[R] Help installing netReg

Jeff Newmiller jdnewm|| @end|ng |rom dcn@d@v|@@c@@u@
Mon Apr 22 06:22:19 CEST 2019 

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.

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