Help installing netReg

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Help installing netReg

Spencer Brackett
Good evening,

 I am having problems with downloading the package used to generate
regression models on R. The following is the error message I received. I
tried installing BiocManager instead as suggested, but this too did not
work. Any ideas?

The downloaded binary packages are in
C:\Users\Spencer\AppData\Local\Temp\Rtmp8YKVqx\downloaded_packages
installation path not writeable, unable to update packages: class, cluster,
codetools, foreign,
  lattice, MASS, Matrix, mgcv, nlme, rpart, survival
Warning message:
'biocLite' is deprecated.
Use 'BiocManager::install' instead.
See help("Deprecated")

Best,

Spencer

        [[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: Help installing netReg

David Winsemius

On 4/14/19 3:20 PM, Spencer Brackett wrote:

> Good evening,
>
>   I am having problems with downloading the package used to generate
> regression models on R. The following is the error message I received. I
> tried installing BiocManager instead as suggested, but this too did not
> work. Any ideas?
>
> The downloaded binary packages are in
> C:\Users\Spencer\AppData\Local\Temp\Rtmp8YKVqx\downloaded_packages
> installation path not writeable, unable to update packages: class, cluster,
> codetools, foreign,
>    lattice, MASS, Matrix, mgcv, nlme, rpart, survival
> Warning message:
> 'biocLite' is deprecated.
> Use 'BiocManager::install' instead.
> See help("Deprecated")


Since you did not include the code that provoked this message we can
only guess that you did in fact use `bioLite`. We also cannot tell what
you mean by "problems with downloading the package used to generate
regression models on R". The typical first step is to use the glm or lm
function for this task and those are both in the stats package which is
installed with the base version of R and is loaded by default when R is
started up.

"

Have you tried following the suggestion at the end of the message?


And do read the Posting Guide and include "commented, minimal,
self-contained, reproducible code."


--

David.

>
> Best,
>
> Spencer
>
> [[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.

______________________________________________
[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: Help installing netReg

Spencer Brackett
My apologies... here is the full code in summary

install.packages("ggplot2")
install.packages("ggplot2")
source("https://bioconductor.org/biocLite.R")
?BiocUpgrade
source("https://bioconductor.org/biocLite.R")biocLite("BiocUpgrade")
source("https://bioconductor.org/biocLite.R")
biocLite("BiocUpgrade")
source("https://bioconductor.org/bioLite.R")
biocLite("netReg")
help("Deprecated")
'BiocManager::install'
biocLite("netReg")
help("oldName-deprecated")
‘??oldName-deprecated’
.Deprecated(new, package=NULL, msg,
old = as.character(sys.call(sys.parent()))[1L])

Best,

Spencer



On Sun, Apr 14, 2019 at 7:20 PM David Winsemius <[hidden email]>
wrote:

>
> On 4/14/19 3:20 PM, Spencer Brackett wrote:
> > Good evening,
> >
> >   I am having problems with downloading the package used to generate
> > regression models on R. The following is the error message I received. I
> > tried installing BiocManager instead as suggested, but this too did not
> > work. Any ideas?
> >
> > The downloaded binary packages are in
> > C:\Users\Spencer\AppData\Local\Temp\Rtmp8YKVqx\downloaded_packages
> > installation path not writeable, unable to update packages: class,
> cluster,
> > codetools, foreign,
> >    lattice, MASS, Matrix, mgcv, nlme, rpart, survival
> > Warning message:
> > 'biocLite' is deprecated.
> > Use 'BiocManager::install' instead.
> > See help("Deprecated")
>
>
> Since you did not include the code that provoked this message we can
> only guess that you did in fact use `bioLite`. We also cannot tell what
> you mean by "problems with downloading the package used to generate
> regression models on R". The typical first step is to use the glm or lm
> function for this task and those are both in the stats package which is
> installed with the base version of R and is loaded by default when R is
> started up.
>
> "
>
> Have you tried following the suggestion at the end of the message?
>
>
> And do read the Posting Guide and include "commented, minimal,
> self-contained, reproducible code."
>
>
> --
>
> David.
>
> >
> > Best,
> >
> > Spencer
> >
> >       [[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.
>

        [[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: Help installing netReg

Spencer Brackett
Good evening,

 I am having problems with downloading the package used to generate
regression models on R. The following is the error message I received. I
tried installing BiocManager instead as suggested, but this too did not
work. Any ideas?

The following is the full summary of what I’ve tried thus far...

install.packages("ggplot2")
install.packages("ggplot2")
source("https://bioconductor.org/biocLite.R")
?BiocUpgrade
source("https://bioconductor.org/biocLite.R")biocLite("BiocUpgrade")
source("https://bioconductor.org/biocLite.R")
biocLite("BiocUpgrade")
source("https://bioconductor.org/bioLite.R")
biocLite("netReg")
help("Deprecated")
'BiocManager::install'
biocLite("netReg")
help("oldName-deprecated")
‘??oldName-deprecated’
.Deprecated(new, package=NULL, msg,
old = as.character(sys.call(sys.parent()))[1L])

Best,

Spencer

On Sun, Apr 14, 2019 at 7:58 PM Spencer Brackett <
[hidden email]> wrote:

> My apologies... here is the full code in summary
>
> install.packages("ggplot2")
> install.packages("ggplot2")
> source("https://bioconductor.org/biocLite.R")
> ?BiocUpgrade
> source("https://bioconductor.org/biocLite.R")biocLite("BiocUpgrade")
> source("https://bioconductor.org/biocLite.R")
> biocLite("BiocUpgrade")
> source("https://bioconductor.org/bioLite.R")
> biocLite("netReg")
> help("Deprecated")
> 'BiocManager::install'
> biocLite("netReg")
> help("oldName-deprecated")
> ‘??oldName-deprecated’
> .Deprecated(new, package=NULL, msg,
> old = as.character(sys.call(sys.parent()))[1L])
>
> Best,
>
> Spencer
>
>
>
> On Sun, Apr 14, 2019 at 7:20 PM David Winsemius <[hidden email]>
> wrote:
>
>>
>> On 4/14/19 3:20 PM, Spencer Brackett wrote:
>> > Good evening,
>> >
>> >   I am having problems with downloading the package used to generate
>> > regression models on R. The following is the error message I received. I
>> > tried installing BiocManager instead as suggested, but this too did not
>> > work. Any ideas?
>> >
>> > The downloaded binary packages are in
>> > C:\Users\Spencer\AppData\Local\Temp\Rtmp8YKVqx\downloaded_packages
>> > installation path not writeable, unable to update packages: class,
>> cluster,
>> > codetools, foreign,
>> >    lattice, MASS, Matrix, mgcv, nlme, rpart, survival
>> > Warning message:
>> > 'biocLite' is deprecated.
>> > Use 'BiocManager::install' instead.
>> > See help("Deprecated")
>>
>>
>> Since you did not include the code that provoked this message we can
>> only guess that you did in fact use `bioLite`. We also cannot tell what
>> you mean by "problems with downloading the package used to generate
>> regression models on R". The typical first step is to use the glm or lm
>> function for this task and those are both in the stats package which is
>> installed with the base version of R and is loaded by default when R is
>> started up.
>>
>> "
>>
>> Have you tried following the suggestion at the end of the message?
>>
>>
>> And do read the Posting Guide and include "commented, minimal,
>> self-contained, reproducible code."
>>
>>
>> --
>>
>> David.
>>
>> >
>> > Best,
>> >
>> > Spencer
>> >
>> >       [[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.
>>
>

        [[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: Help installing netReg

Bert Gunter-2
netReg is not "the package that generates regression models in R." Tons of
packages generate regression models in R, including lm(), which is in the
stats package that is part of R's standard distro.

