Mike Jiang
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/flowCore |
| git_branch: devel |
| git_last_commit: 46f519e |
| git_last_commit_date: 2024-10-29 09:27:02 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
| 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 722/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| flowCore 2.19.0 (landing page) Mike Jiang
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the flowCore package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowCore.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: flowCore |
| Version: 2.19.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:flowCore.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings flowCore_2.19.0.tar.gz |
| StartedAt: 2024-12-24 06:47:06 -0000 (Tue, 24 Dec 2024) |
| EndedAt: 2024-12-24 06:50:09 -0000 (Tue, 24 Dec 2024) |
| EllapsedTime: 183.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: flowCore.Rcheck |
| Warnings: 3 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:flowCore.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings flowCore_2.19.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/flowCore.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowCore/DESCRIPTION’ ... OK
* this is package ‘flowCore’ version ‘2.19.0’
* 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: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking C++ specification ... OK
* checking installed package size ... INFO
installed size is 16.1Mb
sub-directories of 1Mb or more:
R 1.2Mb
data 5.4Mb
extdata 1.1Mb
libs 7.6Mb
* 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 ...Warning: program compiled against libxml 212 using older 211
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 ... OK
* 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 ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/flowCore/libs/flowCore.so’:
Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
Found ‘rand’, possibly from ‘rand’ (C)
Found ‘sprintf’, possibly from ‘sprintf’ (C)
Found ‘srand’, possibly from ‘srand’ (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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
filterResultList-class 6.786 0.132 6.943
flowFrame-class 5.418 0.064 5.496
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 WARNINGs, 3 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/flowCore.Rcheck/00check.log’
for details.
flowCore.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL flowCore ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘flowCore’ ... ** using staged installation ** libs using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ using C++17 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c FastLogicle.cpp -o FastLogicle.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c Hyperlog.cpp -o Hyperlog.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c Logicle.cpp -o Logicle.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c biexponential.cpp -o biexponential.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c convertRawBytes.cpp -o convertRawBytes.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c cpp11.cpp -o cpp11.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c fcsTextParse.cpp -o fcsTextParse.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c hyperlogTransform.cpp -o hyperlogTransform.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c inPolygon.cpp -o inPolygon.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c inPolytope.cpp -o inPolytope.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c logicleTransform.cpp -o logicleTransform.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c poly_centroid.cpp -o poly_centroid.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c sortBytes.cpp -o sortBytes.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c uint2double.cpp -o uint2double.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DBOOST_NO_AUTO_PTR -w -Wfatal-errors -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cpp11/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RProtoBufLib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c zeroin.cpp -o zeroin.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -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 /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/cytolib/lib/libcytolib.a -L/home/biocbuild/R/R/lib -lR 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 /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
