[Bioc-devel] tximport fails to build on Windows

[Obenchain, Valerie]

Hi Mike,

Here is a more informative error from Stangling and sourcing the
vignette on the Windows builder:

...

reading in files with read_tsv
1 Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") :
  cannot open file
'C:/Users/vobencha/Documents/R/win-library/3.4/tximportData/extdata/sailfish/ERR188297/aux/meta_info.
json': No such file or directory
...

The issue lies in readInfRepFish() at this line where file.exists() is
called:

  auxPath <- file.path(fish_dir, aux_dir)
  if (!file.exists(auxPath)) {
    return(NULL)
  }

'auxPath' is
"C:/Users/vobencha/Documents/R/win-library/3.4/tximportData/extdata/sailfish/ERR188297/aux"
which tests TRUE even though no such directory exists. I can reproduce
this weirdness with a simple example. No aux directory or aux file
exists in my home, yet it tests true when there is no trailing slash.
(The trailing slash is not valid in windows and therefore evaluates to
FALSE.)

file.exists("C:/Users/vobencha/aux")
] TRUE
file.exists("C:/Users/vobencha/aux/")
] FALSE

Believe it or not, you simply choose a bad directory name for Windows.
Section 1.1. 'Package Structure' of this link lists aux as a disallowed
file (directory) name:

  https://cran.r-project.org/doc/manuals/r-devel/R-exts.html

You can reproduce this problem with any of the disallowed files names in
that section (disallowed because they are DOS device names). Examples
for the salmon files worked because you named the directory aux_info. If
you rename aux to something else (not listed in Section 1.1!) the
package should build successfully.

Val



On 03/20/2017 01:38 PM, Michael Love wrote:
> Anyone have any ideas for how to debug this?
>
> I get an error from the tximport vignette on tokay2, but I can't
> figure out what could be the issue:
>
> ...
> 1 Quitting from lines 185-189 (tximport.Rmd)
> Error: processing vignette 'tximport.Rmd' failed with diagnostics:
> cannot open the connection
> Execution halted
>
> http://master.bioconductor.org/checkResults/devel/bioc-LATEST/tximport/tokay2-buildsrc.html
>
> Those lines look innocuous to me, and work fine on Linux and Mac:
>
>     184 ```{r}
>     185 files <- file.path(dir,"sailfish", samples$run, "quant.sf")
>     186 names(files) <- paste0("sample",1:6)
>     187 txi.sailfish <- tximport(files, type="sailfish", tx2gene=tx2gene)
>     188 head(txi.sailfish$counts)
>     189 ```
>
> I tried bumping the version and I still get the error from tokay2.
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



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