-bioc-rapid/R/site-library --timings flowCore_2.25.0.tar.gz |
| StartedAt: 2026-05-21 13:08:44 -0400 (Thu, 21 May 2026) |
| EndedAt: 2026-05-21 13:10:50 -0400 (Thu, 21 May 2026) |
| EllapsedTime: 125.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: flowCore.Rcheck |
| Warnings: 4 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/R CMD check --install=check:flowCore.install-out.txt --library=/home/rapidbuild/bbs-3.24-bioc-rapid/R/site-library --timings flowCore_2.25.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/flowCore.Rcheck’
* using R version 4.6.0 (2026-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-21 17:08:44 UTC
* checking for file ‘flowCore/DESCRIPTION’ ... OK
* this is package ‘flowCore’ version ‘2.25.0’
* package encoding: UTF-8
* 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 ‘flowCore’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking C++ specification ... INFO
specified C++17
* checking installed package size ... INFO
installed size is 44.3Mb
sub-directories of 1Mb or more:
R 1.2Mb
data 5.4Mb
extdata 1.1Mb
libs 35.8Mb
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘Rcpp’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
eval,compensatedParameter-missing : <anonymous>: no visible binding for
global variable ‘mat’
eval,compensatedParameter-missing : <anonymous>: no visible binding for
global variable ‘msv’
show,flowFrame: no visible global function definition for
‘capture.output’
Undefined global functions or variables:
capture.output mat msv
Consider adding
importFrom("utils", "capture.output")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) identifier-methods.Rd:36: Escaped LaTeX specials: \^
checkRd: (-1) quadraticTransform.Rd:26: Escaped LaTeX specials: \^
checkRd: (-1) read.FCS.Rd:26: Escaped LaTeX specials: \$
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'flowFrame-class.Rd':
‘[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrame}’
‘[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrames}’
Non-topic package-anchored link(s) in Rd file 'flowSet-class.Rd':
‘[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrame}’
Non-topic package-anchored link(s) in Rd file 'parameters-methods.Rd':
‘[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrame}’
Non-topic package-anchored link(s) in Rd file 'read.flowSet.Rd':
‘[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrame}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘multiRangeGate’
Undocumented S4 classes:
‘multiRangeGate’
Undocumented S4 methods:
generic '%in%' and siglist 'flowFrame,multiRangeGate'
generic 'show' and siglist 'multiRangeGate'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... WARNING
Non-portable flags in variable 'PKG_CPPFLAGS':
-w -Wfatal-errors
* checking for GNU extensions in Makefiles ... INFO
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... WARNING
apparently using $(BLAS_LIBS) without following $(FLIBS) in ‘src/Makevars’
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/flowCore/libs/flowCore.so’:
Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
Found ‘__printf_chk’, possibly from ‘printf’ (C)
Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
Found ‘abort’, possibly from ‘abort’ (C)
Found ‘exit’, possibly from ‘exit’ (C)
Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Found ‘rand’, possibly from ‘rand’ (C)
Found ‘srand’, possibly from ‘srand’ (C)
Found ‘stderr’, possibly from ‘stderr’ (C)
Found ‘stdout’, possibly from ‘stdout’ (C)
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 nor [v]sprintf. 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 sizes of PDF files under ‘inst/doc’ ...* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 4 WARNINGs, 4 NOTEs
See
‘/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/flowCore.Rcheck/00check.log’
for details.
