pdmclass 1.41.0
James W. MacDonald
| Snapshot Date: 2015-08-19 16:24:33 -0700 (Wed, 19 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pdmclass | | Last Changed Rev: 102594 / Revision: 107602 | | Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ WARNINGS ] | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | WARNINGS | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf pdmclass.buildbin-libdir pdmclass.Rcheck && mkdir pdmclass.buildbin-libdir pdmclass.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pdmclass.buildbin-libdir pdmclass_1.41.0.tar.gz >pdmclass.Rcheck\00install.out 2>&1 && cp pdmclass.Rcheck\00install.out pdmclass-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=pdmclass.buildbin-libdir --install="check:pdmclass-install.out" --force-multiarch --no-vignettes --timings pdmclass_1.41.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/pdmclass.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pdmclass/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pdmclass' version '1.41.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [31s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
pdmClass.cv 17.15 0.99 18.15
pdmGenes 9.57 0.17 9.76
** running examples for arch 'x64' ... [35s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
pdmClass.cv 20.46 1.37 21.86
pdmGenes 9.89 0.14 10.04
* 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
'D:/biocbld/bbs-3.2-bioc/meat/pdmclass.Rcheck/00check.log'
for details.
install for i386
* 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.
install for x64
* installing *source* package 'pdmclass' ...
** 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.
* MD5 sums
packaged installation of 'pdmclass' as pdmclass_1.41.0.zip
* DONE (pdmclass)