R help - Aug 2019 - Error exporting dataframe from Julia to R with Feather

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 at 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 at
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 at 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 at 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 at cbs.dk  Priv: PDalgd at gmail.com

That is a better path, I agree.

However, I suspect that RStudio would still like to know about the issue,
even *if* feather/R is what crashes. They probably do not want RStudio to
crash even so.

-- Bert

On Thu, Aug 8, 2019 at 8:29 AM peter dalgaard <pdalgd at 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 at
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 at
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 at 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 at 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 at cbs.dk  Priv: PDalgd at gmail.com
>
>
>
>
>
>
>
>
>
>
	[[alternative HTML version deleted]]

If R crashes, RStudio typically also crashes... so not necessarily news to them.

I will say that reproducible examples are nearly always necessary in cases like
this to obtain meaningful answers from anyone, and the output of sessionInfo()
is also usually needed.

On August 8, 2019 8:35:49 AM PDT, Bert Gunter <bgunter.4567 at gmail.com>
wrote:
>That is a better path, I agree.
>
>However, I suspect that RStudio would still like to know about the
>issue,
>even *if* feather/R is what crashes. They probably do not want RStudio
>to
>crash even so.
>
>-- Bert
>
>On Thu, Aug 8, 2019 at 8:29 AM peter dalgaard <pdalgd at 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 at
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 at 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 at 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 at 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 at cbs.dk  Priv: PDalgd at gmail.com
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>
>	[[alternative HTML version deleted]]
>
>______________________________________________
>R-help at 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.
-- 
Sent from my phone. Please excuse my brevity.

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 at 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 at
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 at
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 at 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 at 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 at cbs.dk  Priv: PDalgd at gmail.com
>
>
>
>
>
>
>
>
>

--
Best regards,
Luigi