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BioC 3.2: CHECK report for plrs on zin1

This page was generated on 2015-08-24 10:49:00 -0700 (Mon, 24 Aug 2015).

Package 761/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
plrs 1.9.0
Gwenael G.R. Leday to
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/plrs
Last Changed Rev: 102594 / Revision: 107696
Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: plrs
Version: 1.9.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings plrs_1.9.0.tar.gz
StartedAt: 2015-08-24 02:37:24 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 02:38:25 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 60.1 seconds
RetCode: 0
Status:  OK 
CheckDir: plrs.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings plrs_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/plrs.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘plrs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘plrs’ version ‘1.9.0’
* 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 ‘plrs’ can be installed ... [4s/4s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘mvtnorm’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
':::' call which should be '::': ‘CGHbase:::calls’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [12s/12s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
plrs.series 7.666      0   7.664
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/plrs.Rcheck/00check.log’
for details.


plrs.Rcheck/00install.out:

* installing *source* package ‘plrs’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘model.matrix’ from package ‘stats’ in package ‘plrs’
Creating a generic function for ‘knots’ from package ‘stats’ in package ‘plrs’
Creating a generic function for ‘print’ from package ‘base’ in package ‘plrs’
Creating a generic function for ‘effects’ from package ‘stats’ in package ‘plrs’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (plrs)

plrs.Rcheck/plrs-Ex.timings:

nameusersystemelapsed
criteria0.3480.0000.348
modify.conf0.0050.0000.005
neveCN170.1500.0040.154
neveGE170.0520.0000.053
plrs0.0170.0000.017
plrs.cb1.4440.0321.495
plrs.series7.6660.0007.664
plrs.sim0.0240.0000.024
plrs.test0.0210.0000.021