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CHECK report for M3C on machv2

This page was generated on 2020-10-17 11:58:49 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE M3C PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 964/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
M3C 1.10.0
Christopher John
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/M3C
Branch: RELEASE_3_11
Last Commit: 34ad0a1
Last Changed Date: 2020-04-27 15:09:30 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: M3C
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:M3C.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings M3C_1.10.0.tar.gz
StartedAt: 2020-10-17 02:33:24 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:35:24 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 120.2 seconds
RetCode: 0
Status:  OK 
CheckDir: M3C.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:M3C.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings M3C_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/M3C.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘M3C/DESCRIPTION’ ... OK
* this is package ‘M3C’ version ‘1.10.0’
* 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 ‘M3C’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
CDF: no visible global function definition for ‘ecdf’
CDF: no visible global function definition for ‘complete.cases’
CDF: no visible binding for global variable ‘consensusindex’
CDF: no visible binding for global variable ‘k’
CDF: no visible binding for global variable ‘K’
CDF: no visible binding for global variable ‘PAC_SCORE’
M3C: no visible global function definition for ‘exprs’
M3C: no visible global function definition for ‘is’
M3C: no visible global function definition for ‘capture.output’
M3C: no visible global function definition for ‘txtProgressBar’
M3C : progress: no visible global function definition for
  ‘setTxtProgressBar’
M3C: no visible global function definition for ‘prcomp’
M3C: no visible global function definition for ‘cov’
M3C: no visible global function definition for ‘rnorm’
M3C: no visible binding for global variable ‘sd’
M3C: no visible binding for global variable ‘var’
M3C : <anonymous>: no visible global function definition for ‘pbeta’
M3C : <anonymous>: no visible global function definition for ‘pnorm’
M3C: no visible binding for global variable ‘K’
M3C: no visible binding for global variable ‘RCSI’
M3C: no visible global function definition for ‘qnorm’
M3C: no visible binding for global variable ‘RCSI_SE’
M3C: no visible binding for global variable ‘P_SCORE’
M3Creal: no visible global function definition for ‘hclust’
M3Creal: no visible global function definition for ‘as.dist’
M3Creal: no visible global function definition for ‘cutree’
M3Creal: no visible global function definition for ‘is’
PCSI_plot: no visible binding for global variable ‘K’
PCSI_plot: no visible binding for global variable ‘PCSI’
ccRun: no visible global function definition for ‘dist’
ccRun: no visible global function definition for ‘as.dist’
ccRun: no visible global function definition for ‘kmeans’
ccRun: no visible global function definition for ‘hclust’
ccRun: no visible global function definition for ‘cutree’
clustersim : addnoise: no visible global function definition for
  ‘rnorm’
clustersim: no visible global function definition for ‘rnorm’
clustersim: no visible binding for global variable ‘X3’
clustersim: no visible global function definition for ‘prcomp’
clustersim: no visible global function definition for ‘kmeans’
clustersim: no visible binding for global variable ‘PC1’
clustersim: no visible binding for global variable ‘PC2’
featurefilter: no visible binding for global variable ‘sd’
featurefilter: no visible global function definition for ‘quantile’
featurefilter: no visible binding for global variable ‘mad’
getl: no visible global function definition for ‘kmeans’
getl: no visible global function definition for ‘dist’
getl: no visible global function definition for ‘hclust’
getl: no visible global function definition for ‘cutree’
pca: no visible global function definition for ‘prcomp’
pca: no visible global function definition for ‘png’
pca: no visible global function definition for ‘dev.off’
pca: no visible binding for global variable ‘label’
rbfkernel: no visible global function definition for ‘dist’
tsne: no visible binding for global variable ‘X1’
tsne: no visible binding for global variable ‘X2’
tsne: no visible global function definition for ‘png’
tsne: no visible global function definition for ‘dev.off’
tsne: no visible binding for global variable ‘label’
umap: no visible binding for global variable ‘X1’
umap: no visible binding for global variable ‘X2’
umap: no visible global function definition for ‘png’
umap: no visible global function definition for ‘dev.off’
umap: no visible binding for global variable ‘label’
Undefined global functions or variables:
  K PAC_SCORE PC1 PC2 PCSI P_SCORE RCSI RCSI_SE X1 X2 X3 as.dist
  capture.output complete.cases consensusindex cov cutree dev.off dist
  ecdf exprs hclust is k kmeans label mad pbeta png pnorm prcomp qnorm
  quantile rnorm sd setTxtProgressBar txtProgressBar var
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("methods", "is")
  importFrom("stats", "as.dist", "complete.cases", "cov", "cutree",
             "dist", "ecdf", "hclust", "kmeans", "mad", "pbeta", "pnorm",
             "prcomp", "qnorm", "quantile", "rnorm", "sd", "var")
  importFrom("utils", "capture.output", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
M3C 2.477  0.106  34.938
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/M3C.Rcheck/00check.log’
for details.



Installation output

M3C.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL M3C
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘M3C’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (M3C)

Tests output


Example timings

M3C.Rcheck/M3C-Ex.timings

nameusersystemelapsed
M3C 2.477 0.10634.938
clustersim0.6890.0210.710
featurefilter0.4910.0070.498
pca0.0710.0050.076
tsne0.1250.0030.127
umap0.4600.0150.476