So what exactly is it that you want to do that you think requires netReg?
And if netReg is required, have you tried addressing your queries to the
Bioconductor list, as it is one of their packages?

Cheers,
Bert


"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 Sun, Apr 21, 2019 at 5:06 PM Spencer Brackett <
[hidden email]> wrote:

> Good evening,
>
>  I am having problems with downloading the package used to generate
> regression models on R. The following is the error message I received. I
> tried installing BiocManager instead as suggested, but this too did not
> work. Any ideas?
>
> The following is the full summary of what I’ve tried thus far...
>
> install.packages("ggplot2")
> install.packages("ggplot2")
> source("https://bioconductor.org/biocLite.R")
> ?BiocUpgrade
> source("https://bioconductor.org/biocLite.R")biocLite("BiocUpgrade")
> source("https://bioconductor.org/biocLite.R")
> biocLite("BiocUpgrade")
> source("https://bioconductor.org/bioLite.R")
> biocLite("netReg")
> help("Deprecated")
> 'BiocManager::install'
> biocLite("netReg")
> help("oldName-deprecated")
> ‘??oldName-deprecated’
> .Deprecated(new, package=NULL, msg,
> old = as.character(sys.call(sys.parent()))[1L])
>
> Best,
>
> Spencer
>
> On Sun, Apr 14, 2019 at 7:58 PM Spencer Brackett <
> [hidden email]> wrote:
>
> > My apologies... here is the full code in summary
> >
> > install.packages("ggplot2")
> > install.packages("ggplot2")
> > source("https://bioconductor.org/biocLite.R")
> > ?BiocUpgrade
> > source("https://bioconductor.org/biocLite.R")biocLite("BiocUpgrade")
> > source("https://bioconductor.org/biocLite.R")
> > biocLite("BiocUpgrade")
> > source("https://bioconductor.org/bioLite.R")
> > biocLite("netReg")
> > help("Deprecated")
> > 'BiocManager::install'
> > biocLite("netReg")
> > help("oldName-deprecated")
> > ‘??oldName-deprecated’
> > .Deprecated(new, package=NULL, msg,
> > old = as.character(sys.call(sys.parent()))[1L])
> >
> > Best,
> >
> > Spencer
> >
> >
> >
> > On Sun, Apr 14, 2019 at 7:20 PM David Winsemius <[hidden email]>
> > wrote:
> >
> >>
> >> On 4/14/19 3:20 PM, Spencer Brackett wrote:
> >> > Good evening,
> >> >
> >> >   I am having problems with downloading the package used to generate
> >> > regression models on R. The following is the error message I
> received. I
> >> > tried installing BiocManager instead as suggested, but this too did
> not
> >> > work. Any ideas?
> >> >
> >> > The downloaded binary packages are in
> >> > C:\Users\Spencer\AppData\Local\Temp\Rtmp8YKVqx\downloaded_packages
> >> > installation path not writeable, unable to update packages: class,
> >> cluster,
> >> > codetools, foreign,
> >> >    lattice, MASS, Matrix, mgcv, nlme, rpart, survival
> >> > Warning message:
> >> > 'biocLite' is deprecated.
> >> > Use 'BiocManager::install' instead.
> >> > See help("Deprecated")
> >>
> >>
> >> Since you did not include the code that provoked this message we can
> >> only guess that you did in fact use `bioLite`. We also cannot tell what
> >> you mean by "problems with downloading the package used to generate
> >> regression models on R". The typical first step is to use the glm or lm
> >> function for this task and those are both in the stats package which is
> >> installed with the base version of R and is loaded by default when R is
> >> started up.
> >>
> >> "
> >>
> >> Have you tried following the suggestion at the end of the message?
> >>
> >>
> >> And do read the Posting Guide and include "commented, minimal,
> >> self-contained, reproducible code."
> >>
> >>
> >> --
> >>
> >> David.
> >>
> >> >
> >> > Best,
> >> >
> >> > Spencer
> >> >
> >> >       [[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.
> >>
> >
>
>         [[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.
>

        [[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: Help installing netReg

Spencer Brackett
Mr. Gunter,

Yes I have reached out to the bioconductor list but was informed that my
inquiry concerning this package was not appropriate for the mailing list.
However, I have since tried re implementing the code which I sent and my R
Studio says that netReg has successfully been unpacked, so for now it
appears that my problem is solved :)

Best,

Spencer Brackett

On Sun, Apr 21, 2019 at 8:35 PM Bert Gunter <[hidden email]> wrote:

> netReg is not "the package that generates regression models in R." Tons of
> packages generate regression models in R, including lm(), which is in the
> stats package that is part of R's standard distro.
>
> So what exactly is it that you want to do that you think requires netReg?
> And if netReg is required, have you tried addressing your queries to the
> Bioconductor list, as it is one of their packages?
>
> Cheers,
> Bert
>
>
> "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 Sun, Apr 21, 2019 at 5:06 PM Spencer Brackett <
> [hidden email]> wrote:
>
>> Good evening,
>>
>>  I am having problems with downloading the package used to generate
>> regression models on R. The following is the error message I received. I
>> tried installing BiocManager instead as suggested, but this too did not
>> work. Any ideas?
>>
>> The following is the full summary of what I’ve tried thus far...
>>
>> install.packages("ggplot2")
>> install.packages("ggplot2")
>> source("https://bioconductor.org/biocLite.R")
>> ?BiocUpgrade
>> source("https://bioconductor.org/biocLite.R")biocLite("BiocUpgrade")
>> source("https://bioconductor.org/biocLite.R")
>> biocLite("BiocUpgrade")
>> source("https://bioconductor.org/bioLite.R")
>> biocLite("netReg")
>> help("Deprecated")
>> 'BiocManager::install'
>> biocLite("netReg")
>> help("oldName-deprecated")
>> ‘??oldName-deprecated’
>> .Deprecated(new, package=NULL, msg,
>> old = as.character(sys.call(sys.parent()))[1L])
>>
>> Best,
>>
>> Spencer
>>
>> On Sun, Apr 14, 2019 at 7:58 PM Spencer Brackett <
>> [hidden email]> wrote:
>>
>> > My apologies... here is the full code in summary
>> >
>> > install.packages("ggplot2")
>> > install.packages("ggplot2")
>> > source("https://bioconductor.org/biocLite.R")
>> > ?BiocUpgrade
>> > source("https://bioconductor.org/biocLite.R")biocLite("BiocUpgrade")
>> > source("https://bioconductor.org/biocLite.R")
>> > biocLite("BiocUpgrade")
>> > source("https://bioconductor.org/bioLite.R")
>> > biocLite("netReg")
>> > help("Deprecated")
>> > 'BiocManager::install'
>> > biocLite("netReg")
>> > help("oldName-deprecated")
>> > ‘??oldName-deprecated’
>> > .Deprecated(new, package=NULL, msg,
>> > old = as.character(sys.call(sys.parent()))[1L])
>> >
>> > Best,
>> >
>> > Spencer
>> >
>> >
>> >
>> > On Sun, Apr 14, 2019 at 7:20 PM David Winsemius <[hidden email]
>> >
>> > wrote:
>> >
>> >>
>> >> On 4/14/19 3:20 PM, Spencer Brackett wrote:
>> >> > Good evening,
>> >> >
>> >> >   I am having problems with downloading the package used to generate
>> >> > regression models on R. The following is the error message I
>> received. I
>> >> > tried installing BiocManager instead as suggested, but this too did
>> not
>> >> > work. Any ideas?
>> >> >
>> >> > The downloaded binary packages are in
>> >> > C:\Users\Spencer\AppData\Local\Temp\Rtmp8YKVqx\downloaded_packages
>> >> > installation path not writeable, unable to update packages: class,
>> >> cluster,
>> >> > codetools, foreign,
>> >> >    lattice, MASS, Matrix, mgcv, nlme, rpart, survival
>> >> > Warning message:
>> >> > 'biocLite' is deprecated.
>> >> > Use 'BiocManager::install' instead.
>> >> > See help("Deprecated")
>> >>
>> >>
>> >> Since you did not include the code that provoked this message we can
>> >> only guess that you did in fact use `bioLite`. We also cannot tell what
>> >> you mean by "problems with downloading the package used to generate
>> >> regression models on R". The typical first step is to use the glm or lm
>> >> function for this task and those are both in the stats package which is
>> >> installed with the base version of R and is loaded by default when R is
>> >> started up.
>> >>
>> >> "
>> >>
>> >> Have you tried following the suggestion at the end of the message?
>> >>
>> >>
>> >> And do read the Posting Guide and include "commented, minimal,
>> >> self-contained, reproducible code."
>> >>
>> >>
>> >> --
>> >>
>> >> David.
>> >>
>> >> >
>> >> > Best,
>> >> >
>> >> > Spencer
>> >> >
>> >> >       [[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.
>> >>
>> >
>>
>>         [[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.
>>
>

