##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:affypdnn.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings affypdnn_1.62.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/affypdnn.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.62.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: Package 'affypdnn' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.11-bioc/meat/affypdnn.Rcheck/00install.out’ for details.
* 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 ... ERROR
Running examples in ‘affypdnn-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: transform.ProbeSet
> ### Title: A function to transform a ProbeSet
> ### Aliases: transform.ProbeSet
> ### Keywords: manip
> 
> ### ** Examples
> 
> library(affydata)
> 
> data(Dilution)
> 
> ppset.name <- sample(featureNames(Dilution), 1)
> ppset <- probeset(Dilution, ppset.name)[[1]]
> ppset.log <- transform(ppset, fun=log)
Error in as.data.frame.default(x[[i]], optional = TRUE) : 
  cannot coerce class ‘structure("ProbeSet", package = "affy")’ to a data.frame
Calls: transform ... data.frame -> as.data.frame -> as.data.frame.default
Execution halted
* 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 ERROR, 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/affypdnn.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL affypdnn
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-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'.
Warning: Package 'affypdnn' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package can be loaded from final location
registering new summary method 'pdnn'.
registering new pmcorrect method 'pdnn' and 'pdnnpredict'.
Warning: Package 'affypdnn' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package keeps a record of temporary installation path
* DONE (affypdnn)