flowCore.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/R CMD INSTALL flowCore ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library’ * installing *source* package ‘flowCore’ ... ** this is package ‘flowCore’ version ‘2.25.0’ ** using staged installation ** libs specified C++17 using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’ using C++17 g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/cpp11/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/BH/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/cytolib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c FastLogicle.cpp -o FastLogicle.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/cpp11/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/BH/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/cytolib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c Hyperlog.cpp -o Hyperlog.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/cpp11/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/BH/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/cytolib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c Logicle.cpp -o Logicle.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/cpp11/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/BH/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/cytolib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c biexponential.cpp -o biexponential.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/cpp11/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/BH/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/cytolib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c convertRawBytes.cpp -o convertRawBytes.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/cpp11/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/BH/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/cytolib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c cpp11.cpp -o cpp11.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/cpp11/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/BH/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/cytolib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c fcsTextParse.cpp -o fcsTextParse.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/cpp11/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/BH/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/cytolib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c hyperlogTransform.cpp -o hyperlogTransform.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/cpp11/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/BH/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/cytolib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c inPolygon.cpp -o inPolygon.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/cpp11/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/BH/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/cytolib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c inPolytope.cpp -o inPolytope.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/cpp11/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/BH/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/cytolib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c logicleTransform.cpp -o logicleTransform.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/cpp11/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/BH/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/cytolib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c poly_centroid.cpp -o poly_centroid.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/cpp11/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/BH/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/cytolib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c sortBytes.cpp -o sortBytes.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/cpp11/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/BH/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/cytolib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c uint2double.cpp -o uint2double.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.24-bioc-rapid/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/cpp11/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/BH/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/cytolib/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/RProtoBufLib/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c zeroin.cpp -o zeroin.o g++ -std=gnu++17 -shared -L/usr/local/lib -o flowCore.so FastLogicle.o Hyperlog.o Logicle.o biexponential.o convertRawBytes.o cpp11.o fcsTextParse.o hyperlogTransform.o inPolygon.o inPolytope.o logicleTransform.o poly_centroid.o sortBytes.o uint2double.o zeroin.o /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/cytolib/lib/libcytolib.a /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/Rhdf5lib/lib/libhdf5_cpp.a /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/Rhdf5lib/lib/libhdf5.a -L/media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/Rhdf5lib/lib -lsz -lm -ldl -lcurl -lssl -lcrypto -llapack -L/home/rapidbuild/bbs-3.24-bioc-rapid/R/lib -lRblas if [ `uname -s` = 'Darwin' ]; then install_name_tool -change /usr/local/clang4/lib/libc++.1.dylib /usr/lib/libc++.1.dylib flowCore.so; fi installing to /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/R/site-library/00LOCK-flowCore/00new/flowCore/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** 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 (flowCore)
