Package: parody

Version: 1.41.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:parody.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings parody_1.41.0.tar.gz

StartedAt: 2019-04-09 04:46:34 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:47:08 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 34.5 seconds

RetCode: 0

Status:  OK

CheckDir: parody.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:parody.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings parody_1.41.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/parody.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'parody/DESCRIPTION' ... OK
* this is package 'parody' version '1.41.0'
* 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 whether package 'parody' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ddcovGen : <anonymous>: warning in matrix(x[i, ], nc = 1): partial
  argument match of 'nc' to 'ncol'
ddcovGen : <anonymous>: warning in matrix((N * mx - om)/(N - 1), nc =
  1): partial argument match of 'nc' to 'ncol'
C.unstr: no visible global function definition for 'var'
C.unstr: no visible global function definition for 'mahalanobis'
MLvarcov: no visible global function definition for 'var'
al: no visible global function definition for 'plogis'
d1S: no visible global function definition for 'var'
ddcovGen: no visible global function definition for 'var'
hamp.scale.4: no visible global function definition for 'qnorm'
hampor : Mad: no visible global function definition for 'median'
hampor: no visible global function definition for 'median'
lams.unstr: no visible global function definition for 'qbeta'
lamtab: no visible global function definition for 'qt'
mlvar: no visible global function definition for 'var'
shorth: no visible global function definition for 'qnorm'
skesd: no visible global function definition for 'median'
skesd: no visible global function definition for 'var'
skesd.old: no visible global function definition for 'var'
Undefined global functions or variables:
  mahalanobis median plogis qbeta qnorm qt var
Consider adding
  importFrom("stats", "mahalanobis", "median", "plogis", "qbeta",
             "qnorm", "qt", "var")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: mv.calout.detect.Rd:40: Dropping empty section \references
* 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
** 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/parody.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/parody_1.41.0.tar.gz && rm -rf parody.buildbin-libdir && mkdir parody.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=parody.buildbin-libdir parody_1.41.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL parody_1.41.0.zip && rm parody_1.41.0.tar.gz parody_1.41.0.zip
###
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install for i386

* installing *source* package 'parody' ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'parody'
    finding HTML links ... done
    box.scale                               html  
    bushfire                                html  
    calout.detect                           html  
    mv.calout.detect                        html  
    shorth                                  html  
    tcost                                   html  
    tukeyor                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'parody' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'parody' as parody_1.41.0.zip
* DONE (parody)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'parody' successfully unpacked and MD5 sums checked