Problem with loaded R packages

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Problem with loaded R packages

Spencer Brackett
Good afternoon,

  I am trying to load the two R packages CGSDR and GAIA which I have
successfully installed onto my R program. Following installation of the two
packages, I proceeded upon recommendation to load both packages via the
library function. Therefore I inputed following...

library(cgdsr)
library(gaia)

This was successfull. Then did the following

source(https://cran.r-project.org/web/packages/cgdsr/vingnettes/cgdsr.pdf

This Bioconductorlink was reported to contain an error and was not loaded
successfully.

Any ideas of what exactly I am doing wrong in my lines?

Many thanks,

Spencer Brackett

        [[alternative HTML version deleted]]

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Re: Problem with loaded R packages

R help mailing list-2
Hi,

The ?source function is intended to read a plain text R source code file into the R console, not a PDF file.

Even if source() could read in a PDF file, you have a typo in the URL, which is CRAN, not BioConductor, and which should be:

  https://cran.r-project.org/web/packages/cgdsr/vignettes/cgdsr.pdf

Regards,

Marc Schwartz

> On Aug 15, 2018, at 2:07 PM, Spencer Brackett <[hidden email]> wrote:
>
> Good afternoon,
>
>  I am trying to load the two R packages CGSDR and GAIA which I have
> successfully installed onto my R program. Following installation of the two
> packages, I proceeded upon recommendation to load both packages via the
> library function. Therefore I inputed following...
>
> library(cgdsr)
> library(gaia)
>
> This was successfull. Then did the following
>
> source(https://cran.r-project.org/web/packages/cgdsr/vingnettes/cgdsr.pdf
>
> This Bioconductorlink was reported to contain an error and was not loaded
> successfully.
>
> Any ideas of what exactly I am doing wrong in my lines?
>
> Many thanks,
>
> Spencer Brackett
>
> [[alternative HTML version deleted]]

______________________________________________
[hidden email] 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.
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Re: Problem with loaded R packages

R help mailing list-2
Hi Spencer,

Please be sure to use reply-all to keep the thread on the list and in the list archives for the future benefit of others. It also allows others to participate with additional information, if needed.

You have already loaded the packages by using the two library() function calls as you have below.

Beyond that, if there are examples from the package vignettes that you want to run, just copy and paste the relevant code from the PDF file, within whatever application you use to view it, into the R console.

Each package also has it's own documentation as well, describing the functions, their arguments, any included datasets, and typically some examples. You can bring up the main package help index by using, for example:

  help(package = "cgdsr")
 
Regards,

Marc


> On Aug 15, 2018, at 2:41 PM, Spencer Brackett <[hidden email]> wrote:
>
> Mr. Schwartz,
>
>   I see. Thank you for the correction! Is there any other line which I could input to load the two packages in question?
>
> Many thanks,
>
> Spencer Brackett
>
> On Wed, Aug 15, 2018 at 2:33 PM Marc Schwartz <[hidden email]> wrote:
> Hi,
>
> The ?source function is intended to read a plain text R source code file into the R console, not a PDF file.
>
> Even if source() could read in a PDF file, you have a typo in the URL, which is CRAN, not BioConductor, and which should be:
>
>   https://cran.r-project.org/web/packages/cgdsr/vignettes/cgdsr.pdf
>
> Regards,
>
> Marc Schwartz
>
> > On Aug 15, 2018, at 2:07 PM, Spencer Brackett <[hidden email]> wrote:
> >
> > Good afternoon,
> >
> >  I am trying to load the two R packages CGSDR and GAIA which I have
> > successfully installed onto my R program. Following installation of the two
> > packages, I proceeded upon recommendation to load both packages via the
> > library function. Therefore I inputed following...
> >
> > library(cgdsr)
> > library(gaia)
> >
> > This was successfull. Then did the following
> >
> > source(https://cran.r-project.org/web/packages/cgdsr/vingnettes/cgdsr.pdf
> >
> > This Bioconductorlink was reported to contain an error and was not loaded
> > successfully.
> >
> > Any ideas of what exactly I am doing wrong in my lines?
> >
> > Many thanks,
> >
> > Spencer Brackett
> >
> >       [[alternative HTML version deleted]]
>

