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CHECK report for kimod on tokay1

This page was generated on 2019-04-13 11:26:10 -0400 (Sat, 13 Apr 2019).

Package 821/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
kimod 1.10.0
M L Zingaretti
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/kimod
Branch: RELEASE_3_8
Last Commit: 126c425
Last Changed Date: 2018-10-30 11:41:59 -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: kimod
Version: 1.10.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:kimod.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings kimod_1.10.0.tar.gz
StartedAt: 2019-04-13 03:20:42 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 03:23:25 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 162.2 seconds
RetCode: 0
Status:  OK  
CheckDir: kimod.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:kimod.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings kimod_1.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/kimod.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 'kimod/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'kimod' version '1.10.0'
* 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 'kimod' 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
Continous: no visible global function definition for 'lm'
Continous: no visible global function definition for 'pf'
Continous: no visible global function definition for 'AIC'
Continous: no visible global function definition for 'BIC'
DiStatis: no visible global function definition for 'as.dist'
compbin: no visible global function definition for 'na.omit'
confelli: no visible global function definition for 'qf'
confelli: no visible global function definition for 'runif'
dist.binary: no visible global function definition for 'as.dist'
distan: no visible global function definition for 'dist'
distan: no visible global function definition for 'cor'
maha: no visible global function definition for 'cov'
Biplot,SelectVar: no visible global function definition for 'cutree'
BootPlot,Bootstrap: no visible global function definition for 'cov'
BootPlot,Bootstrap: no visible global function definition for 'rgb'
Bootstrap,DiStatis: no visible binding for global variable 'sd'
Bootstrap,DiStatis: no visible global function definition for 'qt'
GroupProj,SelectVar: no visible global function definition for 'cutree'
SelectVar,DiStatis: no visible global function definition for
  'p.adjust'
TrajPlot,DiStatis: no visible global function definition for 'rgb'
print,Bootstrap: no visible global function definition for 'head'
print,DiStatis: no visible global function definition for 'head'
print,GroupProj: no visible global function definition for 'head'
print,SelectVar: no visible global function definition for 'head'
Undefined global functions or variables:
  AIC BIC as.dist cor cov cutree dist head lm na.omit p.adjust pf qf qt
  rgb runif sd
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "AIC", "BIC", "as.dist", "cor", "cov", "cutree",
             "dist", "lm", "na.omit", "p.adjust", "pf", "qf", "qt",
             "runif", "sd")
  importFrom("utils", "head")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
DiStatis-Bootstrap 7.22      0    7.22
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
DiStatis-Bootstrap 7.17      0    7.17
* 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
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/kimod.Rcheck/00check.log'
for details.



Installation output

kimod.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/kimod_1.10.0.tar.gz && rm -rf kimod.buildbin-libdir && mkdir kimod.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=kimod.buildbin-libdir kimod_1.10.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL kimod_1.10.0.zip && rm kimod_1.10.0.tar.gz kimod_1.10.0.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
  0  379k    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  379k  100  379k    0     0  6940k      0 --:--:-- --:--:-- --:--:-- 7296k

install for i386

* installing *source* package 'kimod' ...
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'kimod'
    finding HTML links ... done
    BootPlot                                html  
    Bootstrap-Class                         html  
    Bootstrap-print.Boot                    html  
    Bootstrap-summary                       html  
    DiStatis-Bootstrap                      html  
    DiStatis-Class                          html  
    DiStatis-CompPlot                       html  
    DiStatis-DiStatis                       html  
    DiStatis-PanelPlot                      html  
    DiStatis-RVPlot                         html  
    DiStatis-SelectVar                      html  
    DiStatis-TrajPlot                       html  
    DiStatis-print                          html  
    DiStatis-summary                        html  
    GroupProj-Class                         html  
    GroupProj-print                         html  
    GroupProj-summary                       html  
    GroupProj                               html  
    NCI60Selec                              html  
    NCI60Selec_ESet                         html  
    SelectVar-Biplot                        html  
    SelectVar-Class                         html  
    SelectVar-print                         html  
    SelectVar-summary                       html  
    winesassesors                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'kimod' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'kimod' as kimod_1.10.0.zip
* DONE (kimod)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'kimod' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

kimod.Rcheck/examples_i386/kimod-Ex.timings

nameusersystemelapsed
BootPlot1.820.051.87
Bootstrap-Class000
Bootstrap-print.Boot1.690.001.69
Bootstrap-summary1.880.011.89
DiStatis-Bootstrap7.220.007.22
DiStatis-Class000
DiStatis-CompPlot000
DiStatis-DiStatis0.150.000.16
DiStatis-PanelPlot0.110.000.11
DiStatis-RVPlot0.050.000.05
DiStatis-SelectVar2.930.002.94
DiStatis-TrajPlot0.080.020.09
DiStatis-print0.080.000.08
DiStatis-summary0.450.160.61
GroupProj-Class000
GroupProj-print1.780.001.80
GroupProj-summary2.240.002.23
GroupProj1.620.011.64
NCI60Selec000
NCI60Selec_ESet000
SelectVar-Biplot1.780.021.80
SelectVar-Class000
SelectVar-print1.820.001.81
SelectVar-summary2.480.012.50
winesassesors000

kimod.Rcheck/examples_x64/kimod-Ex.timings

nameusersystemelapsed
BootPlot1.850.021.86
Bootstrap-Class000
Bootstrap-print.Boot2.490.012.50
Bootstrap-summary2.980.023.00
DiStatis-Bootstrap7.170.007.17
DiStatis-Class000
DiStatis-CompPlot000
DiStatis-DiStatis0.160.000.15
DiStatis-PanelPlot0.170.020.19
DiStatis-RVPlot0.100.020.11
DiStatis-SelectVar3.720.003.72
DiStatis-TrajPlot0.070.010.09
DiStatis-print0.080.000.08
DiStatis-summary0.500.060.56
GroupProj-Class000
GroupProj-print1.910.001.91
GroupProj-summary2.060.022.08
GroupProj2.080.002.08
NCI60Selec000
NCI60Selec_ESet000
SelectVar-Biplot2.390.002.39
SelectVar-Class000
SelectVar-print1.750.001.75
SelectVar-summary2.150.022.16
winesassesors000