Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:45 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 721/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
flowCyBar 1.41.0 (landing page) Joachim Schumann
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the flowCyBar package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/flowCyBar.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: flowCyBar |
Version: 1.41.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowCyBar.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowCyBar_1.41.0.tar.gz |
StartedAt: 2024-08-26 21:18:03 -0400 (Mon, 26 Aug 2024) |
EndedAt: 2024-08-26 21:18:22 -0400 (Mon, 26 Aug 2024) |
EllapsedTime: 19.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: flowCyBar.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowCyBar.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowCyBar_1.41.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/flowCyBar.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 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘flowCyBar/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘flowCyBar’ version ‘1.41.0’ * 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 ‘flowCyBar’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 ... NOTE correlation,data.frame : <anonymous>: no visible global function definition for ‘as.dist’ correlation,data.frame : est: no visible global function definition for ‘cor.test’ correlation,data.frame : pval: no visible global function definition for ‘cor.test’ correlation,matrix : <anonymous>: no visible global function definition for ‘as.dist’ correlation,matrix : est: no visible global function definition for ‘cor.test’ correlation,matrix : pval: no visible global function definition for ‘cor.test’ cybar_plot,data.frame-data.frame: no visible global function definition for ‘layout’ cybar_plot,data.frame-data.frame: no visible global function definition for ‘par’ cybar_plot,data.frame-data.frame: no visible global function definition for ‘boxplot’ cybar_plot,data.frame-matrix: no visible global function definition for ‘layout’ cybar_plot,data.frame-matrix: no visible global function definition for ‘par’ cybar_plot,data.frame-matrix: no visible global function definition for ‘boxplot’ cybar_plot,matrix-data.frame: no visible global function definition for ‘layout’ cybar_plot,matrix-data.frame: no visible global function definition for ‘par’ cybar_plot,matrix-data.frame: no visible global function definition for ‘boxplot’ cybar_plot,matrix-matrix: no visible global function definition for ‘layout’ cybar_plot,matrix-matrix: no visible global function definition for ‘par’ cybar_plot,matrix-matrix: no visible global function definition for ‘boxplot’ cybar_plot,missing-data.frame: no visible global function definition for ‘boxplot’ cybar_plot,missing-matrix: no visible global function definition for ‘boxplot’ nmds,data.frame: no visible global function definition for ‘text’ nmds,data.frame: no visible global function definition for ‘points’ nmds,data.frame: no visible global function definition for ‘legend’ nmds,matrix: no visible global function definition for ‘text’ nmds,matrix: no visible global function definition for ‘points’ nmds,matrix: no visible global function definition for ‘legend’ normalize,data.frame : <anonymous>: no visible global function definition for ‘head’ normalize,matrix : <anonymous>: no visible global function definition for ‘head’ Undefined global functions or variables: as.dist boxplot cor.test head layout legend par points text Consider adding importFrom("graphics", "boxplot", "layout", "legend", "par", "points", "text") importFrom("stats", "as.dist", "cor.test") importFrom("utils", "head") 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... 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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/flowCyBar.Rcheck/00check.log’ for details.
flowCyBar.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL flowCyBar ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘flowCyBar’ ... files ‘build/vignette.rds’, ‘inst/doc/flowCyBar-manual.R’, ‘inst/doc/flowCyBar-manual.Rnw’, ‘inst/doc/flowCyBar-manual.bib’, ‘inst/doc/flowCyBar-manual.pdf’ are missing files ‘DESCRIPTION’, ‘R/correlation.R’, ‘R/cybar_plot.R’, ‘R/nmds.R’, ‘R/normalize.R’, ‘man/correlation.Rd’, ‘man/cybar_plot.Rd’, ‘man/flowCyBar-package.Rd’, ‘man/nmds.Rd’, ‘man/normalize.Rd’, ‘vignettes/flowCyBar-manual.Rnw’ have the wrong MD5 checksums ** using staged installation ** R ** data ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (flowCyBar)
flowCyBar.Rcheck/flowCyBar-Ex.timings
name | user | system | elapsed | |
correlation | 0.509 | 0.010 | 0.519 | |
cybar_plot | 0.062 | 0.004 | 0.066 | |
nmds | 0.123 | 0.013 | 0.136 | |
normalize | 0.008 | 0.003 | 0.011 | |