Requesting R and Octave Packages

[Elimboto Yohana]

Hi Andrey,

I have been testing R and Octave with SageCell. I think it is worth installing these R libraries shall that be possible:

1. ggplot2 (https://ggplot2.tidyverse.org/)

2. deSolve (https://cran.r-project.org/web/packages/deSolve/index.html)

3. Is it possible to install the swirl package with its associated courses?

Install swirl package:

install.packages("swirl")

Install courses:

library("swirl")

install_course("Course Name")

Courses are found at https://swirlstats.com/scn/title.html

Instructions on how to install courses are described at https://github.com/swirldev/swirl_courses

It would however be great to install these Octave Packages:

1. statistics

2. econometrics

I tried to check if they are installed by loading them,

pkg load statistics                
pkg load econometrics

but the server executes for a long time without any response.

Kind regards,

Elimboto

[Andrey Novoseltsev]

Hi Elimboto,

octave-statistics was installed before, I've also installed octave-econometrics, can you please test again?

For R - do you know how to install packages without any user interaction? As long as we are using R shipped with Sage, I can't directly use system ones. It seems there are now options to use a system one instead, but I didn't look into it closely, there were more pressing issues ;-)

[Elimboto Yohana]

Hi Andrey,

Thank you very much, both Octave packages are working fine.

As for R packages, I'm not sure if what you asked may be close to what is being discussed here! https://stackoverflow.com/questions/51510644/how-to-not-need-user-input-for-install-packagestype-both

Kind regards,

Elimboto

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[Andrey Novoseltsev]

Hi Elimboto,

I've installed these packages and they work to some extent https://sagecell.sagemath.org/?q=dvvfai

I am unclear however, what do you expect from swirl, given that it tries to work interactively.

On a related note - have you tried to setup SageMathCell for yourself just so that you can experiment with it and its capabilities, including what happens with extra packages install in the system or Sage itself?

Best,

Andrey

[Andrey Novoseltsev]

On Tue, Apr 6, 2021 at 4:17 AM Elimboto Yohana <e...@tssfl.com> wrote:

Thank you for installing deSolve and ggplot2. Why I'm I encountering the runtime error?

RRuntimeError: Error in library(ggplot2) : there is no package called ‘ggplot2’

RRuntimeError: Error in library(deSolve) : there is no package called ‘deSolve’

But this only happens with "https://www.tssfl.com/programming-and-computing-with-python-right-from-the-forum-6300" and not https://sagecell.sagemath.org!

No idea - it works fine for me on your site as well. Can you give detailed steps to reproduce the error? 

[Elimboto Yohana]

Hi Andrey,

This has been inconsistent, sometimes it works, sometimes not. I have been getting such an error by just importing the library only: library(ggplot2), library(deSolve). It is somehow stable currently.

Kind regards,

Elimboto

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[Elimboto Yohana]

This error keeps coming up. library(ggplot2) yields the following error message (similarly for other R packages, e.g., deSolve):

---------------------------------------------------------------------------
RRuntimeError                             Traceback (most recent call last)
<ipython-input-1-0c929c793351> in <module>
----> 1 r.eval("options(bitmapType='cairo')"); print(r.eval("""library(ggplot2)""").strip())
      2 r.eval("graphics.off()"); None

/home/sc_serv/sage/local/lib/python3.8/site-packages/sage/interfaces/r.py in eval(self, code, *args, **kwds)
   1337         """
   1338         self._lazy_init()
-> 1339         return str(robjects.r(code)).rstrip()
   1340 
   1341 

/home/sc_serv/sage/local/lib/python3.8/site-packages/rpy2/robjects/__init__.py in __call__(self, string)
    414     def __call__(self, string):
    415         p = rinterface.parse(string)
--> 416         res = self.eval(p)
    417         return conversion.rpy2py(res)
    418 

/home/sc_serv/sage/local/lib/python3.8/site-packages/rpy2/robjects/functions.py in __call__(self, *args, **kwargs)
    195                 v = kwargs.pop(k)
    196                 kwargs[r_k] = v
--> 197         return (super(SignatureTranslatedFunction, self)
    198                 .__call__(*args, **kwargs))
    199 

/home/sc_serv/sage/local/lib/python3.8/site-packages/rpy2/robjects/functions.py in __call__(self, *args, **kwargs)
    123             else:
    124                 new_kwargs[k] = conversion.py2rpy(v)
--> 125         res = super(Function, self).__call__(*new_args, **new_kwargs)
    126         res = conversion.rpy2py(res)
    127         return res

/home/sc_serv/sage/local/lib/python3.8/site-packages/rpy2/rinterface_lib/conversion.py in _(*args, **kwargs)
     42 def _cdata_res_to_rinterface(function):
     43     def _(*args, **kwargs):
---> 44         cdata = function(*args, **kwargs)
     45         # TODO: test cdata is of the expected CType
     46         return _cdata_to_rinterface(cdata)

/home/sc_serv/sage/local/lib/python3.8/site-packages/rpy2/rinterface.py in __call__(self, *args, **kwargs)
    622                     error_occured))
    623             if error_occured[0]:
--> 624                 raise embedded.RRuntimeError(_rinterface._geterrmessage())
    625         return res
    626 

RRuntimeError: Error in library(ggplot2) : there is no package called ‘ggplot2’

What is wrong?

Kind regards,

Elimboto

[Andrey Novoseltsev]

Hi Elimboto,

Turns out one of the servers didn't install these packages, thank you for your persistent complaints, should be working now!

Andrey

[Elimboto Yohana]

Hi Andrey,

Thank you for solving an issue. Tested and libraries seem to be working consistently.

Kind regards,

Elimboto

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[Angel Serrano]

Hi! we`re using a sagecell embeded on a moodle course, but we need to use a package called "survey", is there any way to install it? 

[Elimboto Yohana]

Yes, a number of R packages that were previously  installed not available.

Elimboto

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[Elimboto Yohana]

Hi Andrey,

I would appreciate if you could install the R package 'deSolve", it is missing, but was previously installed:

RRuntimeError: Error in library(deSolve) : there is no package called ‘deSolve’

Kind regards,

Elimboto

[Andrey Novoseltsev]

Perhaps R packages didn't get installed after the last update again for some reason, although it has been a while. I won't do anything right now as I will be away from computers for a few days, but will look into it when I am back.

[Andrey Novoseltsev]

Seems to work now and I have added some code to check that R packages are actually installed, hopefully it will prevent reoccurrences of this issue.

[Elimboto Yohana]

Hi Andrey,

Thanks. Packages seem to work.

Elimboto

On Wed, Jul 27, 2022 at 8:06 AM Andrey Novoseltsev <novo...@gmail.com> wrote:

Seems to work now and I have added some code to check that R packages are actually installed, hopefully it will prevent reoccurrences of this issue.

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