        [[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: Help installing netReg

Spencer Brackett
R users,

  I am trying to download R Studio onto my Chrombook for convenience, but
exited out of the Linux terminal that had opened upon my turning on of
Linux(Beta) through my settings. Because of this I am unable to prompt the
same type of Linex terminal and can only enable a new one via ctrl alt t .
Running the same line of commands (as shown below) that I was following
before encountering my error w/ the first terminal is not working. Note,
the hostname for the new terminal that I have prompted is crosh> if that
effects anything.

Commands I was instructed to make after enabling Linux on my Chrome...

lsb_release
sudo apt search r-base | grep ^r-base (to download R)

-y gnupg2
—keyserver keys.gnupg.net —recv-key ‘ ‘
***where my terminal experienced some sort of error causing me to abandon
it***

Any pointers for how I may proceed or alternative tutorials that I may
follow?

Best,

Spencer Brackett


On Sun, Apr 21, 2019 at 9:35 PM Spencer Brackett <
[hidden email]> wrote:

> Mr. Gunter,
>
> Yes I have reached out to the bioconductor list but was informed that my
> inquiry concerning this package was not appropriate for the mailing list.
> However, I have since tried re implementing the code which I sent and my R
> Studio says that netReg has successfully been unpacked, so for now it
> appears that my problem is solved :)
>
> Best,
>
> Spencer Brackett
>
> On Sun, Apr 21, 2019 at 8:35 PM Bert Gunter <[hidden email]>
> wrote:
>
>> netReg is not "the package that generates regression models in R." Tons
>> of packages generate regression models in R, including lm(), which is in
>> the stats package that is part of R's standard distro.
>>
>> So what exactly is it that you want to do that you think requires netReg?
>> And if netReg is required, have you tried addressing your queries to the
>> Bioconductor list, as it is one of their packages?
>>
>> Cheers,
>> Bert
>>
>>
>> "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 Sun, Apr 21, 2019 at 5:06 PM Spencer Brackett <
>> [hidden email]> wrote:
>>
>>> Good evening,
>>>
>>>  I am having problems with downloading the package used to generate
>>> regression models on R. The following is the error message I received. I
>>> tried installing BiocManager instead as suggested, but this too did not
>>> work. Any ideas?
>>>
>>> The following is the full summary of what I’ve tried thus far...
>>>
>>> install.packages("ggplot2")
>>> install.packages("ggplot2")
>>> source("https://bioconductor.org/biocLite.R")
>>> ?BiocUpgrade
>>> source("https://bioconductor.org/biocLite.R")biocLite("BiocUpgrade")
>>> source("https://bioconductor.org/biocLite.R")
>>> biocLite("BiocUpgrade")
>>> source("https://bioconductor.org/bioLite.R")
>>> biocLite("netReg")
>>> help("Deprecated")
>>> 'BiocManager::install'
>>> biocLite("netReg")
>>> help("oldName-deprecated")
>>> ‘??oldName-deprecated’
>>> .Deprecated(new, package=NULL, msg,
>>> old = as.character(sys.call(sys.parent()))[1L])
>>>
>>> Best,
>>>
>>> Spencer
>>>
>>> On Sun, Apr 14, 2019 at 7:58 PM Spencer Brackett <
>>> [hidden email]> wrote:
>>>
>>> > My apologies... here is the full code in summary
>>> >
>>> > install.packages("ggplot2")
>>> > install.packages("ggplot2")
>>> > source("https://bioconductor.org/biocLite.R")
>>> > ?BiocUpgrade
>>> > source("https://bioconductor.org/biocLite.R")biocLite("BiocUpgrade")
>>> > source("https://bioconductor.org/biocLite.R")
>>> > biocLite("BiocUpgrade")
>>> > source("https://bioconductor.org/bioLite.R")
>>> > biocLite("netReg")
>>> > help("Deprecated")
>>> > 'BiocManager::install'
>>> > biocLite("netReg")
>>> > help("oldName-deprecated")
>>> > ‘??oldName-deprecated’
>>> > .Deprecated(new, package=NULL, msg,
>>> > old = as.character(sys.call(sys.parent()))[1L])
>>> >
>>> > Best,
>>> >
>>> > Spencer
>>> >
>>> >
>>> >
>>> > On Sun, Apr 14, 2019 at 7:20 PM David Winsemius <
>>> [hidden email]>
>>> > wrote:
>>> >
>>> >>
>>> >> On 4/14/19 3:20 PM, Spencer Brackett wrote:
>>> >> > Good evening,
>>> >> >
>>> >> >   I am having problems with downloading the package used to generate
>>> >> > regression models on R. The following is the error message I
>>> received. I
>>> >> > tried installing BiocManager instead as suggested, but this too did
>>> not
>>> >> > work. Any ideas?
>>> >> >
>>> >> > The downloaded binary packages are in
>>> >> > C:\Users\Spencer\AppData\Local\Temp\Rtmp8YKVqx\downloaded_packages
>>> >> > installation path not writeable, unable to update packages: class,
>>> >> cluster,
>>> >> > codetools, foreign,
>>> >> >    lattice, MASS, Matrix, mgcv, nlme, rpart, survival
>>> >> > Warning message:
>>> >> > 'biocLite' is deprecated.
>>> >> > Use 'BiocManager::install' instead.
>>> >> > See help("Deprecated")
>>> >>
>>> >>
>>> >> Since you did not include the code that provoked this message we can
>>> >> only guess that you did in fact use `bioLite`. We also cannot tell
>>> what
>>> >> you mean by "problems with downloading the package used to generate
>>> >> regression models on R". The typical first step is to use the glm or
>>> lm
>>> >> function for this task and those are both in the stats package which
>>> is
>>> >> installed with the base version of R and is loaded by default when R
>>> is
>>> >> started up.
>>> >>
>>> >> "
>>> >>
>>> >> Have you tried following the suggestion at the end of the message?
>>> >>
>>> >>
>>> >> And do read the Posting Guide and include "commented, minimal,
>>> >> self-contained, reproducible code."
>>> >>
>>> >>
>>> >> --
>>> >>
>>> >> David.
>>> >>
>>> >> >
>>> >> > Best,
>>> >> >
>>> >> > Spencer
>>> >> >
>>> >> >       [[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.
>>> >>
>>> >
>>>
>>>         [[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.
>>>
>>

        [[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: Help installing netReg

Boris Steipe
This is unrelated to the question on the subject line, we call this "thread hijacking" and that's one of the Things Not To Do. Post a new question.

