[R] Help installing netReg

[Spencer Brackett]

I updated my rStudio to the newest version. "netReg" is apparently
unavailable here but I will try to use another function to generate the
regression models I am looking for.

Thanks,

Spencer

On Mon, Apr 22, 2019 at 6:35 AM Jeff Newmiller <jdnewmil using dcn.davis.ca.us>
wrote:

> Spoken like someone who hasn't encountered the nightmare that ensues when
> some schmuck fails to limit their actions to only updating the system R
> library while following it. It is straightforward and painless to simply
> update the user library instead, and so much the better if they don't have
> Admin privileges and think they "need" to harass their sysadmins to deal
> with this for them.
>
> library(fortunes)
> fortune(337)
>
> On April 21, 2019 11:34:16 PM PDT, Caitlin Gibbons <
> bioprogrammer using gmail.com> wrote:
> >Hi Spencer.
> >
> >On a Windows machine, the message “Installation path not writeable” can
> >be solved by starting RStudio as an administrator. Right click the
> >RStudio icon and select “Run as Administrator”. This should solve that
> >problem.
> >
> >Hope this helps.
> >
> >~Caitlin
> >
> >
> >Sent from my iPhone
> >
> >> On Apr 21, 2019, at 9:22 PM, Jeff Newmiller
> ><jdnewmil using dcn.davis.ca.us> wrote:
> >>
> >> 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
> ><spbrackett20 using saintjosephhs.com> 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
> >>> <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.
> >>>>
> >>>>
> >>>
> >>>    [[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.
> >>
> >> --
> >> Sent from my phone. Please excuse my brevity.
> >>
> >> ______________________________________________
> >> 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.
>
> --
> Sent from my phone. Please excuse my brevity.
>

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