[R] 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 <boris.steipe using utoronto.ca>
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 <
> spbrackett20 using saintjosephhs.com> 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 <
> > spbrackett20 using saintjosephhs.com> 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 <bgunter.4567 using gmail.com>
> >> 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 <
> >>> spbrackett20 using saintjosephhs.com> 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 <
> >>>> spbrackett20 using saintjosephhs.com> 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 <
> >>>> dwinsemius using comcast.net>
> >>>>> 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]]
> >>>>>>>
> >>>>>>> ______________________________________________
> >>>>>>> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> >>>>>>> https://stat.ethz.ch/mailman/listinfo/r-help
> >>>>>>> PLEASE do read the posting guide
> >>>>>> http://www.R-project.org/posting-guide.html
> >>>>>>> and provide commented, minimal, self-contained, reproducible code.
> >>>>>>
> >>>>>
> >>>>
> >>>>        [[alternative HTML version deleted]]
> >>>>
> >>>> ______________________________________________
> >>>> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> >>>> https://stat.ethz.ch/mailman/listinfo/r-help
> >>>> PLEASE do read the posting guide
> >>>> http://www.R-project.org/posting-guide.html
> >>>> and provide commented, minimal, self-contained, reproducible code.
> >>>>
> >>>
> >
> >       [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
>

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