I just wanted to give you the proper incantation for Bioconductor packages. As you already know, don't use bioclite(), which needed to be sourced from an URL. Instead install.packages("Biocmanager") from CRAN, then - there's no need to load it - use Biocmanager::install(<package name>) from there on. I usually have it in scripts like so:

if (! requireNamespace("BiocManager", quietly = TRUE)) {
  install.packages("BiocManager")
}
if (! requireNamespace("biomaRt", quietly = TRUE)) {
  BiocManager::install("biomaRt")
}


Cheers,
Boris

> On 2019-04-21, at 22:27, Spencer Brackett <[hidden email]> wrote:
>
> R users,
>
>  I am trying to download R Studio onto my Chrombook for convenience, but
> exited out of the Linux terminal that had opened upon my turning on of
> Linux(Beta) through my settings. Because of this I am unable to prompt the
> same type of Linex terminal and can only enable a new one via ctrl alt t .
> Running the same line of commands (as shown below) that I was following
> before encountering my error w/ the first terminal is not working. Note,
> the hostname for the new terminal that I have prompted is crosh> if that
> effects anything.
>
> Commands I was instructed to make after enabling Linux on my Chrome...
>
> lsb_release
> sudo apt search r-base | grep ^r-base (to download R)
>
> -y gnupg2
> —keyserver keys.gnupg.net —recv-key ‘ ‘
> ***where my terminal experienced some sort of error causing me to abandon
> it***
>
> Any pointers for how I may proceed or alternative tutorials that I may
> follow?
>
> Best,
>
> Spencer Brackett
>
>
> On Sun, Apr 21, 2019 at 9:35 PM Spencer Brackett <
> [hidden email]> wrote:
>
>> Mr. Gunter,
>>
>> Yes I have reached out to the bioconductor list but was informed that my
>> inquiry concerning this package was not appropriate for the mailing list.
>> However, I have since tried re implementing the code which I sent and my R
>> Studio says that netReg has successfully been unpacked, so for now it
>> appears that my problem is solved :)
>>
>> Best,
>>
>> Spencer Brackett
>>
>> On Sun, Apr 21, 2019 at 8:35 PM Bert Gunter <[hidden email]>
>> wrote:
>>
>>> netReg is not "the package that generates regression models in R." Tons
>>> of packages generate regression models in R, including lm(), which is in
>>> the stats package that is part of R's standard distro.
>>>
>>> So what exactly is it that you want to do that you think requires netReg?
>>> And if netReg is required, have you tried addressing your queries to the
>>> Bioconductor list, as it is one of their packages?
>>>
>>> Cheers,
>>> Bert
>>>
>>>
>>> "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 Sun, Apr 21, 2019 at 5:06 PM Spencer Brackett <
>>> [hidden email]> wrote:
>>>
>>>> Good evening,
>>>>
>>>> I am having problems with downloading the package used to generate
>>>> regression models on R. The following is the error message I received. I
>>>> tried installing BiocManager instead as suggested, but this too did not
>>>> work. Any ideas?
>>>>
>>>> The following is the full summary of what I’ve tried thus far...
>>>>
>>>> install.packages("ggplot2")
>>>> install.packages("ggplot2")
>>>> source("https://bioconductor.org/biocLite.R")
>>>> ?BiocUpgrade
>>>> source("https://bioconductor.org/biocLite.R")biocLite("BiocUpgrade")
>>>> source("https://bioconductor.org/biocLite.R")
>>>> biocLite("BiocUpgrade")
>>>> source("https://bioconductor.org/bioLite.R")
>>>> biocLite("netReg")
>>>> help("Deprecated")
>>>> 'BiocManager::install'
>>>> biocLite("netReg")
>>>> help("oldName-deprecated")
>>>> ‘??oldName-deprecated’
>>>> .Deprecated(new, package=NULL, msg,
>>>> old = as.character(sys.call(sys.parent()))[1L])
>>>>
>>>> Best,
>>>>
>>>> Spencer
>>>>
>>>> On Sun, Apr 14, 2019 at 7:58 PM Spencer Brackett <
>>>> [hidden email]> wrote:
>>>>
>>>>> My apologies... here is the full code in summary
>>>>>
>>>>> install.packages("ggplot2")
>>>>> install.packages("ggplot2")
>>>>> source("https://bioconductor.org/biocLite.R")
>>>>> ?BiocUpgrade
>>>>> source("https://bioconductor.org/biocLite.R")biocLite("BiocUpgrade")
>>>>> source("https://bioconductor.org/biocLite.R")
>>>>> biocLite("BiocUpgrade")
>>>>> source("https://bioconductor.org/bioLite.R")
>>>>> biocLite("netReg")
>>>>> help("Deprecated")
>>>>> 'BiocManager::install'
>>>>> biocLite("netReg")
>>>>> help("oldName-deprecated")
>>>>> ‘??oldName-deprecated’
>>>>> .Deprecated(new, package=NULL, msg,
>>>>> old = as.character(sys.call(sys.parent()))[1L])
>>>>>
>>>>> Best,
>>>>>
>>>>> Spencer
>>>>>
>>>>>
>>>>>
>>>>> On Sun, Apr 14, 2019 at 7:20 PM David Winsemius <
>>>> [hidden email]>
>>>>> wrote:
>>>>>
>>>>>>
>>>>>> On 4/14/19 3:20 PM, Spencer Brackett wrote:
>>>>>>> Good evening,
>>>>>>>
>>>>>>>  I am having problems with downloading the package used to generate
>>>>>>> regression models on R. The following is the error message I
>>>> received. I
>>>>>>> tried installing BiocManager instead as suggested, but this too did
>>>> not
>>>>>>> work. Any ideas?
>>>>>>>
>>>>>>> The downloaded binary packages are in
>>>>>>> C:\Users\Spencer\AppData\Local\Temp\Rtmp8YKVqx\downloaded_packages
>>>>>>> installation path not writeable, unable to update packages: class,
>>>>>> cluster,
>>>>>>> codetools, foreign,
>>>>>>>   lattice, MASS, Matrix, mgcv, nlme, rpart, survival
>>>>>>> Warning message:
>>>>>>> 'biocLite' is deprecated.
>>>>>>> Use 'BiocManager::install' instead.
>>>>>>> See help("Deprecated")
>>>>>>
>>>>>>
>>>>>> Since you did not include the code that provoked this message we can
>>>>>> only guess that you did in fact use `bioLite`. We also cannot tell
>>>> what
>>>>>> you mean by "problems with downloading the package used to generate
>>>>>> regression models on R". The typical first step is to use the glm or
>>>> lm
>>>>>> function for this task and those are both in the stats package which
>>>> is
>>>>>> installed with the base version of R and is loaded by default when R
>>>> is
>>>>>> started up.
>>>>>>
>>>>>> "
>>>>>>
>>>>>> Have you tried following the suggestion at the end of the message?
>>>>>>
>>>>>>
>>>>>> And do read the Posting Guide and include "commented, minimal,
>>>>>> self-contained, reproducible code."
>>>>>>
>>>>>>
>>>>>> --
>>>>>>
>>>>>> David.
>>>>>>
>>>>>>>
>>>>>>> Best,
>>>>>>>
>>>>>>> Spencer
>>>>>>>
>>>>>>>      [[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.
>>>>>>
>>>>>
>>>>
>>>>        [[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.
>>>>
>>>
>
> [[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.

