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BioC 3.4: CHECK report for parody on malbec1

This page was generated on 2017-04-15 16:09:45 -0400 (Sat, 15 Apr 2017).

Package 890/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
parody 1.32.0
VJ Carey
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/parody
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: parody
Version: 1.32.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings parody_1.32.0.tar.gz
StartedAt: 2017-04-15 00:18:49 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 00:19:12 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 22.4 seconds
RetCode: 0
Status:  OK 
CheckDir: parody.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings parody_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/parody.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.32.0’
* 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 installed files from ‘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
  ‘/home/biocbuild/bbs-3.4-bioc/meat/parody.Rcheck/00check.log’
for details.


parody.Rcheck/00install.out:

* installing *source* package ‘parody’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (parody)

parody.Rcheck/parody-Ex.timings:

nameusersystemelapsed
box.scale000
bushfire0.0080.0000.008
calout.detect0.0040.0000.003
mv.calout.detect0.0120.0000.012
tcost0.0080.0000.006
tukeyor0.0000.0000.002