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BioC 3.6: CHECK report for affypdnn on tokay1

This page was generated on 2017-08-16 13:26:19 -0400 (Wed, 16 Aug 2017).

Package 26/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affypdnn 1.51.0
Laurent Gautier
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affypdnn
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: affypdnn
Version: 1.51.0
Command: rm -rf affypdnn.buildbin-libdir affypdnn.Rcheck && mkdir affypdnn.buildbin-libdir affypdnn.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affypdnn.buildbin-libdir affypdnn_1.51.0.tar.gz >affypdnn.Rcheck\00install.out 2>&1 && cp affypdnn.Rcheck\00install.out affypdnn-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=affypdnn.buildbin-libdir --install="check:affypdnn-install.out" --force-multiarch --no-vignettes --timings affypdnn_1.51.0.tar.gz
StartedAt: 2017-08-15 21:39:39 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 21:42:50 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 191.0 seconds
RetCode: 0
Status:  OK  
CheckDir: affypdnn.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf affypdnn.buildbin-libdir affypdnn.Rcheck && mkdir affypdnn.buildbin-libdir affypdnn.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affypdnn.buildbin-libdir affypdnn_1.51.0.tar.gz >affypdnn.Rcheck\00install.out 2>&1 && cp affypdnn.Rcheck\00install.out affypdnn-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=affypdnn.buildbin-libdir --install="check:affypdnn-install.out" --force-multiarch --no-vignettes --timings affypdnn_1.51.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/affypdnn.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'affypdnn/DESCRIPTION' ... OK
* this is package 'affypdnn' version '1.51.0'
* 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 'affypdnn' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  11.7Mb
* 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 'affy' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'affy'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File 'affypdnn/R/zzz.R':
  .onLoad calls:
    require(affy)
    cat("registering new summary method 'pdnn'.\n")
    cat("registering new pmcorrect method 'pdnn' and 'pdnnpredict'.\n")

Package startup functions should not change the search path.
Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.

registering new summary method 'pdnn'.
registering new pmcorrect method 'pdnn' and 'pdnnpredict'.
pmcorrect.pdnn: warning in matrix(as.logical(NA), nr = nrow(probes), nc
  = ncol(probes)): partial argument match of 'nr' to 'nrow'
pmcorrect.pdnn: warning in matrix(as.logical(NA), nr = nrow(probes), nc
  = ncol(probes)): partial argument match of 'nc' to 'ncol'
* 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
Examples with CPU or elapsed time > 5s
                             user system elapsed
expressopdnn                29.15   2.69   31.84
generateExprVal.method.pdnn 23.93   2.23   26.16
find.params.pdnn             7.64   0.41    8.04
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
expressopdnn                27.97   2.75   30.72
generateExprVal.method.pdnn 16.22   1.83   18.05
find.params.pdnn             6.27   0.53    6.80
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/affypdnn.Rcheck/00check.log'
for details.


affypdnn.Rcheck/00install.out:


install for i386

* installing *source* package 'affypdnn' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
registering new summary method 'pdnn'.
registering new pmcorrect method 'pdnn' and 'pdnnpredict'.

install for x64

* installing *source* package 'affypdnn' ...
** testing if installed package can be loaded
registering new summary method 'pdnn'.
registering new pmcorrect method 'pdnn' and 'pdnnpredict'.
* MD5 sums
packaged installation of 'affypdnn' as affypdnn_1.51.0.zip
* DONE (affypdnn)

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

nameusersystemelapsed
chiptype.pdnn.params000
expressopdnn29.15 2.6931.84
find.params.pdnn7.640.418.04
generateExprVal.method.pdnn23.93 2.2326.16
matplotProbesPDNN000
params.dilution0.660.000.66
pdnn.params.chiptype000
transform.ProbeSet0.420.000.42

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

nameusersystemelapsed
chiptype.pdnn.params000
expressopdnn27.97 2.7530.72
find.params.pdnn6.270.536.80
generateExprVal.method.pdnn16.22 1.8318.05
matplotProbesPDNN000
params.dilution0.560.020.57
pdnn.params.chiptype000
transform.ProbeSet0.360.010.38