______________________________________________
[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: Help installing netReg

Spencer Brackett
Boris,
'
My apologies. Thanks for the tip! I tried the command you suggested in your
response and got the following...

> BiocManager::install("netReg")
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.1 (2018-07-02)
Installing package(s) 'BiocVersion', 'netReg'
trying URL '
https://bioconductor.org/packages/3.8/bioc/bin/windows/contrib/3.5/BiocVersion_3.8.0.zip
'
Content type 'application/zip' length 8843 bytes
downloaded 8843 bytes

trying URL '
https://bioconductor.org/packages/3.8/bioc/bin/windows/contrib/3.5/netReg_1.6.0.zip
'
Content type 'application/zip' length 4143315 bytes (4.0 MB)
downloaded 4.0 MB

package ‘BiocVersion’ successfully unpacked and MD5 sums checked
package ‘netReg’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
C:\Users\Spencer\AppData\Local\Temp\RtmpW6FwPY\downloaded_packages
installation path not writeable, unable to update packages: class, cluster,
codetools, foreign,
  lattice, MASS, Matrix, mgcv, nlme, rpart, survival

***Does it matter that the packages above are unable to be updated? For
insight, I am trying to generate linear regression models that model
expression of methylation w/ in a TCGA dataset.***

Best,

Spencer

On Sun, Apr 21, 2019 at 10:57 PM Boris Steipe <[hidden email]>
wrote:

> This is unrelated to the question on the subject line, we call this
> "thread hijacking" and that's one of the Things Not To Do. Post a new
> question.
>
> I just wanted to give you the proper incantation for Bioconductor
> packages. As you already know, don't use bioclite(), which needed to be
> sourced from an URL. Instead install.packages("Biocmanager") from CRAN,
> then - there's no need to load it - use Biocmanager::install(<package
> name>) from there on. I usually have it in scripts like so:
>
> if (! requireNamespace("BiocManager", quietly = TRUE)) {
>   install.packages("BiocManager")
> }
> if (! requireNamespace("biomaRt", quietly = TRUE)) {
>   BiocManager::install("biomaRt")
> }
>
>
> Cheers,
> Boris
>
> > On 2019-04-21, at 22:27, Spencer Brackett <
> [hidden email]> wrote:
> >
> > R users,
> >
> >  I am trying to download R Studio onto my Chrombook for convenience, but
> > exited out of the Linux terminal that had opened upon my turning on of
> > Linux(Beta) through my settings. Because of this I am unable to prompt
> the
> > same type of Linex terminal and can only enable a new one via ctrl alt t
> .
> > Running the same line of commands (as shown below) that I was following
> > before encountering my error w/ the first terminal is not working. Note,
> > the hostname for the new terminal that I have prompted is crosh> if that
> > effects anything.
> >
> > Commands I was instructed to make after enabling Linux on my Chrome...
> >
> > lsb_release
> > sudo apt search r-base | grep ^r-base (to download R)
> >
> > -y gnupg2
> > —keyserver keys.gnupg.net —recv-key ‘ ‘
> > ***where my terminal experienced some sort of error causing me to abandon
> > it***
> >
> > Any pointers for how I may proceed or alternative tutorials that I may
> > follow?
> >
> > Best,
> >
> > Spencer Brackett
> >
> >
> > On Sun, Apr 21, 2019 at 9:35 PM Spencer Brackett <
> > [hidden email]> wrote:
> >
> >> Mr. Gunter,
> >>
> >> Yes I have reached out to the bioconductor list but was informed that my
> >> inquiry concerning this package was not appropriate for the mailing
> list.
> >> However, I have since tried re implementing the code which I sent and
> my R
> >> Studio says that netReg has successfully been unpacked, so for now it
> >> appears that my problem is solved :)
> >>
> >> Best,
> >>
> >> Spencer Brackett
> >>
> >> On Sun, Apr 21, 2019 at 8:35 PM Bert Gunter <[hidden email]>
> >> wrote:
> >>
> >>> netReg is not "the package that generates regression models in R." Tons
> >>> of packages generate regression models in R, including lm(), which is
> in
> >>> the stats package that is part of R's standard distro.
> >>>
> >>> So what exactly is it that you want to do that you think requires
> netReg?
> >>> And if netReg is required, have you tried addressing your queries to
> the
> >>> Bioconductor list, as it is one of their packages?
> >>>
> >>> Cheers,
> >>> Bert
> >>>
> >>>
> >>> "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 Sun, Apr 21, 2019 at 5:06 PM Spencer Brackett <
> >>> [hidden email]> wrote:
> >>>
> >>>> Good evening,
> >>>>
> >>>> I am having problems with downloading the package used to generate
> >>>> regression models on R. The following is the error message I
> received. I
> >>>> tried installing BiocManager instead as suggested, but this too did
> not
> >>>> work. Any ideas?
> >>>>
> >>>> The following is the full summary of what I’ve tried thus far...
> >>>>
> >>>> install.packages("ggplot2")
> >>>> install.packages("ggplot2")
> >>>> source("https://bioconductor.org/biocLite.R")
> >>>> ?BiocUpgrade
> >>>> source("https://bioconductor.org/biocLite.R")biocLite("BiocUpgrade")
> >>>> source("https://bioconductor.org/biocLite.R")
> >>>> biocLite("BiocUpgrade")
> >>>> source("https://bioconductor.org/bioLite.R")
> >>>> biocLite("netReg")
> >>>> help("Deprecated")
> >>>> 'BiocManager::install'
> >>>> biocLite("netReg")
> >>>> help("oldName-deprecated")
> >>>> ‘??oldName-deprecated’
> >>>> .Deprecated(new, package=NULL, msg,
> >>>> old = as.character(sys.call(sys.parent()))[1L])
> >>>>
> >>>> Best,
> >>>>
> >>>> Spencer
> >>>>
> >>>> On Sun, Apr 14, 2019 at 7:58 PM Spencer Brackett <
> >>>> [hidden email]> wrote:
> >>>>
> >>>>> My apologies... here is the full code in summary
> >>>>>
> >>>>> install.packages("ggplot2")
> >>>>> install.packages("ggplot2")
> >>>>> source("https://bioconductor.org/biocLite.R")
> >>>>> ?BiocUpgrade
> >>>>> source("https://bioconductor.org/biocLite.R")biocLite("BiocUpgrade")
> >>>>> source("https://bioconductor.org/biocLite.R")
> >>>>> biocLite("BiocUpgrade")
> >>>>> source("https://bioconductor.org/bioLite.R")
> >>>>> biocLite("netReg")
> >>>>> help("Deprecated")
> >>>>> 'BiocManager::install'
> >>>>> biocLite("netReg")
> >>>>> help("oldName-deprecated")
> >>>>> ‘??oldName-deprecated’
> >>>>> .Deprecated(new, package=NULL, msg,
> >>>>> old = as.character(sys.call(sys.parent()))[1L])
> >>>>>
> >>>>> Best,
> >>>>>
> >>>>> Spencer
> >>>>>
> >>>>>
> >>>>>
> >>>>> On Sun, Apr 14, 2019 at 7:20 PM David Winsemius <
> >>>> [hidden email]>
> >>>>> wrote:
> >>>>>
> >>>>>>
> >>>>>> On 4/14/19 3:20 PM, Spencer Brackett wrote:
> >>>>>>> Good evening,
> >>>>>>>
> >>>>>>>  I am having problems with downloading the package used to generate
> >>>>>>> regression models on R. The following is the error message I
> >>>> received. I
> >>>>>>> tried installing BiocManager instead as suggested, but this too did
> >>>> not
> >>>>>>> work. Any ideas?
> >>>>>>>
> >>>>>>> The downloaded binary packages are in
> >>>>>>> C:\Users\Spencer\AppData\Local\Temp\Rtmp8YKVqx\downloaded_packages
> >>>>>>> installation path not writeable, unable to update packages: class,
> >>>>>> cluster,
> >>>>>>> codetools, foreign,
> >>>>>>>   lattice, MASS, Matrix, mgcv, nlme, rpart, survival
> >>>>>>> Warning message:
> >>>>>>> 'biocLite' is deprecated.
> >>>>>>> Use 'BiocManager::install' instead.
> >>>>>>> See help("Deprecated")
> >>>>>>
> >>>>>>
> >>>>>> Since you did not include the code that provoked this message we can
> >>>>>> only guess that you did in fact use `bioLite`. We also cannot tell
> >>>> what
> >>>>>> you mean by "problems with downloading the package used to generate
> >>>>>> regression models on R". The typical first step is to use the glm or
> >>>> lm
> >>>>>> function for this task and those are both in the stats package which
> >>>> is
> >>>>>> installed with the base version of R and is loaded by default when R
> >>>> is
> >>>>>> started up.
> >>>>>>
> >>>>>> "
> >>>>>>
> >>>>>> Have you tried following the suggestion at the end of the message?
> >>>>>>
> >>>>>>
> >>>>>> And do read the Posting Guide and include "commented, minimal,
> >>>>>> self-contained, reproducible code."
> >>>>>>
> >>>>>>
> >>>>>> --
> >>>>>>
> >>>>>> David.
> >>>>>>
> >>>>>>>
> >>>>>>> Best,
> >>>>>>>
> >>>>>>> Spencer
> >>>>>>>
> >>>>>>>      [[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.
> >>>>>>
> >>>>>
> >>>>
> >>>>        [[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.
> >>>>
> >>>
> >
> >       [[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.
>
>

