[R] Help installing netReg

Boris Steipe bor|@@@te|pe @end|ng |rom utoronto@c@
Mon Apr 22 06:04:50 CEST 2019 

"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 <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.
>

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