[R] Help installing netReg

Jeff Newmiller jdnewm|| @end|ng |rom dcn@d@v|@@c@@u@
Mon Apr 22 12:35:14 CEST 2019 

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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