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BioC 3.6: CHECK report for pcaMethods on malbec1

This page was generated on 2017-08-16 13:17:44 -0400 (Wed, 16 Aug 2017).

Package 977/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pcaMethods 1.69.0
Henning Redestig
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: pcaMethods
Version: 1.69.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings pcaMethods_1.69.0.tar.gz
StartedAt: 2017-08-16 01:18:09 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:20:15 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 125.8 seconds
RetCode: 0
Status:  OK 
CheckDir: pcaMethods.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings pcaMethods_1.69.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/pcaMethods.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.69.0’
* 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 ‘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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
kEstimate 61.368  0.004  61.419
robustSvd 11.596  0.004  11.608
robustPca  5.236  0.012   5.254
* 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
  ‘/home/biocbuild/bbs-3.6-bioc/meat/pcaMethods.Rcheck/00check.log’
for details.


pcaMethods.Rcheck/00install.out:

* installing *source* package ‘pcaMethods’ ...
** libs
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c nipals.cpp -o nipals.o
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o pcaMethods.so RcppExports.o nipals.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/pcaMethods.Rcheck/pcaMethods/libs
** R
** data
** inst
** preparing 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
* DONE (pcaMethods)

pcaMethods.Rcheck/pcaMethods-Ex.timings:

nameusersystemelapsed
DModX-pcaRes-method0.1520.0000.154
Q20.3840.0040.387
R2VX-pcaRes-method0.0120.0000.015
RnipalsPca0.2440.0000.244
biplot-methods0.0080.0000.009
bpca0.8160.0000.813
cvseg0.0280.0000.028
fitted-methods0.0040.0000.006
kEstimate61.368 0.00461.419
kEstimateFast0.420.000.42
leverage-pcaRes-method0.0080.0000.008
llsImpute0.2440.0000.244
nipalsPca0.0040.0040.009
nlpca1.9440.0001.947
nni0.1840.0000.180
pca1.2400.0001.242
plot.pcaRes0.2280.0000.232
plotPcs0.0160.0000.016
ppca0.2160.0000.216
predict-methods0.0080.0000.009
prep0.0000.0000.001
rediduals-methods0.0040.0000.007
robustPca5.2360.0125.254
robustSvd11.596 0.00411.608
slplot-pcaRes-method0.0160.0000.016
svdImpute0.0800.0000.079
svdPca0.0160.0000.014
wasna-pcaRes-method0.0120.0000.013