        [[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: Help installing netReg

Boris Steipe
"installation path not writeable" tells you that there is a permissions problem with your setup. Sounds like a pretty standard problem. Someone who works with Windows will know the standard solution.

Cheers,
B.



> On 2019-04-21, at 23:49, Spencer Brackett <[hidden email]> wrote:
>
> Boris,
> '
> My apologies. Thanks for the tip! I tried the command you suggested in your response and got the following...
>
> > BiocManager::install("netReg")
> Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.1 (2018-07-02)
> Installing package(s) 'BiocVersion', 'netReg'
> trying URL 'https://bioconductor.org/packages/3.8/bioc/bin/windows/contrib/3.5/BiocVersion_3.8.0.zip'
> Content type 'application/zip' length 8843 bytes
> downloaded 8843 bytes
>
> trying URL 'https://bioconductor.org/packages/3.8/bioc/bin/windows/contrib/3.5/netReg_1.6.0.zip'
> Content type 'application/zip' length 4143315 bytes (4.0 MB)
> downloaded 4.0 MB
>
> package ‘BiocVersion’ successfully unpacked and MD5 sums checked
> package ‘netReg’ successfully unpacked and MD5 sums checked
>
> The downloaded binary packages are in
> C:\Users\Spencer\AppData\Local\Temp\RtmpW6FwPY\downloaded_packages
> installation path not writeable, unable to update packages: class, cluster, codetools, foreign,
>   lattice, MASS, Matrix, mgcv, nlme, rpart, survival
>
> ***Does it matter that the packages above are unable to be updated? For insight, I am trying to generate linear regression models that model expression of methylation w/ in a TCGA dataset.***
>
> Best,
>
> Spencer
>
> On Sun, Apr 21, 2019 at 10:57 PM Boris Steipe <[hidden email]> wrote:
> This is unrelated to the question on the subject line, we call this "thread hijacking" and that's one of the Things Not To Do. Post a new question.
>
> I just wanted to give you the proper incantation for Bioconductor packages. As you already know, don't use bioclite(), which needed to be sourced from an URL. Instead install.packages("Biocmanager") from CRAN, then - there's no need to load it - use Biocmanager::install(<package name>) from there on. I usually have it in scripts like so:
>
> if (! requireNamespace("BiocManager", quietly = TRUE)) {
>   install.packages("BiocManager")
> }
> if (! requireNamespace("biomaRt", quietly = TRUE)) {
>   BiocManager::install("biomaRt")
> }
>
>
> Cheers,
> Boris
>
> > On 2019-04-21, at 22:27, Spencer Brackett <[hidden email]> wrote:
> >
> > R users,
> >
> >  I am trying to download R Studio onto my Chrombook for convenience, but
> > exited out of the Linux terminal that had opened upon my turning on of
> > Linux(Beta) through my settings. Because of this I am unable to prompt the
> > same type of Linex terminal and can only enable a new one via ctrl alt t .
> > Running the same line of commands (as shown below) that I was following
> > before encountering my error w/ the first terminal is not working. Note,
> > the hostname for the new terminal that I have prompted is crosh> if that
> > effects anything.
> >
> > Commands I was instructed to make after enabling Linux on my Chrome...
> >
> > lsb_release
> > sudo apt search r-base | grep ^r-base (to download R)
> >
> > -y gnupg2
> > —keyserver keys.gnupg.net —recv-key ‘ ‘
> > ***where my terminal experienced some sort of error causing me to abandon
> > it***
> >
> > Any pointers for how I may proceed or alternative tutorials that I may
> > follow?
> >
> > Best,
> >
> > Spencer Brackett
> >
> >
> > On Sun, Apr 21, 2019 at 9:35 PM Spencer Brackett <
> > [hidden email]> wrote:
> >
> >> Mr. Gunter,
> >>
> >> Yes I have reached out to the bioconductor list but was informed that my
> >> inquiry concerning this package was not appropriate for the mailing list.
> >> However, I have since tried re implementing the code which I sent and my R
> >> Studio says that netReg has successfully been unpacked, so for now it
> >> appears that my problem is solved :)
> >>
> >> Best,
> >>
> >> Spencer Brackett
> >>
> >> On Sun, Apr 21, 2019 at 8:35 PM Bert Gunter <[hidden email]>
> >> wrote:
> >>
> >>> netReg is not "the package that generates regression models in R." Tons
> >>> of packages generate regression models in R, including lm(), which is in
> >>> the stats package that is part of R's standard distro.
> >>>
> >>> So what exactly is it that you want to do that you think requires netReg?
> >>> And if netReg is required, have you tried addressing your queries to the
> >>> Bioconductor list, as it is one of their packages?
> >>>
> >>> Cheers,
> >>> Bert
> >>>
> >>>
> >>> "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 Sun, Apr 21, 2019 at 5:06 PM Spencer Brackett <
> >>> [hidden email]> wrote:
> >>>
> >>>> Good evening,
> >>>>
> >>>> I am having problems with downloading the package used to generate
> >>>> regression models on R. The following is the error message I received. I
> >>>> tried installing BiocManager instead as suggested, but this too did not
> >>>> work. Any ideas?
> >>>>
> >>>> The following is the full summary of what I’ve tried thus far...
> >>>>
> >>>> install.packages("ggplot2")
> >>>> install.packages("ggplot2")
> >>>> source("https://bioconductor.org/biocLite.R")
> >>>> ?BiocUpgrade
> >>>> source("https://bioconductor.org/biocLite.R")biocLite("BiocUpgrade")
> >>>> source("https://bioconductor.org/biocLite.R")
> >>>> biocLite("BiocUpgrade")
> >>>> source("https://bioconductor.org/bioLite.R")
> >>>> biocLite("netReg")
> >>>> help("Deprecated")
> >>>> 'BiocManager::install'
> >>>> biocLite("netReg")
> >>>> help("oldName-deprecated")
> >>>> ‘??oldName-deprecated’
> >>>> .Deprecated(new, package=NULL, msg,
> >>>> old = as.character(sys.call(sys.parent()))[1L])
> >>>>
> >>>> Best,
> >>>>
> >>>> Spencer
> >>>>
> >>>> On Sun, Apr 14, 2019 at 7:58 PM Spencer Brackett <
> >>>> [hidden email]> wrote:
> >>>>
> >>>>> My apologies... here is the full code in summary
> >>>>>
> >>>>> install.packages("ggplot2")
> >>>>> install.packages("ggplot2")
> >>>>> source("https://bioconductor.org/biocLite.R")
> >>>>> ?BiocUpgrade
> >>>>> source("https://bioconductor.org/biocLite.R")biocLite("BiocUpgrade")
> >>>>> source("https://bioconductor.org/biocLite.R")
> >>>>> biocLite("BiocUpgrade")
> >>>>> source("https://bioconductor.org/bioLite.R")
> >>>>> biocLite("netReg")
> >>>>> help("Deprecated")
> >>>>> 'BiocManager::install'
> >>>>> biocLite("netReg")
> >>>>> help("oldName-deprecated")
> >>>>> ‘??oldName-deprecated’
> >>>>> .Deprecated(new, package=NULL, msg,
> >>>>> old = as.character(sys.call(sys.parent()))[1L])
> >>>>>
> >>>>> Best,
> >>>>>
> >>>>> Spencer
> >>>>>
> >>>>>
> >>>>>
> >>>>> On Sun, Apr 14, 2019 at 7:20 PM David Winsemius <
> >>>> [hidden email]>
> >>>>> wrote:
> >>>>>
> >>>>>>
> >>>>>> On 4/14/19 3:20 PM, Spencer Brackett wrote:
> >>>>>>> Good evening,
> >>>>>>>
> >>>>>>>  I am having problems with downloading the package used to generate
> >>>>>>> regression models on R. The following is the error message I
> >>>> received. I
> >>>>>>> tried installing BiocManager instead as suggested, but this too did
> >>>> not
> >>>>>>> work. Any ideas?
> >>>>>>>
> >>>>>>> The downloaded binary packages are in
> >>>>>>> C:\Users\Spencer\AppData\Local\Temp\Rtmp8YKVqx\downloaded_packages
> >>>>>>> installation path not writeable, unable to update packages: class,
> >>>>>> cluster,
> >>>>>>> codetools, foreign,
> >>>>>>>   lattice, MASS, Matrix, mgcv, nlme, rpart, survival
> >>>>>>> Warning message:
> >>>>>>> 'biocLite' is deprecated.
> >>>>>>> Use 'BiocManager::install' instead.
> >>>>>>> See help("Deprecated")
> >>>>>>
> >>>>>>
> >>>>>> Since you did not include the code that provoked this message we can
> >>>>>> only guess that you did in fact use `bioLite`. We also cannot tell
> >>>> what
> >>>>>> you mean by "problems with downloading the package used to generate
> >>>>>> regression models on R". The typical first step is to use the glm or
> >>>> lm
> >>>>>> function for this task and those are both in the stats package which
> >>>> is
> >>>>>> installed with the base version of R and is loaded by default when R
> >>>> is
> >>>>>> started up.
> >>>>>>
> >>>>>> "
> >>>>>>
> >>>>>> Have you tried following the suggestion at the end of the message?
> >>>>>>
> >>>>>>
> >>>>>> And do read the Posting Guide and include "commented, minimal,
> >>>>>> self-contained, reproducible code."
> >>>>>>
> >>>>>>
> >>>>>> --
> >>>>>>
> >>>>>> David.
> >>>>>>
> >>>>>>>
> >>>>>>> Best,
> >>>>>>>
> >>>>>>> Spencer
> >>>>>>>
> >>>>>>>      [[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.
> >>>>>>
> >>>>>
> >>>>
> >>>>        [[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.
> >>>>
> >>>
> >
> >       [[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.
>

