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CHECK report for pcaMethods on tokay1

This page was generated on 2019-04-13 11:20:03 -0400 (Sat, 13 Apr 2019).

Package 1134/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pcaMethods 1.74.0
Henning Redestig
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/pcaMethods
Branch: RELEASE_3_8
Last Commit: 1b8f0a5
Last Changed Date: 2018-10-30 11:41:43 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 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
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: pcaMethods
Version: 1.74.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pcaMethods.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings pcaMethods_1.74.0.tar.gz
StartedAt: 2019-04-13 04:26:00 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 04:31:14 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 314.3 seconds
RetCode: 0
Status:  OK  
CheckDir: pcaMethods.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:pcaMethods.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings pcaMethods_1.74.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/pcaMethods.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pcaMethods/DESCRIPTION' ... OK
* this is package 'pcaMethods' version '1.74.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.8-bioc/R/library/pcaMethods/libs/i386/pcaMethods.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
kEstimate 55.59   0.14   55.74
robustSvd 13.31   0.00   13.31
robustPca  6.41   0.02    6.42
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
kEstimate 78.89   0.00   78.95
robustSvd 20.99   0.01   21.00
robustPca  8.97   0.00    8.97
* 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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/pcaMethods.Rcheck/00check.log'
for details.



Installation output

pcaMethods.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/pcaMethods_1.74.0.tar.gz && rm -rf pcaMethods.buildbin-libdir && mkdir pcaMethods.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=pcaMethods.buildbin-libdir pcaMethods_1.74.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL pcaMethods_1.74.0.zip && rm pcaMethods_1.74.0.tar.gz pcaMethods_1.74.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  171k  100  171k    0     0  3480k      0 --:--:-- --:--:-- --:--:-- 3800k

install for i386

* installing *source* package 'pcaMethods' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c nipals.cpp -o nipals.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o pcaMethods.dll tmp.def RcppExports.o nipals.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/pcaMethods.buildbin-libdir/pcaMethods/libs/i386
** 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
  converting help for package 'pcaMethods'
    finding HTML links ... done
    BPCA_dostep                             html  
    BPCA_initmodel                          html  
    DModX-pcaRes-method                     html  
    Q2                                      html  
    R2VX-pcaRes-method                      html  
    R2cum-pcaRes-method                     html  
    RnipalsPca                              html  
    asExprSet                               html  
    biplot-methods                          html  
    bpca                                    html  
    center-pcaRes-method                    html  
    centered-pcaRes-method                  html  
    checkData                               html  
    completeObs-nniRes-method               html  
    cvseg                                   html  
    cvstat-pcaRes-method                    html  
    deletediagonals                         html  
    derrorHierarchic                        html  
    dim.pcaRes                              html  
    errorHierarchic                         html  
    fitted-methods                          html  
    forkNlpcaNet                            html  
    getHierarchicIdx                        html  
    helix                                   html  
    kEstimate                               html  
    kEstimateFast                           html  
    leverage-pcaRes-method                  html  
    lineSearch                              html  
    linr                                    html  
    listPcaMethods                          html  
    llsImpute                               html  
    loadings-ANY-method                     html  
    loadings-pcaRes-method                  html  
    loadings.pcaRes                         html  
    metaboliteData                          html  
    metaboliteDataComplete                  html  
    method-pcaRes-method                    html  
    nObs-pcaRes-method                      html  
    nP-pcaRes-method                        html  
    nPcs-pcaRes-method                      html  
    nVar-pcaRes-method                      html  
    nipalsPca                               html  
    nlpca                                   html  
    nmissing-pcaRes-method                  html  
    nni                                     html  
    nniRes                                  html  
    optiAlgCgd                              html  
    orth                                    html  
    pca                                     html  
    pcaMethods-deprecated                   html  
    pcaMethods                              html  
    pcaNet                                  html  
    pcaRes                                  html  
    plot.pcaRes                             html  
    plotPcs                                 html  
    ppca                                    html  
    predict-methods                         html  
    prep                                    html  
    rediduals-methods                       html  
    repmat                                  html  
    robustPca                               html  
    robustSvd                               html  
    sDev-pcaRes-method                      html  
    scaled-pcaRes-method                    html  
    scl-pcaRes-method                       html  
    scores-pcaRes-method                    html  
    scores.pcaRes                           html  
    show-methods                            html  
    showNniRes                              html  
    simpleEllipse                           html  
    slplot-pcaRes-method                    html  
    sortFeatures                            html  
    summary                                 html  
    svdImpute                               html  
    svdPca                                  html  
    tempFixNas                              html  
    vector2matrices-matrix-method           html  
    vector2matrices-nlpcaNet-method         html  
    wasna-pcaRes-method                     html  
    weightsAccount                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'pcaMethods' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c nipals.cpp -o nipals.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o pcaMethods.dll tmp.def RcppExports.o nipals.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/pcaMethods.buildbin-libdir/pcaMethods/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pcaMethods' as pcaMethods_1.74.0.zip
* DONE (pcaMethods)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'pcaMethods' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

pcaMethods.Rcheck/examples_i386/pcaMethods-Ex.timings

nameusersystemelapsed
DModX-pcaRes-method0.050.000.05
Q20.140.000.20
R2VX-pcaRes-method0.010.000.02
RnipalsPca0.220.000.21
biplot-methods000
bpca0.750.000.75
cvseg0.010.000.02
fitted-methods0.020.000.01
kEstimate55.59 0.1455.74
kEstimateFast0.380.000.37
leverage-pcaRes-method0.010.000.02
llsImpute0.180.000.17
nipalsPca0.000.020.01
nlpca3.150.013.18
nni0.220.000.21
pca1.240.031.27
plot.pcaRes0.290.000.30
plotPcs0.020.000.01
ppca0.120.030.16
predict-methods0.020.000.01
prep000
rediduals-methods0.010.000.02
robustPca6.410.026.42
robustSvd13.31 0.0013.31
slplot-pcaRes-method0.000.010.02
svdImpute0.080.020.09
svdPca0.020.000.02
wasna-pcaRes-method0.010.000.02

pcaMethods.Rcheck/examples_x64/pcaMethods-Ex.timings

nameusersystemelapsed
DModX-pcaRes-method0.060.010.08
Q20.200.000.26
R2VX-pcaRes-method0.030.000.03
RnipalsPca0.350.030.37
biplot-methods0.010.000.02
bpca1.320.021.33
cvseg0.010.000.01
fitted-methods0.020.000.02
kEstimate78.89 0.0078.95
kEstimateFast0.580.000.58
leverage-pcaRes-method0.010.000.01
llsImpute0.270.000.28
nipalsPca0.010.010.04
nlpca3.320.003.31
nni0.150.020.17
pca1.130.051.17
plot.pcaRes0.610.010.63
plotPcs0.010.020.03
ppca0.220.010.23
predict-methods0.020.000.02
prep000
rediduals-methods0.010.020.03
robustPca8.970.008.97
robustSvd20.99 0.0121.00
slplot-pcaRes-method0.030.020.05
svdImpute0.120.000.12
svdPca0.050.000.05
wasna-pcaRes-method0.010.010.03