Package: mdqc

Version: 1.44.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mdqc.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings mdqc_1.44.0.tar.gz

StartedAt: 2019-04-13 03:35:28 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 03:36:56 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 87.8 seconds

RetCode: 0

Status:  OK

CheckDir: mdqc.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:mdqc.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings mdqc_1.44.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/mdqc.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 'mdqc/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'mdqc' version '1.44.0'
* 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 'mdqc' 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
Tbsb: no visible global function definition for 'pchisq'
Tbsc: no visible global function definition for 'qchisq'
ksiint: no visible global function definition for 'pgamma'
mdqc: no visible global function definition for 'as.dist'
mdqc: no visible global function definition for 'mahalanobis'
mySm: no visible global function definition for 'var'
mySm: no visible global function definition for 'mahalanobis'
plot.mdqc: no visible global function definition for 'par'
plot.mdqc: no visible global function definition for 'plot'
plot.mdqc: no visible global function definition for 'abline'
plot.mdqc: no visible global function definition for 'qchisq'
plot.mdqc: no visible global function definition for 'points'
plot.mdqc: no visible global function definition for 'text'
print.mdqc: no visible global function definition for 'qchisq'
summary.mdqc: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  abline as.dist mahalanobis par pchisq pgamma plot points qchisq text
  var
Consider adding
  importFrom("graphics", "abline", "par", "plot", "points", "text")
  importFrom("stats", "as.dist", "mahalanobis", "pchisq", "pgamma",
             "qchisq", "var")
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 ... NOTE
S3 methods shown with full name in documentation object 'prcomp.robust':
  'prcomp.robust'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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
** running examples for arch 'x64' ... OK
* 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/mdqc.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/mdqc_1.44.0.tar.gz && rm -rf mdqc.buildbin-libdir && mkdir mdqc.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mdqc.buildbin-libdir mdqc_1.44.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL mdqc_1.44.0.zip && rm mdqc_1.44.0.tar.gz mdqc_1.44.0.zip
###
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install for i386

* installing *source* package 'mdqc' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'mdqc'
    finding HTML links ... done
    allQC                                   html  
    mdqc-package                            html  
    mdqc                                    html  
    plot.mdqc                               html  
    prcomp.robust                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'mdqc' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mdqc' as mdqc_1.44.0.zip
* DONE (mdqc)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'mdqc' successfully unpacked and MD5 sums checked
In R CMD INSTALL