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This page was generated on 2023-10-20 09:38:02 -0400 (Fri, 20 Oct 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
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 710/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
flowCHIC 1.34.0 (landing page) Author: Joachim Schumann
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the flowCHIC 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: flowCHIC |
Version: 1.34.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowCHIC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowCHIC_1.34.0.tar.gz |
StartedAt: 2023-10-17 19:47:46 -0400 (Tue, 17 Oct 2023) |
EndedAt: 2023-10-17 19:51:16 -0400 (Tue, 17 Oct 2023) |
EllapsedTime: 210.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: flowCHIC.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowCHIC.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowCHIC_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/flowCHIC.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘flowCHIC/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘flowCHIC’ version ‘1.34.0’ * 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 ‘flowCHIC’ can be installed ... OK * checking installed package size ... NOTE installed size is 5.9Mb sub-directories of 1Mb or more: extdata 5.7Mb * 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 R 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 fcs_to_img,character: warning in hexbin(x, y, xbin = 128): partial argument match of 'xbin' to 'xbins' img_sub,character: warning in hexbin(x, y, xbin = xbin): partial argument match of 'xbin' to 'xbins' fcs_to_img,character: no visible global function definition for ‘png’ fcs_to_img,character: no visible binding for global variable ‘count’ fcs_to_img,character: no visible global function definition for ‘dev.off’ img_sub,character: no visible global function definition for ‘png’ img_sub,character: no visible binding for global variable ‘count’ img_sub,character: no visible global function definition for ‘dev.off’ plot_nmds,data.frame-data.frame: no visible global function definition for ‘as.dist’ plot_nmds,data.frame-data.frame: no visible global function definition for ‘par’ plot_nmds,data.frame-data.frame: no visible global function definition for ‘hclust’ plot_nmds,data.frame-data.frame: no visible global function definition for ‘points’ plot_nmds,data.frame-data.frame: no visible global function definition for ‘text’ plot_nmds,data.frame-data.frame: no visible global function definition for ‘legend’ Undefined global functions or variables: as.dist count dev.off hclust legend par png points text Consider adding importFrom("grDevices", "dev.off", "png") importFrom("graphics", "legend", "par", "points", "text") importFrom("stats", "as.dist", "hclust") 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed calculate_overlaps_xor 9.601 0.295 17.634 plot_nmds 5.481 0.173 9.455 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/flowCHIC.Rcheck/00check.log’ for details.
flowCHIC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL flowCHIC ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘flowCHIC’ ... ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (flowCHIC)
flowCHIC.Rcheck/flowCHIC-Ex.timings
name | user | system | elapsed | |
calculate_overlaps_xor | 9.601 | 0.295 | 17.634 | |
fcs_to_img | 1.315 | 0.047 | 2.369 | |
img_sub | 2.406 | 0.058 | 3.873 | |
plot_nmds | 5.481 | 0.173 | 9.455 | |