______________________________________________
[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: Help installing netReg

Jeff Newmiller
In reply to this post by Spencer Brackett
I don't know anything about the Bioconductor installation, but it is normal practice on Windows to install updates to packages distributed with R (such as those below) by "superceding" them in your user library. This happens automatically if you don't specify the destination library to install to. Just do a normal update.packages and the Program Files library will stay unchanged but your user library versions of the base R packages will be loaded instead.

On April 21, 2019 8:49:08 PM PDT, Spencer Brackett <[hidden email]> wrote:

>Boris,
>'
>My apologies. Thanks for the tip! I tried the command you suggested in
>your
>response and got the following...
>
>> BiocManager::install("netReg")
>Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.1 (2018-07-02)
>Installing package(s) 'BiocVersion', 'netReg'
>trying URL '
>https://bioconductor.org/packages/3.8/bioc/bin/windows/contrib/3.5/BiocVersion_3.8.0.zip
>'
>Content type 'application/zip' length 8843 bytes
>downloaded 8843 bytes
>
>trying URL '
>https://bioconductor.org/packages/3.8/bioc/bin/windows/contrib/3.5/netReg_1.6.0.zip
>'
>Content type 'application/zip' length 4143315 bytes (4.0 MB)
>downloaded 4.0 MB
>
>package ‘BiocVersion’ successfully unpacked and MD5 sums checked
>package ‘netReg’ successfully unpacked and MD5 sums checked
>
>The downloaded binary packages are in
>C:\Users\Spencer\AppData\Local\Temp\RtmpW6FwPY\downloaded_packages
>installation path not writeable, unable to update packages: class,
>cluster,
>codetools, foreign,
>  lattice, MASS, Matrix, mgcv, nlme, rpart, survival
>
>***Does it matter that the packages above are unable to be updated? For
>insight, I am trying to generate linear regression models that model
>expression of methylation w/ in a TCGA dataset.***
>
>Best,
>
>Spencer
>
>On Sun, Apr 21, 2019 at 10:57 PM Boris Steipe
><[hidden email]>
>wrote:
>
>> This is unrelated to the question on the subject line, we call this
>> "thread hijacking" and that's one of the Things Not To Do. Post a new
>> question.
>>
>> I just wanted to give you the proper incantation for Bioconductor
>> packages. As you already know, don't use bioclite(), which needed to
>be
>> sourced from an URL. Instead install.packages("Biocmanager") from
>CRAN,
>> then - there's no need to load it - use Biocmanager::install(<package
>> name>) from there on. I usually have it in scripts like so:
>>
>> if (! requireNamespace("BiocManager", quietly = TRUE)) {
>>   install.packages("BiocManager")
>> }
>> if (! requireNamespace("biomaRt", quietly = TRUE)) {
>>   BiocManager::install("biomaRt")
>> }
>>
>>
>> Cheers,
>> Boris
>>
>> > On 2019-04-21, at 22:27, Spencer Brackett <
>> [hidden email]> wrote:
>> >
>> > R users,
>> >
>> >  I am trying to download R Studio onto my Chrombook for
>convenience, but
>> > exited out of the Linux terminal that had opened upon my turning on
>of
>> > Linux(Beta) through my settings. Because of this I am unable to
>prompt
>> the
>> > same type of Linex terminal and can only enable a new one via ctrl
>alt t
>> .
>> > Running the same line of commands (as shown below) that I was
>following
>> > before encountering my error w/ the first terminal is not working.
>Note,
>> > the hostname for the new terminal that I have prompted is crosh> if
>that
>> > effects anything.
>> >
>> > Commands I was instructed to make after enabling Linux on my
>Chrome...
>> >
>> > lsb_release
>> > sudo apt search r-base | grep ^r-base (to download R)
>> >
>> > -y gnupg2
>> > —keyserver keys.gnupg.net —recv-key ‘ ‘
>> > ***where my terminal experienced some sort of error causing me to
>abandon
>> > it***
>> >
>> > Any pointers for how I may proceed or alternative tutorials that I
>may
>> > follow?
>> >
>> > Best,
>> >
>> > Spencer Brackett
>> >
>> >
>> > On Sun, Apr 21, 2019 at 9:35 PM Spencer Brackett <
>> > [hidden email]> wrote:
>> >
>> >> Mr. Gunter,
>> >>
>> >> Yes I have reached out to the bioconductor list but was informed
>that my
>> >> inquiry concerning this package was not appropriate for the
>mailing
>> list.
>> >> However, I have since tried re implementing the code which I sent
>and
>> my R
>> >> Studio says that netReg has successfully been unpacked, so for now
>it
>> >> appears that my problem is solved :)
>> >>
>> >> Best,
>> >>
>> >> Spencer Brackett
>> >>
>> >> On Sun, Apr 21, 2019 at 8:35 PM Bert Gunter
><[hidden email]>
>> >> wrote:
>> >>
>> >>> netReg is not "the package that generates regression models in
>R." Tons
>> >>> of packages generate regression models in R, including lm(),
>which is
>> in
