Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-08-13 17:39 -0400 (Tue, 13 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4758 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4493 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4522 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4471 |
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 755/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
flowViz 1.68.0 (landing page) Mike Jiang
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
To the developers/maintainers of the flowViz package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowViz.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. |
Package: flowViz |
Version: 1.68.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:flowViz.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings flowViz_1.68.0.tar.gz |
StartedAt: 2024-08-11 23:18:38 -0400 (Sun, 11 Aug 2024) |
EndedAt: 2024-08-11 23:21:41 -0400 (Sun, 11 Aug 2024) |
EllapsedTime: 182.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: flowViz.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:flowViz.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings flowViz_1.68.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/flowViz.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘flowViz/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘flowViz’ version ‘1.68.0’ * 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 ‘flowViz’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘flowCore’ ‘lattice’ A package should be listed in only one of these fields. * 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 Unexported objects imported by ':::' calls: ‘lattice:::hist.constructor’ ‘lattice:::updateList’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .process_overlay_flowSet : <anonymous>: no visible global function definition for ‘extends’ .xyplot.flowSet: no visible global function definition for ‘as.formula’ panel.densityplot.flowset.stack: no visible binding for global variable ‘rl’ panel.xyplot.flowframe: no visible global function definition for ‘densCols’ panel.xyplot.flowframe.old: no visible global function definition for ‘densCols’ prepanel.densityplot.flowset.stack: no visible global function definition for ‘extends’ contour,flowFrame: no visible global function definition for ‘contourLines’ densityplot,formula-ncdfFlowList: no visible global function definition for ‘selectMethod’ densityplot,formula-view: no visible global function definition for ‘Data’ flowPlot,flowFrame: no visible global function definition for ‘rainbow’ glpoints,filter-flowFrame-missing: no visible binding for global variable ‘parms’ glpoints,filter-flowFrame-missing: no visible binding for global variable ‘strict’ gpoints,quadGate-flowFrame-character: no visible binding for global variable ‘filterResult’ gpolygon,ellipsoidGate-character: no visible binding for global variable ‘fd’ histogram,formula-ncdfFlowList: no visible global function definition for ‘selectMethod’ xyplot,formula-gateView: no visible global function definition for ‘action’ xyplot,formula-gateView: no visible global function definition for ‘Data’ xyplot,formula-gateView: no visible global function definition for ‘parent’ xyplot,formula-ncdfFlowList: no visible global function definition for ‘selectMethod’ xyplot,formula-view: no visible global function definition for ‘Data’ xyplot,view-missing: no visible global function definition for ‘Data’ Undefined global functions or variables: Data action as.formula contourLines densCols extends fd filterResult parent parms rainbow rl selectMethod strict Consider adding importFrom("grDevices", "contourLines", "densCols", "rainbow") importFrom("methods", "extends", "selectMethod") importFrom("stats", "as.formula") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE prepare_Rd: glines-methods.Rd:150-152: Dropping empty section ‘Methods’ prepare_Rd: timeLinePlot.Rd:72-74: Dropping empty section ‘Methods’ * 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... NOTE Files named as vignettes but with no recognized vignette engine: ‘vignettes/densityplot_vs_histogram.Rmd’ (Is a VignetteBuilder field missing?) * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed xyplot 9.558 0.120 9.679 densityplot 9.365 0.215 9.581 splom 8.892 0.107 9.000 lattice-methods 6.938 0.152 7.090 timeLinePlot 6.204 0.060 6.265 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... NOTE Package vignette with \VignetteEngine{} not specifying an engine package: ‘filters.Rmd’ Engines should be specified as \VignetteEngine{PKG::ENG}. * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 6 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/flowViz.Rcheck/00check.log’ for details.
flowViz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL flowViz ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘flowViz’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading in method for ‘densityplot’ with signature ‘x="formula",data="view"’: no definition for class “view” in method for ‘densityplot’ with signature ‘x="formula",data="ncdfFlowSet"’: no definition for class “ncdfFlowSet” in method for ‘densityplot’ with signature ‘x="formula",data="ncdfFlowList"’: no definition for class “ncdfFlowList” in method for ‘histogram’ with signature ‘x="formula",data="ncdfFlowSet"’: no definition for class “ncdfFlowSet” in method for ‘histogram’ with signature ‘x="formula",data="ncdfFlowList"’: no definition for class “ncdfFlowList” in method for ‘glines’ with signature ‘x="norm2Filter",data="ANY"’: no definition for class “norm2Filter” in method for ‘glines’ with signature ‘x="norm2Filter",data="logicalFilterResult"’: no definition for class “norm2Filter” in method for ‘glines’ with signature ‘x="norm2Filter",data="flowFrame"’: no definition for class “norm2Filter” in method for ‘glpoints’ with signature ‘x="norm2Filter",data="flowFrame",channels="character"’: no definition for class “norm2Filter” in method for ‘glpolygon’ with signature ‘x="norm2Filter",data="ANY"’: no definition for class “norm2Filter” in method for ‘glpolygon’ with signature ‘x="norm2Filter",data="logicalFilterResult"’: no definition for class “norm2Filter” in method for ‘glpolygon’ with signature ‘x="norm2Filter",data="flowFrame"’: no definition for class “norm2Filter” in method for ‘gpoints’ with signature ‘x="norm2Filter",data="flowFrame",channels="character"’: no definition for class “norm2Filter” in method for ‘gpolygon’ with signature ‘x="norm2Filter",data="ANY"’: no definition for class “norm2Filter” in method for ‘gpolygon’ with signature ‘x="norm2Filter",data="logicalFilterResult"’: no definition for class “norm2Filter” in method for ‘gpolygon’ with signature ‘x="norm2Filter",data="flowFrame"’: no definition for class “norm2Filter” in method for ‘xyplot’ with signature ‘x="formula",data="view"’: no definition for class “view” in method for ‘xyplot’ with signature ‘x="view",data="missing"’: no definition for class “view” in method for ‘xyplot’ with signature ‘x="formula",data="gateView"’: no definition for class “gateView” in method for ‘xyplot’ with signature ‘x="formula",data="ncdfFlowSet"’: no definition for class “ncdfFlowSet” in method for ‘xyplot’ with signature ‘x="formula",data="ncdfFlowList"’: no definition for class “ncdfFlowList” ** help *** installing help indices ** 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 * DONE (flowViz)
flowViz.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 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(flowViz) Loading required package: flowCore Loading required package: lattice > > test_check("flowViz") [ FAIL 0 | WARN 1 | SKIP 0 | PASS 9 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 9 ] > > proc.time() user system elapsed 7.370 0.384 7.744
flowViz.Rcheck/flowViz-Ex.timings
name | user | system | elapsed | |
contour-methods | 1.866 | 0.052 | 1.918 | |
densityplot | 9.365 | 0.215 | 9.581 | |
ecdfplot | 4.751 | 0.008 | 4.759 | |
flowPlot | 1.505 | 0.004 | 1.508 | |
flowViz-package | 0 | 0 | 0 | |
flowViz.par.get | 2.041 | 0.032 | 2.072 | |
lattice-methods | 6.938 | 0.152 | 7.090 | |
splom | 8.892 | 0.107 | 9.000 | |
timeLinePlot | 6.204 | 0.060 | 6.265 | |
xyplot | 9.558 | 0.120 | 9.679 | |