| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:02 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| 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 715/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| flowCyBar 1.36.0 (landing page) Joachim Schumann
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK |  | |||||||
|
To the developers/maintainers of the flowCyBar 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: flowCyBar |
| Version: 1.36.0 |
| 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_1.36.0.tar.gz |
| StartedAt: 2023-10-17 19:57:46 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 19:59:12 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 86.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: flowCyBar.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_1.36.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/flowCyBar.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 ‘flowCyBar/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowCyBar’ version ‘1.36.0’
* 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 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
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 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/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/4.3-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 | 2.009 | 0.042 | 3.127 | |
| cybar_plot | 0.217 | 0.014 | 0.350 | |
| nmds | 0.502 | 0.046 | 0.830 | |
| normalize | 0.029 | 0.006 | 0.055 | |