______________________________________________
[hidden email] 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.
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Re: Problem with loaded R packages

Jeff Newmiller
In reply to this post by Spencer Brackett
a) Raw URL text is not legal in R code. URLs MUST ALWAYS be enclosed in single (') or double (") quotes in R.

b) The source function expects to go where you tell it to go and retrieve text composed of R statements. A PDF is a binary file... even if it happened to contain some R code that you could read with your PDF viewer it would be inaccessible to the R interpreter because it is not in a text file.

c) I can't really tell where you are headed with this code you gave us... if you want to read the vignette you could use your web browser to download that PDF and use your viewer to open it. If you want to run any of the code shown in it you can copy it to the console interactively.

d) The Bioconductor project has a different mailing list... for questions not generically about R you should look at https://www.bioconductor.org/help/support

On August 15, 2018 11:07:39 AM PDT, Spencer Brackett <[hidden email]> wrote:

>Good afternoon,
>
>  I am trying to load the two R packages CGSDR and GAIA which I have
>successfully installed onto my R program. Following installation of the
>two
>packages, I proceeded upon recommendation to load both packages via the
>library function. Therefore I inputed following...
>
>library(cgdsr)
>library(gaia)
>
>This was successfull. Then did the following
>
>source(https://cran.r-project.org/web/packages/cgdsr/vingnettes/cgdsr.pdf
>
>This Bioconductorlink was reported to contain an error and was not
>loaded
>successfully.
>
>Any ideas of what exactly I am doing wrong in my lines?
>
>Many thanks,
>
>Spencer Brackett
>
> [[alternative HTML version deleted]]
>
>______________________________________________
>[hidden email] 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.

______________________________________________
[hidden email] 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.
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Re: Problem with loaded R packages

Spencer Brackett
 Many thanks! I will look into apply the advice given.

-Spencer Brackett

On Wed, Aug 15, 2018 at 3:03 PM Jeff Newmiller <[hidden email]>
wrote:

> a) Raw URL text is not legal in R code. URLs MUST ALWAYS be enclosed in
> single (') or double (") quotes in R.
>
> b) The source function expects to go where you tell it to go and retrieve
> text composed of R statements. A PDF is a binary file... even if it
> happened to contain some R code that you could read with your PDF viewer it
> would be inaccessible to the R interpreter because it is not in a text file.
>
> c) I can't really tell where you are headed with this code you gave us...
> if you want to read the vignette you could use your web browser to download
> that PDF and use your viewer to open it. If you want to run any of the code
> shown in it you can copy it to the console interactively.
>
> d) The Bioconductor project has a different mailing list... for questions
> not generically about R you should look at
> https://www.bioconductor.org/help/support
>
> On August 15, 2018 11:07:39 AM PDT, Spencer Brackett <
> [hidden email]> wrote:
> >Good afternoon,
> >
> >  I am trying to load the two R packages CGSDR and GAIA which I have
> >successfully installed onto my R program. Following installation of the
> >two
> >packages, I proceeded upon recommendation to load both packages via the
> >library function. Therefore I inputed following...
> >
> >library(cgdsr)
> >library(gaia)
> >
> >This was successfull. Then did the following
> >
> >source(https://cran.r-project.org/web/packages/cgdsr/vingnettes/cgdsr.pdf
> >
> >This Bioconductorlink was reported to contain an error and was not
> >loaded
> >successfully.
> >
> >Any ideas of what exactly I am doing wrong in my lines?
> >
> >Many thanks,
> >
> >Spencer Brackett
> >
> >       [[alternative HTML version deleted]]
> >
> >______________________________________________
> >[hidden email] 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.
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] 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.