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CHECK report for affypdnn on malbec1

This page was generated on 2020-04-15 12:04:06 -0400 (Wed, 15 Apr 2020).

Package 33/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affypdnn 1.60.0
Laurent Gautier
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/affypdnn
Branch: RELEASE_3_10
Last Commit: 9f8998f
Last Changed Date: 2019-10-29 13:07:26 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: affypdnn
Version: 1.60.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:affypdnn.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings affypdnn_1.60.0.tar.gz
StartedAt: 2020-04-15 00:10:37 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 00:12:09 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 92.6 seconds
RetCode: 0
Status:  OK 
CheckDir: affypdnn.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:affypdnn.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings affypdnn_1.60.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/affypdnn.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affypdnn/DESCRIPTION’ ... OK
* this is package ‘affypdnn’ version ‘1.60.0’
* 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 ‘affypdnn’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.9Mb
  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
* 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
'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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  transform.ProbeSet
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
expressopdnn                24.328  0.372  24.770
generateExprVal.method.pdnn 18.448  0.128  18.609
find.params.pdnn             7.824  0.044   7.880
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/affypdnn.Rcheck/00check.log’
for details.



Installation output

affypdnn.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL affypdnn
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘affypdnn’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
registering new summary method 'pdnn'.
registering new pmcorrect method 'pdnn' and 'pdnnpredict'.
** testing if installed package can be loaded from final location
registering new summary method 'pdnn'.
registering new pmcorrect method 'pdnn' and 'pdnnpredict'.
** testing if installed package keeps a record of temporary installation path
* DONE (affypdnn)

Tests output


Example timings

affypdnn.Rcheck/affypdnn-Ex.timings

nameusersystemelapsed
chiptype.pdnn.params0.0000.0000.002
expressopdnn24.328 0.37224.770
find.params.pdnn7.8240.0447.880
generateExprVal.method.pdnn18.448 0.12818.609
matplotProbesPDNN000
params.dilution0.7280.0120.741
pdnn.params.chiptype0.0000.0000.001
transform.ProbeSet0.4440.0120.458