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CHECK report for pcaMethods on malbec1

This page was generated on 2021-05-06 12:28:31 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the pcaMethods package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1314/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pcaMethods 1.82.0  (landing page)
Henning Redestig
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/pcaMethods
Branch: RELEASE_3_12
Last Commit: d500b33
Last Changed Date: 2020-10-27 10:29:37 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: pcaMethods
Version: 1.82.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:pcaMethods.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings pcaMethods_1.82.0.tar.gz
StartedAt: 2021-05-06 04:20:56 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 04:23:21 -0400 (Thu, 06 May 2021)
EllapsedTime: 144.2 seconds
RetCode: 0
Status:   OK  
CheckDir: pcaMethods.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:pcaMethods.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings pcaMethods_1.82.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/pcaMethods.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pcaMethods/DESCRIPTION’ ... OK
* this is package ‘pcaMethods’ version ‘1.82.0’
* 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 ‘pcaMethods’ 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
BPCA_initmodel: no visible global function definition for ‘cov’
Q2: no visible global function definition for ‘txtProgressBar’
Q2: no visible global function definition for ‘setTxtProgressBar’
Q2: no visible global function definition for ‘cor’
RnipalsPca: no visible global function definition for ‘na.omit’
cvseg : <anonymous>: no visible global function definition for
  ‘na.omit’
llsImpute: no visible global function definition for ‘cor’
nlpca: no visible global function definition for ‘runif’
nlpca: no visible global function definition for ‘rnorm’
plot.pcaRes: no visible global function definition for ‘gray’
plot.pcaRes: no visible global function definition for ‘barplot’
plot.pcaRes: no visible global function definition for ‘legend’
plotPcs : panel: no visible global function definition for ‘abline’
plotPcs : panel: no visible global function definition for ‘lines’
plotPcs : panel: no visible global function definition for ‘points’
plotPcs : panel: no visible global function definition for ‘text’
plotPcs: no visible global function definition for ‘pairs’
ppca: no visible global function definition for ‘rnorm’
ppca: no visible global function definition for ‘cov’
robustSvd: no visible binding for global variable ‘median’
simpleEllipse: no visible global function definition for ‘qf’
svdImpute: no visible global function definition for ‘prcomp’
svdPca: no visible global function definition for ‘prcomp’
plot,pcaRes: no visible global function definition for ‘gray’
plot,pcaRes: no visible global function definition for ‘barplot’
plot,pcaRes: no visible global function definition for ‘legend’
slplot,pcaRes: no visible global function definition for ‘par’
slplot,pcaRes: no visible global function definition for ‘layout’
slplot,pcaRes: no visible global function definition for ‘abline’
slplot,pcaRes: no visible global function definition for ‘lines’
Undefined global functions or variables:
  abline barplot cor cov gray layout legend lines median na.omit pairs
  par points prcomp qf rnorm runif setTxtProgressBar text
  txtProgressBar
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "barplot", "layout", "legend",
             "lines", "pairs", "par", "points", "text")
  importFrom("stats", "cor", "cov", "median", "na.omit", "prcomp", "qf",
             "rnorm", "runif")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
kEstimate 67.008  0.048  67.186
robustSvd 17.912  0.000  17.937
robustPca  8.288  0.004   8.306
* 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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/pcaMethods.Rcheck/00check.log’
for details.



Installation output

pcaMethods.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL pcaMethods
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘pcaMethods’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c nipals.cpp -o nipals.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o pcaMethods.so RcppExports.o nipals.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/library/00LOCK-pcaMethods/00new/pcaMethods/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘loadings’ in package ‘pcaMethods’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pcaMethods)

Tests output


Example timings

pcaMethods.Rcheck/pcaMethods-Ex.timings

nameusersystemelapsed
DModX-pcaRes-method0.0600.0080.069
Q20.2360.0000.236
R2VX-pcaRes-method0.0280.0000.027
RnipalsPca0.3000.0000.298
biplot-methods0.0120.0000.014
bpca1.1080.0041.113
cvseg0.0160.0000.018
fitted-methods0.0080.0000.011
kEstimate67.008 0.04867.186
kEstimateFast0.4560.0040.461
leverage-pcaRes-method0.0160.0000.013
llsImpute0.2640.0000.268
nipalsPca0.0120.0000.013
nlpca2.6960.0002.701
nni0.2080.0000.205
pca1.3520.0161.371
plot.pcaRes0.2840.0280.314
plotPcs0.0320.0080.039
ppca0.1680.0320.197
predict-methods0.0120.0000.012
prep0.0000.0000.001
rediduals-methods0.0080.0000.008
robustPca8.2880.0048.306
robustSvd17.912 0.00017.937
slplot-pcaRes-method0.0320.0000.031
svdImpute0.1200.0040.126
svdPca0.0200.0000.023
wasna-pcaRes-method0.0280.0080.036