BioC 3.2: CHECK report for pdmclass on zin1

Package: pdmclass

Version: 1.42.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings pdmclass_1.42.0.tar.gz

StartedAt: 2016-04-23 03:46:39 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 03:47:20 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 41.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: pdmclass.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings pdmclass_1.42.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/pdmclass.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-linux-gnu (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 ‘1.42.0’
* 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 ‘pdmclass’ can be installed ... [2s/2s] 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 ... [23s/23s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
pdmClass.cv 13.745  0.107  13.930
pdmGenes     6.843  0.024   6.879
* 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
  ‘/home/biocbuild/bbs-3.2-bioc/meat/pdmclass.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
pdmClass	0.643	0.028	0.672
pdmClass.cv	13.745	0.107	13.930
pdmGenes	6.843	0.024	6.879
predict.pls	0.384	0.012	0.394