pdmclass 1.45.0
James W. MacDonald
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pdmclass | | Last Changed Rev: 117081 / Revision: 121152 | | Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | WARNINGS | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ WARNINGS ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pdmclass_1.45.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/pdmclass.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.45.0’
* 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 sizes of PDF files under ‘inst/doc’ ... 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 13.983 0.626 14.623
pdmGenes 8.314 0.446 8.762
* 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-3.4-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)