>> >>> the stats package that is part of R's standard distro.
>> >>>
>> >>> So what exactly is it that you want to do that you think requires
>> netReg?
>> >>> And if netReg is required, have you tried addressing your queries
>to
>> the
>> >>> Bioconductor list, as it is one of their packages?
>> >>>
>> >>> Cheers,
>> >>> Bert
>> >>>
>> >>>
>> >>> "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 Sun, Apr 21, 2019 at 5:06 PM Spencer Brackett <
>> >>> [hidden email]> wrote:
>> >>>
>> >>>> Good evening,
>> >>>>
>> >>>> I am having problems with downloading the package used to
>generate
>> >>>> regression models on R. The following is the error message I
>> received. I
>> >>>> tried installing BiocManager instead as suggested, but this too
>did
>> not
>> >>>> work. Any ideas?
>> >>>>
>> >>>> The following is the full summary of what I’ve tried thus far...
>> >>>>
>> >>>> install.packages("ggplot2")
>> >>>> install.packages("ggplot2")
>> >>>> source("https://bioconductor.org/biocLite.R")
>> >>>> ?BiocUpgrade
>> >>>>
>source("https://bioconductor.org/biocLite.R")biocLite("BiocUpgrade")
>> >>>> source("https://bioconductor.org/biocLite.R")
>> >>>> biocLite("BiocUpgrade")
>> >>>> source("https://bioconductor.org/bioLite.R")
>> >>>> biocLite("netReg")
>> >>>> help("Deprecated")
>> >>>> 'BiocManager::install'
>> >>>> biocLite("netReg")
>> >>>> help("oldName-deprecated")
>> >>>> ‘??oldName-deprecated’
>> >>>> .Deprecated(new, package=NULL, msg,
>> >>>> old = as.character(sys.call(sys.parent()))[1L])
>> >>>>
>> >>>> Best,
>> >>>>
>> >>>> Spencer
>> >>>>
>> >>>> On Sun, Apr 14, 2019 at 7:58 PM Spencer Brackett <
>> >>>> [hidden email]> wrote:
>> >>>>
>> >>>>> My apologies... here is the full code in summary
>> >>>>>
>> >>>>> install.packages("ggplot2")
>> >>>>> install.packages("ggplot2")
>> >>>>> source("https://bioconductor.org/biocLite.R")
>> >>>>> ?BiocUpgrade
>> >>>>>
>source("https://bioconductor.org/biocLite.R")biocLite("BiocUpgrade")
>> >>>>> source("https://bioconductor.org/biocLite.R")
>> >>>>> biocLite("BiocUpgrade")
>> >>>>> source("https://bioconductor.org/bioLite.R")
>> >>>>> biocLite("netReg")
>> >>>>> help("Deprecated")
>> >>>>> 'BiocManager::install'
>> >>>>> biocLite("netReg")
>> >>>>> help("oldName-deprecated")
>> >>>>> ‘??oldName-deprecated’
>> >>>>> .Deprecated(new, package=NULL, msg,
>> >>>>> old = as.character(sys.call(sys.parent()))[1L])
>> >>>>>
>> >>>>> Best,
>> >>>>>
>> >>>>> Spencer
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>> On Sun, Apr 14, 2019 at 7:20 PM David Winsemius <
>> >>>> [hidden email]>
>> >>>>> wrote:
>> >>>>>
>> >>>>>>
>> >>>>>> On 4/14/19 3:20 PM, Spencer Brackett wrote:
>> >>>>>>> Good evening,
>> >>>>>>>
>> >>>>>>>  I am having problems with downloading the package used to
>generate
>> >>>>>>> regression models on R. The following is the error message I
>> >>>> received. I
>> >>>>>>> tried installing BiocManager instead as suggested, but this
>too did
>> >>>> not
>> >>>>>>> work. Any ideas?
>> >>>>>>>
>> >>>>>>> The downloaded binary packages are in
>> >>>>>>>
>C:\Users\Spencer\AppData\Local\Temp\Rtmp8YKVqx\downloaded_packages
>> >>>>>>> installation path not writeable, unable to update packages:
>class,
>> >>>>>> cluster,
>> >>>>>>> codetools, foreign,
>> >>>>>>>   lattice, MASS, Matrix, mgcv, nlme, rpart, survival
>> >>>>>>> Warning message:
>> >>>>>>> 'biocLite' is deprecated.
>> >>>>>>> Use 'BiocManager::install' instead.
>> >>>>>>> See help("Deprecated")
>> >>>>>>
>> >>>>>>
>> >>>>>> Since you did not include the code that provoked this message
>we can
>> >>>>>> only guess that you did in fact use `bioLite`. We also cannot
>tell
>> >>>> what
>> >>>>>> you mean by "problems with downloading the package used to
>generate
>> >>>>>> regression models on R". The typical first step is to use the
>glm or
>> >>>> lm
>> >>>>>> function for this task and those are both in the stats package
>which
>> >>>> is
>> >>>>>> installed with the base version of R and is loaded by default
>when R
>> >>>> is
>> >>>>>> started up.
>> >>>>>>
>> >>>>>> "
>> >>>>>>
>> >>>>>> Have you tried following the suggestion at the end of the
>message?
>> >>>>>>
>> >>>>>>
>> >>>>>> And do read the Posting Guide and include "commented, minimal,
>> >>>>>> self-contained, reproducible code."
>> >>>>>>
>> >>>>>>
>> >>>>>> --
>> >>>>>>
>> >>>>>> David.
>> >>>>>>
>> >>>>>>>
>> >>>>>>> Best,
>> >>>>>>>
>> >>>>>>> Spencer
>> >>>>>>>
>> >>>>>>>      [[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.
>> >>>>>>
>> >>>>>
>> >>>>
>> >>>>        [[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.
>> >>>>
>> >>>
>> >
>> >       [[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.
>>
>>
>
> [[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.