Package: mdqc

Version: 1.45.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:mdqc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings mdqc_1.45.0.tar.gz

StartedAt: 2019-04-09 02:00:55 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:01:22 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 27.8 seconds

RetCode: 0

Status:  OK

CheckDir: mdqc.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:mdqc.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings mdqc_1.45.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/mdqc.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 ‘mdqc/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mdqc’ version ‘1.45.0’
* 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 ‘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
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  prcomp.robust
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/mdqc.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 mdqc
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘mdqc’ ...
** 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 (mdqc)

name	user	system	elapsed
allQC	0.021	0.003	0.024
mdqc	2.736	0.024	2.791
plot.mdqc	0.637	0.008	0.651
prcomp.robust	0.438	0.004	0.448