28.224 0.533 28.826
flowCore.Rcheck/flowCore-Ex.timings
| name | user | system | elapsed | |
| EHtrans-class | 0.082 | 0.004 | 0.087 | |
| FCSTransTransform | 1.733 | 0.028 | 1.764 | |
| Subset-methods | 0.261 | 0.000 | 0.265 | |
| arcsinhTransform | 0.062 | 0.004 | 0.066 | |
| asinht-class | 0.035 | 0.000 | 0.035 | |
| asinhtGml2-class | 0.040 | 0.004 | 0.045 | |
| biexponentialTransform | 4.246 | 0.020 | 4.275 | |
| boundaryFilter-class | 0.098 | 0.000 | 0.099 | |
| characterOrNumeric-class | 0.001 | 0.000 | 0.001 | |
| characterOrParameters-class | 0.001 | 0.000 | 0.000 | |
| characterOrTransformation-class | 0.001 | 0.000 | 0.001 | |
| coerce | 0.065 | 0.000 | 0.065 | |
| collapse_desc | 1.827 | 0.012 | 1.842 | |
| compensatedParameter-class | 0.164 | 0.000 | 0.175 | |
| compensation-class | 0.389 | 0.000 | 0.390 | |
| decompensate | 0.066 | 0.000 | 0.066 | |
| dg1polynomial-class | 0.046 | 0.000 | 0.046 | |
| each_col | 0.04 | 0.00 | 0.04 | |
| ellipsoidGate-class | 0.078 | 0.000 | 0.079 | |
| exponential-class | 0.032 | 0.000 | 0.033 | |
| expressionFilter-class | 0.108 | 0.000 | 0.108 | |
| filter-methods | 1.950 | 0.000 | 1.954 | |
| filter-on-methods | 0.105 | 0.000 | 0.105 | |
| filterList-class | 0.006 | 0.000 | 0.005 | |
| filterResult-class | 0.001 | 0.000 | 0.001 | |
| filterResultList-class | 6.786 | 0.132 | 6.943 | |
| filterSummary-class | 0.099 | 0.004 | 0.103 | |
| filterSummaryList-class | 2.411 | 0.032 | 2.447 | |
| flowFrame-class | 5.418 | 0.064 | 5.496 | |
| flowSet-class | 4.007 | 0.068 | 4.083 | |
| fr_append_cols | 1.912 | 0.008 | 1.923 | |
| fsApply | 0.179 | 0.003 | 0.183 | |
| getIndexSort | 0.031 | 0.000 | 0.032 | |
| hyperlog-class | 1.181 | 0.007 | 1.192 | |
| hyperlogtGml2-class | 0.037 | 0.000 | 0.037 | |
| identifier-methods | 0.03 | 0.00 | 0.03 | |
| inverseLogicleTransform | 2.063 | 0.004 | 2.070 | |
| invsplitscale-class | 0.035 | 0.000 | 0.035 | |
| keyword-methods | 1.793 | 0.003 | 1.800 | |
| kmeansFilter-class | 0.157 | 0.000 | 0.157 | |
| linearTransform | 0.042 | 0.000 | 0.041 | |
| lintGml2-class | 0.034 | 0.000 | 0.034 | |
| lnTransform | 2.421 | 0.032 | 2.457 | |
| logTransform | 0.057 | 0.000 | 0.057 | |
| logarithm-class | 0.036 | 0.000 | 0.035 | |
| logicalFilterResult-class | 0.000 | 0.000 | 0.001 | |
| logicleTransform | 1.964 | 0.012 | 1.979 | |
| logicletGml2-class | 0.056 | 0.000 | 0.056 | |
| logtGml2-class | 0.037 | 0.000 | 0.038 | |
| manyFilterResult-class | 0.001 | 0.000 | 0.000 | |
| markernames | 1.915 | 0.004 | 1.922 | |
| multipleFilterResult-class | 0 | 0 | 0 | |
| parameters-methods | 0.033 | 0.000 | 0.033 | |
| polygonGate-class | 0.077 | 0.003 | 0.081 | |
| quadGate-class | 0.665 | 0.024 | 0.691 | |
| quadratic-class | 0.035 | 0.000 | 0.035 | |
| quadraticTransform | 0.042 | 0.000 | 0.043 | |
| ratio-class | 0.043 | 0.000 | 0.043 | |
| ratiotGml2-class | 0.034 | 0.000 | 0.034 | |
| read.FCS | 0.103 | 0.000 | 0.103 | |
| read.FCSheader | 0.007 | 0.000 | 0.006 | |
| read.flowSet | 0.126 | 0.000 | 0.125 | |
| rectangleGate-class | 0.111 | 0.000 | 0.112 | |
| rotate_gate | 0 | 0 | 0 | |
| sampleFilter-class | 0.066 | 0.000 | 0.066 | |
| scaleTransform | 0.042 | 0.000 | 0.042 | |
| scale_gate | 0 | 0 | 0 | |
| shift_gate | 0.001 | 0.000 | 0.001 | |
| singleParameterTransform-class | 0.001 | 0.000 | 0.001 | |
| sinht-class | 0.035 | 0.000 | 0.036 | |
| split-methods | 2.346 | 0.008 | 2.358 | |
| splitScaleTransform | 2.520 | 0.008 | 2.531 | |
| splitscale-class | 0.036 | 0.000 | 0.036 | |
| squareroot-class | 0.033 | 0.000 | 0.034 | |
| timeFilter-class | 2.931 | 0.016 | 2.950 | |
| transform-class | 0.001 | 0.000 | 0.001 | |
| transform | 2.444 | 0.004 | 2.452 | |
| transformFilter-class | 0.183 | 0.012 | 0.195 | |
| transformList-class | 1.943 | 0.004 | 1.950 | |
| transformMap-class | 0.001 | 0.000 | 0.000 | |
| transform_gate | 0 | 0 | 0 | |
| truncateTransform | 0.041 | 0.000 | 0.042 | |
| unitytransform-class | 0.031 | 0.000 | 0.032 | |
| write.FCS | 0.057 | 0.000 | 0.058 | |
| write.flowSet | 2.156 | 0.000 | 2.160 | |