Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:08:00 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
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 |
To the developers/maintainers of the flowBin package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/flowBin.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 651/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
flowBin 1.30.0 (landing page) Kieran O'Neill
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: flowBin |
Version: 1.30.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowBin.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowBin_1.30.0.tar.gz |
StartedAt: 2022-04-12 13:20:28 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 13:22:29 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 120.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: flowBin.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowBin.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowBin_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/flowBin.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘flowBin/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘flowBin’ version ‘1.30.0’ * 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 ‘flowBin’ can be installed ... OK * checking installed package size ... OK * 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 ... 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 ... NOTE Package in Depends field not imported from: ‘flowCore’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .getBinExpr.def : getBinFrame: no visible global function definition for ‘exprs<-’ .getBinExpr.def : getBinFrame: no visible global function definition for ‘exprs’ .getBinExpr.def : scaleData: no visible global function definition for ‘pData’ .getBinExpr.def : getOnePopExpr : extractOneTube : <anonymous>: no visible global function definition for ‘exprs’ .getBinExpr.def : getOnePopExpr : extractOneTube: no visible global function definition for ‘pData’ .getBinExpr.def : getOneBinMeds : <anonymous>: no visible global function definition for ‘median’ .getBinExpr.def : getOneBinMeds : <anonymous>: no visible global function definition for ‘exprs’ .getBinExpr.def : getOneBinMeds: no visible global function definition for ‘pData’ checkQNorm.func: no visible global function definition for ‘flowSet’ checkQNorm.func: no visible global function definition for ‘par’ checkQNorm.func: no visible binding for global variable ‘sd’ flowFPBin.def: no visible global function definition for ‘flowSet’ kMeansBin.def: no visible global function definition for ‘exprs’ kMeansBin.def: no visible global function definition for ‘pData’ kMeansBin.def: no visible global function definition for ‘kmeans’ mapBinsKNN.def : mapClustersKNN: no visible global function definition for ‘exprs’ mapBinsKNN.def: no visible global function definition for ‘capture.output’ mapBinsKNN.def: no visible global function definition for ‘parLapply’ medianFI: no visible global function definition for ‘median’ medianFIDist: no visible global function definition for ‘median’ proportionPositive: no visible global function definition for ‘quantile’ qnorm.func : normCol : <anonymous>: no visible global function definition for ‘exprs’ qnorm.func : normCol : getCol: no visible global function definition for ‘exprs’ qnorm.func : normCol : getCol: no visible global function definition for ‘runif’ qnorm.func : normCol : setCol: no visible global function definition for ‘exprs’ qnorm.func : normCol : setCol: no visible global function definition for ‘exprs<-’ checkQNorm,FlowSample-FlowSample: no visible global function definition for ‘flowSet’ checkQNorm,FlowSample-FlowSample: no visible global function definition for ‘par’ checkQNorm,FlowSample-FlowSample: no visible binding for global variable ‘sd’ flowFPBin,FlowSample: no visible global function definition for ‘flowSet’ getBinExpr,BinnedFlowSample : getBinFrame: no visible global function definition for ‘exprs<-’ getBinExpr,BinnedFlowSample : getBinFrame: no visible global function definition for ‘exprs’ getBinExpr,BinnedFlowSample : scaleData: no visible global function definition for ‘pData’ getBinExpr,BinnedFlowSample : getOnePopExpr : extractOneTube : <anonymous>: no visible global function definition for ‘exprs’ getBinExpr,BinnedFlowSample : getOnePopExpr : extractOneTube: no visible global function definition for ‘pData’ getBinExpr,BinnedFlowSample : getOneBinMeds : <anonymous>: no visible global function definition for ‘median’ getBinExpr,BinnedFlowSample : getOneBinMeds : <anonymous>: no visible global function definition for ‘exprs’ getBinExpr,BinnedFlowSample : getOneBinMeds: no visible global function definition for ‘pData’ kMeansBin,FlowSample: no visible global function definition for ‘exprs’ kMeansBin,FlowSample: no visible global function definition for ‘pData’ kMeansBin,FlowSample: no visible global function definition for ‘kmeans’ mapBinsKNN,FlowSample : mapClustersKNN: no visible global function definition for ‘exprs’ mapBinsKNN,FlowSample: no visible global function definition for ‘capture.output’ mapBinsKNN,FlowSample: no visible global function definition for ‘parLapply’ quantileNormalise,FlowSample : normCol : <anonymous>: no visible global function definition for ‘exprs’ quantileNormalise,FlowSample : normCol : getCol: no visible global function definition for ‘exprs’ quantileNormalise,FlowSample : normCol : getCol: no visible global function definition for ‘runif’ quantileNormalise,FlowSample : normCol : setCol: no visible global function definition for ‘exprs’ quantileNormalise,FlowSample : normCol : setCol: no visible global function definition for ‘exprs<-’ show,FlowSample: no visible global function definition for ‘str’ Undefined global functions or variables: capture.output exprs exprs<- flowSet kmeans median pData par parLapply quantile runif sd str Consider adding importFrom("graphics", "par") importFrom("stats", "kmeans", "median", "quantile", "runif", "sd") importFrom("utils", "capture.output", "str") 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 flowBin 10.018 0.051 10.084 getBinExpr 9.432 0.065 9.510 * 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-3.14-bioc/meat/flowBin.Rcheck/00check.log’ for details.
flowBin.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL flowBin ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘flowBin’ ... ** 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 (flowBin)
flowBin.Rcheck/flowBin-Ex.timings
name | user | system | elapsed | |
checkQNorm | 0.760 | 0.019 | 0.783 | |
flowBin | 10.018 | 0.051 | 10.084 | |
flowFPBin | 0.448 | 0.009 | 0.458 | |
getBinExpr | 9.432 | 0.065 | 9.510 | |
kMeansBin | 0.466 | 0.011 | 0.477 | |
mapBinsKNN | 0.411 | 0.008 | 0.419 | |
quantileNormalise | 0.527 | 0.015 | 0.543 | |