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CHECK report for parody on merida1

This page was generated on 2019-04-16 11:54:56 -0400 (Tue, 16 Apr 2019).

Package 1119/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
parody 1.40.0
VJ Carey
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/parody
Branch: RELEASE_3_8
Last Commit: 72c42dc
Last Changed Date: 2018-10-30 11:41:45 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: parody
Version: 1.40.0
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_1.40.0.tar.gz
StartedAt: 2019-04-16 01:46:09 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:46:34 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 25.0 seconds
RetCode: 0
Status:  OK 
CheckDir: parody.Rcheck
Warnings: 0

Command output

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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_1.40.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/parody.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.40.0’
* 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-3.8-bioc/meat/parody.Rcheck/00check.log’
for details.



Installation output

parody.Rcheck/00install.out

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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/3.5/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)

Tests output


Example timings

parody.Rcheck/parody-Ex.timings

nameusersystemelapsed
box.scale0.0010.0000.001
bushfire0.0180.0030.025
calout.detect0.0050.0010.006
mv.calout.detect0.0220.0030.027
tcost0.0160.0010.017
tukeyor0.0030.0020.005