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BioC 3.4: CHECK report for DFP on moscato1

This page was generated on 2016-09-21 03:42:34 -0700 (Wed, 21 Sep 2016).

Package 315/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DFP 1.31.0
Rodrigo Alvarez-Glez
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DFP
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  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DFP
Version: 1.31.0
Command: rm -rf DFP.buildbin-libdir DFP.Rcheck && mkdir DFP.buildbin-libdir DFP.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DFP.buildbin-libdir DFP_1.31.0.tar.gz >DFP.Rcheck\00install.out 2>&1 && cp DFP.Rcheck\00install.out DFP-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=DFP.buildbin-libdir --install="check:DFP-install.out" --force-multiarch --no-vignettes --timings DFP_1.31.0.tar.gz
StartedAt: 2016-09-20 07:07:01 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 07:07:54 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 53.0 seconds
RetCode: 0
Status:  OK  
CheckDir: DFP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DFP.buildbin-libdir DFP.Rcheck && mkdir DFP.buildbin-libdir DFP.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DFP.buildbin-libdir DFP_1.31.0.tar.gz >DFP.Rcheck\00install.out 2>&1 && cp DFP.Rcheck\00install.out DFP-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=DFP.buildbin-libdir --install="check:DFP-install.out" --force-multiarch --no-vignettes --timings DFP_1.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/DFP.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DFP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DFP' version '1.31.0'
* 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 'DFP' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'Biobase' which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotDiscriminantFuzzyPattern: warning in matrix(x, nr = ly, nc = lx,
  byrow = TRUE): partial argument match of 'nr' to 'nrow'
plotDiscriminantFuzzyPattern: warning in matrix(x, nr = ly, nc = lx,
  byrow = TRUE): partial argument match of 'nc' to 'ncol'
plotDiscriminantFuzzyPattern: warning in matrix(y, nr = ly, nc = lx):
  partial argument match of 'nr' to 'nrow'
plotDiscriminantFuzzyPattern: warning in matrix(y, nr = ly, nc = lx):
  partial argument match of 'nc' to 'ncol'
.plotGeneMF: no visible global function definition for 'curve'
.plotGeneMF: no visible binding for global variable 'x'
.plotGeneMF: no visible global function definition for 'abline'
.plotGeneMF: no visible global function definition for 'palette'
.plotGeneMF: no visible global function definition for 'rainbow'
.plotGeneMF: no visible global function definition for 'legend'
calculateFuzzyPatterns: no visible global function definition for
  'head'
discretizeExpressionValues: no visible global function definition for
  'head'
discriminantFuzzyPattern: no visible global function definition for
  'head'
plotDiscriminantFuzzyPattern: no visible global function definition for
  'image'
plotDiscriminantFuzzyPattern: no visible global function definition for
  'par'
plotDiscriminantFuzzyPattern: no visible global function definition for
  'axis'
plotDiscriminantFuzzyPattern: no visible global function definition for
  'text'
plotMembershipFunctions: no visible global function definition for
  'par'
readCSV: no visible global function definition for 'read.table'
readCSV: no visible global function definition for 'head'
Undefined global functions or variables:
  abline axis curve head image legend palette par rainbow read.table
  text x
Consider adding
  importFrom("grDevices", "palette", "rainbow")
  importFrom("graphics", "abline", "axis", "curve", "image", "legend",
             "par", "text")
  importFrom("utils", "head", "read.table")
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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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: 2 NOTEs
See
  'D:/biocbld/bbs-3.4-bioc/meat/DFP.Rcheck/00check.log'
for details.


DFP.Rcheck/00install.out:


install for i386

* installing *source* package 'DFP' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'DFP' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DFP' as DFP_1.31.0.zip
* DONE (DFP)

DFP.Rcheck/examples_i386/DFP-Ex.timings:

nameusersystemelapsed
DFP-package1.940.001.94
ExpressionLevel-class000
HighExpressionLevel-class000
LowExpressionLevel-class0.010.000.01
MediumExpressionLevel-class000
discriminantFuzzyPattern1.660.001.66
readCSV0.090.000.09
rmadataset0.000.020.02

DFP.Rcheck/examples_x64/DFP-Ex.timings:

nameusersystemelapsed
DFP-package2.310.002.31
ExpressionLevel-class0.010.000.01
HighExpressionLevel-class000
LowExpressionLevel-class000
MediumExpressionLevel-class000
discriminantFuzzyPattern2.060.002.06
readCSV0.080.020.10
rmadataset000