* using log directory 'd:/RCompile/CRANincoming/R-devel/FSAtools.Rcheck'
* using R Under development (unstable) (2023-08-16 r84968 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'FSAtools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'FSAtools' version '2.0.4'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Sylvain Mareschal <mareschal@ovsa.fr>'

New submission

Possibly misspelled words in DESCRIPTION:
  Biosystems (14:42)
  MLPA (14:131)
  Mareschal (14:213, 14:343)
  Palau (14:354)
  Ruminy (14:224)
  al (14:234, 14:363)
  et (14:231, 14:360)
  genotyping (14:439)

The Date field is over a month old.
* 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 serialization versions ... OK
* checking whether package 'FSAtools' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... NOTE
Mismatches for apparent methods not registered:
identify:
  function(x, ...)
identify.fusions:
  function(forward, reverse, design, top, extra)

plot:
  function(x, ...)
plot.fusions:
  function(sampleName, forward, reverse, forwardFile, reverseFile,
           identified, design, pal)
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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 examples ... ERROR
Running examples in 'FSAtools-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: generic.log
> ### Title: Wrapper for 'generic.process'
> ### Aliases: generic.log
> 
> ### ** Examples
> 
>   # Working in temporary directory
>   output <- sprintf("%s/GEP", tempdir())
>   logFile <- sprintf("%s.log", output)
>   
>   # Direct analysis
>   generic.process(
+     input = system.file("extdata/fsa_GEP", package="FSAtools"),
+     design = system.file("extdata/design_GEP.conf", package="FSAtools"),
+     output = output
+   )
Thu Aug 17 10:05:44 2023
FSAtools 2.0.4

Design file : D:\RCompile\CRANincoming\R-devel\lib\FSAtools\extdata\design_GEP.conf [e6265cb968d792e36da0640d68ce45fa]
Design setting(s) set to default for function pdf : onefile, family, fonts, version, paper, encoding, bg, fg, pagecentre, colormodel, useDingbats, useKerning, fillOddEven, compress
Design setting(s) set to default for function multiplot : heights, indexes, byrow, respect, cex
Design setting(s) set to default for function read.fsa : lowess, lowess.top, processed, meta.extra, quiet
Design setting(s) set to default for function align.fsa : channel, fullLadder, useLadder, outThreshold, noiseLevel, surePeaks, leakingRatios, trim, maskOffScale, rMin, rescue, ylim
Design setting(s) set to default for function peaks.fsa : names, size.min, size.max, channels, colors, logTransform, lowThreshold, noiseRange
Design setting(s) set to default for function plot.fsa : units, ladder, offScaleCol, offScalePch, offScaleCex, bg, fg, title.adj, title.line, xlab, ylab, ylim, xaxt, yaxt, bty, xaxp, nticks, all.bp, peaks.alpha, peaks.srt, peaks.adj, peaks.cex, peaks.font, legend.x
Design setting(s) set to default for function add.model : groupMeans, groupSDs, groupNames, groupColors, threshold, geneNames, geneTs, geneMs
Design setting(s) set to default for function classify : plot
Design setting(s) set to default for function export.attr : sep, dec, quote
Design setting(s) set to default for function export.attr : sep, dec, quote
Design setting(s) set to default for function export.attr : sep, dec, quote
Design setting(s) set to default for function dev.off : which
Processing D:/RCompile/CRANincoming/R-devel/lib/FSAtools/extdata/fsa_GEP/A1270.fsa
- file.remove
- pdf
Error in pdf(file = "D:tempRtmpaox2xs/GEP.pdf", title = "GEP", width = 24L,  : 
  cannot open file 'D:tempRtmpaox2xs/GEP.pdf'
Calls: generic.process -> do.call -> pdf
Execution halted
* checking PDF version of manual ... [19s] OK
* checking HTML version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs