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

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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.

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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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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