Package: parody

Version: 1.41.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:parody.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings parody_1.41.0.tar.gz

StartedAt: 2019-04-09 02:43:36 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:44:16 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 40.0 seconds

RetCode: 0

Status:  OK

CheckDir: parody.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:parody.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings parody_1.41.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/parody.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/parody.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL parody
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘parody’ ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (parody)

name	user	system	elapsed
box.scale	0.001	0.000	0.000
bushfire	0.018	0.002	0.020
calout.detect	0.006	0.001	0.007
mv.calout.detect	0.026	0.003	0.030
tcost	0.009	0.001	0.010
tukeyor	0.003	0.002	0.004