[R] Error exporting dataframe from Julia to R with Feather

[Luigi Marongiu]

Hi, I ran from terminal:
```
$ Rscript try.R
[1] "library feather loaded"
[1] "open file"

 *** caught segfault ***
address (nil), cause 'memory not mapped'

Traceback:
 1: .Call(`_feather_openFeather`, path)
 2: openFeather(path)
 3: feather(path)
 4: read_feather("Hits_dedupl.feather")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)
```

Perhaps is the problem with the original database rather than feather.
When I save the dataframe made with Julia with CSV.write and reload in
R with read.table I get the error
```
Warning message:
In scan(file = file, what = what, sep = sep, quote = quote, dec = dec,
: EOF within quoted string > str(hit) 'data.frame': 81365 obs. of 1
variable: $ Group.Sample.Start.Match_len.Read_len.Hit_len.Hit.ID: chr
"Normal\tA4\t6064657\t27\t101\t13669\tNC_038931.1 Thermoproteus tenax
virus 1 (TTV1) genome\tNC_038931"
"Normal\tA0\t6064658\t29\t101\t13669\tNC_038931.1 Thermoproteus tenax
virus 1 (TTV1) genome\tNC_038931"
"Normal\tA0\t6064659\t28\t101\t13669\tNC_038931.1 Thermoproteus tenax
virus 1 (TTV1) genome\tNC_038931"
"Normal\tA0\t6064660\t27\t101\t13669\tNC_038931.1 Thermoproteus tenax
virus 1 (TTV1) genome\tNC_038931" ...
```


On Thu, Aug 8, 2019 at 5:29 PM peter dalgaard <pdalgd using gmail.com> wrote:
>
> Alternatively, try running your example from plain R (in a terminal, R.app, or Rgui, depending on your platform), and see if the problem occurs without RStudio in the equation. If it does, then the feather package probably owns the problem.
>
> -pd
>
> > On 8 Aug 2019, at 16:34 , Bert Gunter <bgunter.4567 using gmail.com> wrote:
> >
> > You may have to contact RStudio about this. RStudio is a separate IDE
> > independent of R -- i.e. developed and maintained by a separate
> > organization from the R project.
> >
> > Bert Gunter
> >
> > "The trouble with having an open mind is that people keep coming along and
> > sticking things into it."
> > -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
> >
> >
> > On Thu, Aug 8, 2019 at 7:08 AM Luigi Marongiu <marongiu.luigi using gmail.com>
> > wrote:
> >
> >> Hello,
> >>
> >> since I am encountering a lot of problems exporting dataframes from
> >> julia to R (there is always something wrong with the formatting,
> >> probably a missing quote) so I am trying to use Feather to do the job.
> >>
> >> I have installed Feather in Julia with `pkg.add("Feather")` and
> >> imported it with `using Feather`. I created a dataframe and saved it
> >> with `Feather.write("/dir/dataframe.feather", df)` and it worked. I
> >> can even open it back with `df =
> >> Feather.read("/dir/dataframe.feather")` and get: `julia> nrow(df)
> >> 128544`.
> >> The problem is with R. I am using Rstudio to test each step.
> >> I installed the package, imported it with `library(feather)` and used it
> >> as:
> >> ```
> >> df = read_feather("/dir/dataframe.feather")
> >> ```
> >> and then Rstudio simply crashes.
> >> any idea why?
> >> Thank you
> >>
> >> ______________________________________________
> >> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guide
> >> http://www.R-project.org/posting-guide.html
> >> and provide commented, minimal, self-contained, reproducible code.
> >>
> >
> >       [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
> --
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Office: A 4.23
> Email: pd.mes using cbs.dk  Priv: PDalgd using gmail.com
>
>
>
>
>
>
>
>
>


--
Best regards,
Luigi