flowCore.Rcheck/tests/testthat.Rout
R version 4.6.0 (2026-04-24) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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.
> library(testthat)
> library(flowCore)
> library(flowStats)
Warning message:
replacing previous import 'flowViz::contour' by 'graphics::contour' when loading 'flowStats'
>
>
> test_check("flowCore")
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following object is masked from 'package:flowStats':
normalize
The following object is masked from 'package:flowCore':
normalize
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
[ FAIL 0 | WARN 2 | SKIP 3 | PASS 324 ]
══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• dir.exists(dataPath) is not TRUE (1): 'test-IO-internal.R:4:1'
• file.exists(filename) is not TRUE (2): 'test-IO.R:32:3', 'test-IO.R:40:3'
[ FAIL 0 | WARN 2 | SKIP 3 | PASS 324 ]
>
> #devtools::test("~/rglab/workspace/flowCore")
>
> proc.time()
user system elapsed
16.444 0.697 17.149
flowCore.Rcheck/flowCore-Ex.timings
| name | user | system | elapsed | |
| EHtrans-class | 0.045 | 0.011 | 0.060 | |
| FCSTransTransform | 1.016 | 0.039 | 1.055 | |
| Subset-methods | 0.138 | 0.001 | 0.143 | |
| arcsinhTransform | 0.036 | 0.001 | 0.039 | |
| asinht-class | 0.022 | 0.002 | 0.024 | |
| asinhtGml2-class | 0.022 | 0.007 | 0.029 | |
| biexponentialTransform | 2.371 | 0.047 | 2.417 | |
| boundaryFilter-class | 0.049 | 0.003 | 0.051 | |
| characterOrNumeric-class | 0.001 | 0.000 | 0.000 | |
| characterOrParameters-class | 0.000 | 0.000 | 0.001 | |
| characterOrTransformation-class | 0.001 | 0.000 | 0.000 | |
| coerce | 0.037 | 0.004 | 0.041 | |
| collapse_desc | 1.094 | 0.023 | 1.117 | |
| compensatedParameter-class | 0.094 | 0.002 | 0.177 | |
| compensation-class | 0.182 | 0.001 | 0.183 | |
| decompensate | 0.030 | 0.003 | 0.034 | |
| dg1polynomial-class | 0.028 | 0.002 | 0.030 | |
| each_col | 0.022 | 0.000 | 0.022 | |
| ellipsoidGate-class | 0.041 | 0.000 | 0.041 | |
| exponential-class | 0.019 | 0.000 | 0.019 | |
| expressionFilter-class | 0.054 | 0.000 | 0.054 | |
| filter-methods | 1.052 | 0.012 | 1.064 | |
| filter-on-methods | 0.050 | 0.001 | 0.052 | |
| filterList-class | 0.002 | 0.000 | 0.003 | |
| filterResult-class | 0 | 0 | 0 | |
| filterResultList-class | 3.796 | 0.108 | 3.903 | |
| filterSummary-class | 0.047 | 0.001 | 0.048 | |
| filterSummaryList-class | 1.432 | 0.019 | 1.451 | |
| flowFrame-class | 2.909 | 0.045 | 2.955 | |
| flowSet-class | 2.199 | 0.112 | 2.313 | |
| fr_append_cols | 0.986 | 0.021 | 1.007 | |
| fsApply | 0.088 | 0.009 | 0.096 | |
| getIndexSort | 0.019 | 0.003 | 0.022 | |
| hyperlog-class | 0.531 | 0.002 | 0.533 | |
| hyperlogtGml2-class | 0.023 | 0.001 | 0.023 | |
| identifier-methods | 0.018 | 0.000 | 0.018 | |
| inverseLogicleTransform | 1.002 | 0.001 | 1.004 | |
| invsplitscale-class | 0.021 | 0.000 | 0.022 | |
| keyword-methods | 0.995 | 0.010 | 1.006 | |
| kmeansFilter-class | 0.077 | 0.001 | 0.078 | |
| linearTransform | 0.023 | 0.000 | 0.024 | |
| lintGml2-class | 0.021 | 0.000 | 0.020 | |
| lnTransform | 1.190 | 0.014 | 1.204 | |
| logTransform | 0.03 | 0.00 | 0.03 | |
| logarithm-class | 0.020 | 0.000 | 0.021 | |
| logicalFilterResult-class | 0.000 | 0.000 | 0.001 | |
| logicleTransform | 1.010 | 0.006 | 1.016 | |
| logicletGml2-class | 0.029 | 0.000 | 0.030 | |
| logtGml2-class | 0.021 | 0.000 | 0.022 | |
| manyFilterResult-class | 0.000 | 0.001 | 0.000 | |
| markernames | 0.989 | 0.004 | 0.993 | |
| multipleFilterResult-class | 0 | 0 | 0 | |
| parameters-methods | 0.018 | 0.001 | 0.020 | |
| polygonGate-class | 0.041 | 0.000 | 0.042 | |
| quadGate-class | 0.481 | 0.007 | 0.488 | |
| quadratic-class | 0.023 | 0.000 | 0.022 | |
| quadraticTransform | 0.023 | 0.001 | 0.024 | |
| ratio-class | 0.021 | 0.000 | 0.021 | |
| ratiotGml2-class | 0.02 | 0.00 | 0.02 | |
| read.FCS | 0.053 | 0.000 | 0.053 | |
| read.FCSheader | 0.003 | 0.001 | 0.003 | |
| read.flowSet | 0.069 | 0.001 | 0.070 | |
| rectangleGate-class | 0.055 | 0.000 | 0.055 | |
| rotate_gate | 0 | 0 | 0 | |
| sampleFilter-class | 0.034 | 0.000 | 0.034 | |
| scaleTransform | 0.023 | 0.000 | 0.024 | |
| scale_gate | 0.001 | 0.000 | 0.000 | |
| shift_gate | 0 | 0 | 0 | |
| singleParameterTransform-class | 0.000 | 0.001 | 0.001 | |
| sinht-class | 0.019 | 0.001 | 0.020 | |
| split-methods | 1.157 | 0.002 | 1.160 | |
| splitScaleTransform | 1.188 | 0.007 | 1.195 | |
| splitscale-class | 0.021 | 0.000 | 0.021 | |
| squareroot-class | 0.02 | 0.00 | 0.02 | |
| timeFilter-class | 1.721 | 0.005 | 1.726 | |
| transform-class | 0.001 | 0.000 | 0.001 | |
| transform | 1.217 | 0.004 | 1.222 | |
| transformFilter-class | 0.091 | 0.001 | 0.092 | |
| transformList-class | 0.978 | 0.004 | 0.983 | |
| transformMap-class | 0 | 0 | 0 | |
| transform_gate | 0 | 0 | 0 | |
| truncateTransform | 0.022 | 0.001 | 0.023 | |
| unitytransform-class | 0.018 | 0.000 | 0.018 | |
| write.FCS | 0.028 | 0.001 | 0.029 | |
| write.flowSet | 1.085 | 0.005 | 1.091 | |