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BioC 3.1: CHECK report for pdmclass on petty

This page was generated on 2015-10-09 09:32:51 -0700 (Fri, 09 Oct 2015).

Package 709/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pdmclass 1.40.0
James W. MacDonald
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/pdmclass
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: pdmclass
Version: 1.40.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pdmclass_1.40.0.tar.gz
StartedAt: 2015-10-09 01:03:13 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 01:04:35 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 82.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: pdmclass.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pdmclass_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/pdmclass.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pdmclass/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pdmclass’ 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 ‘pdmclass’ can be installed ... [3s/3s] 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 ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘fibroEset’ ‘mda’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘mda:::contr.fda’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... WARNING
Foreign function call to a base package:
  .Fortran(if (!cmplx) "dsvdc" else "zsvdc", ..., PACKAGE = "base")
Packages should not make .C/.Call/.External/.Fortran calls to a base
package. They are not part of the API, for use only by R itself and
subject to change without notice.
* checking R code for possible problems ... NOTE
pdmGenes: warning in match.call(expand = FALSE): partial argument match
  of 'expand' to 'expand.dots'
pdmGenes: warning in matrix(NA, nc = dim(x)[2], nr = dim(x)[1]):
  partial argument match of 'nr' to 'nrow'
pdmGenes: warning in matrix(NA, nc = dim(x)[2], nr = dim(x)[1]):
  partial argument match of 'nc' to 'ncol'
pdmGenes: warning in matrix(NA, nc = B, nr = list.length): partial
  argument match of 'nr' to 'nrow'
pdmGenes: warning in matrix(NA, nc = B, nr = list.length): partial
  argument match of 'nc' to 'ncol'
pdmClass: no visible global function definition for ‘fda’
pdmClass: no visible binding for global variable ‘gen.ridge’
pdmGenes: no visible global function definition for ‘gen.ridge’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [43s/43s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
pdmClass.cv 23.061  1.151  24.228
pdmGenes    14.025  0.845  14.879
* 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: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/pdmclass.Rcheck/00check.log’
for details.


pdmclass.Rcheck/00install.out:

* installing *source* package ‘pdmclass’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in fun(libname, pkgname) :
  
*** Deprecation warning ***
The pdmclass package is deprecated and will be removed from
Bioconductor 3.2.

* DONE (pdmclass)

pdmclass.Rcheck/pdmclass-Ex.timings:

nameusersystemelapsed
pdmClass1.2470.0731.404
pdmClass.cv23.061 1.15124.228
pdmGenes14.025 0.84514.879
predict.pls0.7350.0510.787