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CHECK report for parody on malbec2

This page was generated on 2019-10-16 11:57:07 -0400 (Wed, 16 Oct 2019).

Package 1170/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
parody 1.42.0
VJ Carey
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/parody
Branch: RELEASE_3_9
Last Commit: 662422a
Last Changed Date: 2019-05-02 11:53:11 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: parody
Version: 1.42.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:parody.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings parody_1.42.0.tar.gz
StartedAt: 2019-10-16 03:46:55 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:47:35 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 39.7 seconds
RetCode: 0
Status:  OK 
CheckDir: parody.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:parody.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings parody_1.42.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/parody.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘parody/DESCRIPTION’ ... OK
* this is package ‘parody’ version ‘1.42.0’
* 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 : : warning in matrix(x[i, ], nc = 1): partial
  argument match of 'nc' to 'ncol'
ddcovGen : : 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 ... 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/parody.Rcheck/00check.log’
for details.



Installation output

parody.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL parody
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘parody’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (parody)

Tests output


Example timings

parody.Rcheck/parody-Ex.timings

nameusersystemelapsed
box.scale0.0010.0010.001
bushfire0.0090.0030.013
calout.detect0.0050.0010.005
mv.calout.detect0.0160.0000.016
tcost0.0120.0000.012
tukeyor0.0020.0000.002