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BioC 3.4: CHECK report for pdmclass on malbec1

This page was generated on 2017-04-15 16:09:03 -0400 (Sat, 15 Apr 2017).

Package 908/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pdmclass 1.46.0
James W. MacDonald
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/pdmclass
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 [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  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: 1.46.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings pdmclass_1.46.0.tar.gz
StartedAt: 2017-04-15 00:22:25 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 00:23:03 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 37.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: pdmclass.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings pdmclass_1.46.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/pdmclass.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 ‘pdmclass/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pdmclass’ version ‘1.46.0’
* 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 ... 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’
pdmClass.cv: no visible global function definition for ‘predict’
pdmGenes: no visible global function definition for ‘model.extract’
pdmGenes: no visible global function definition for ‘model.matrix’
pdmGenes: no visible global function definition for ‘contr.treatment’
pdmGenes: no visible global function definition for ‘gen.ridge’
pdmGenes: no visible global function definition for ‘coef’
predict.pls: no visible global function definition for ‘fitted’
predict.svd: no visible global function definition for ‘fitted’
svdr: no visible global function definition for ‘lm.fit’
Undefined global functions or variables:
  coef contr.treatment fda fitted gen.ridge lm.fit model.extract
  model.matrix predict
Consider adding
  importFrom("stats", "coef", "contr.treatment", "fitted", "lm.fit",
             "model.extract", "model.matrix", "predict")
to your NAMESPACE file.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
pdmClass.cv 9.760  0.076   9.842
pdmGenes    5.392  0.040   5.436
* 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-3.4-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
pdmClass0.6000.0080.607
pdmClass.cv9.7600.0769.842
pdmGenes5.3920.0405.436
predict.pls0.3000.0000.304