Package: pcaMethods

Version: 1.79.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pcaMethods.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pcaMethods_1.79.1.tar.gz

StartedAt: 2020-01-16 07:18:14 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 07:22:16 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 242.7 seconds

RetCode: 0

Status:  OK

CheckDir: pcaMethods.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:pcaMethods.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings pcaMethods_1.79.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/pcaMethods.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pcaMethods/DESCRIPTION’ ... OK
* this is package ‘pcaMethods’ version ‘1.79.1’
* 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 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
kEstimate 93.764 17.720 112.282
robustSvd 28.310  2.665  31.038
robustPca 13.088  1.211  14.433
* 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-3.11-bioc/meat/pcaMethods.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL pcaMethods
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘pcaMethods’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c nipals.cpp -o nipals.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o pcaMethods.so RcppExports.o nipals.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/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)

name	user	system	elapsed
DModX-pcaRes-method	0.070	0.014	0.084
Q2	0.315	0.018	0.336
R2VX-pcaRes-method	0.038	0.002	0.039
RnipalsPca	0.408	0.034	0.442
biplot-methods	0.014	0.004	0.018
bpca	1.675	0.214	1.890
cvseg	0.021	0.001	0.026
fitted-methods	0.012	0.000	0.013
kEstimate	93.764	17.720	112.282
kEstimateFast	0.637	0.079	0.736
leverage-pcaRes-method	0.017	0.003	0.020
llsImpute	0.320	0.031	0.353
nipalsPca	0.012	0.003	0.014
nlpca	3.224	0.082	3.507
nni	0.278	0.007	0.346
pca	1.571	0.094	1.778
plot.pcaRes	0.548	0.026	0.575
plotPcs	0.024	0.003	0.027
ppca	0.186	0.037	0.225
predict-methods	0.021	0.003	0.024
prep	0.003	0.000	0.004
rediduals-methods	0.017	0.003	0.021
robustPca	13.088	1.211	14.433
robustSvd	28.310	2.665	31.038
slplot-pcaRes-method	0.025	0.003	0.030
svdImpute	0.136	0.024	0.162
svdPca	0.020	0.001	0.022
wasna-pcaRes-method	0.020	0.005	0.026