[R] Help installing the finalfit package

Bill Poling B|||@Po||ng @end|ng |rom ze||@@com
Wed Jun 13 18:38:31 CEST 2018


Ok, thank you David, I understand better now. I will start with the mice package issue and move any further questions to the forum you suggested.

Really appreciate your help.

Cheers.

WHP

From: David Winsemius [mailto:dwinsemius using comcast.net]
Sent: Wednesday, June 13, 2018 11:33 AM
To: Bill Poling <Bill.Poling using zelis.com>
Cc: r-help (r-help using r-project.org) <r-help using r-project.org>
Subject: Re: [R] Help installing the finalfit package


> On Jun 13, 2018, at 3:20 AM, Bill Poling <Bill.Poling using zelis.com<mailto:Bill.Poling using zelis.com>> wrote:
>
> Good morning David, thank you for your reply.
>
> However, I am not sure what you mean regarding the windows error?

I'm not a Windows user, but the first indication of a problem was when the installation procedure tried to replace an older version of mice with a newer version and failed. I only chimed in from my place on the sidelines of an R-Windows game because no one else had responded.

I tried finding the finalfit package on CRAN but it doesn't seem to have yet been submitted in a version that can be installed on a Mac. So I followed the advice on the blog you linked to and I can now see the package DESCRIPTION file. It has these dependencies:

Imports: Hmisc, ggplot2, grid, gridExtra, lme4, magrittr, mice, pROC,
plyr, scales, stats, stringr, survival, survminer
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown, rstan, boot


> Where or what is the windows error?

It appears you have an older version of mice but I cannot tell why it is unacceptable to this version of 'finalfit' since there is no version requirement in the deescription 'Imports:' line.

You might try to update your 'mice'-package. The current version on CRAN is 3.0.0, and attempting to make that available might illuminate the problem.


> And how would I remedy this issue please?

Fixing permissions on windows is not actually on-topic for Rhelp. Perhaps you could ask on the SuperUser forum where advice about Windows system maintenance is on-topic: https://superuser.com/<https://superuser.com/>


Best of luck.

David.
> Thanks
>
> WHP
>
> From: David Winsemius [mailto:dwinsemius using comcast.net]
> Sent: Wednesday, June 13, 2018 12:48 AM
> To: Bill Poling <Bill.Poling using zelis.com<mailto:Bill.Poling using zelis.com>>
> Cc: r-help (r-help using r-project.org<mailto:r-help using r-project.org>) <r-help using r-project.org<mailto:r-help using r-project.org>>
> Subject: Re: [R] Help installing the finalfit package
>
>
> > On Jun 12, 2018, at 5:00 AM, Bill Poling <Bill.Poling using zelis.com<mailto:Bill.Poling using zelis.com>> wrote:
> >
> > Good morning. Over the weekend I worked through this tutorial on bloggers.com<http://bloggers.com> at home where I am on 3.5.5:
> >
> > #Elegant regression results tables and plots in R: the finalfit package
> >
> > https://www.r-bloggers.com/elegant-regression-results-tables-and-plots-in-r-the-finalfit-package/<https://www.r-bloggers.com/elegant-regression-results-tables-and-plots-in-r-the-finalfit-package/>
> >
> > Here at my office I am on "R version 3.4.4 (2018-03-15)" and wish to use some of what I learned.
> >
> > The tutorial ran splendidly at home but here at office, not so much, big smile.
> >
> >> devtools::install_github("ewenharrison/finalfit")
> > Downloading GitHub repo ewenharrison/finalfit using master
> > from URL https://api.github.com/repos/ewenharrison/finalfit/zipball/master<https://api.github.com/repos/ewenharrison/finalfit/zipball/master>
> > Installing finalfit
> > Installing 1 package: mice
> > trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/mice_3.0.0.zip<https://cran.rstudio.com/bin/windows/contrib/3.4/mice_3.0.0.zip>'
> > Content type 'application/zip' length 1490726 bytes (1.4 MB)
> > downloaded 1.4 MB
> >
> > package 'mice' successfully unpacked and MD5 sums checked
> > Warning: cannot remove prior installation of package 'mice'
>
> Generally the first task is to address the first error, which in this case appears to be a windows permission issue.
>
> --
> David
>
>
> >
> > The downloaded binary packages are in
> > C:\Users\bpoling\AppData\Local\Temp\RtmpWYkyVd\downloaded_packages
> > "C:/Users/bpoling/DOCUME~1/R/R-34~1.4/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \
> > "C:/Users/bpoling/AppData/Local/Temp/RtmpWYkyVd/devtools1b0436122944/ewenharrison-finalfit-9438bc2" --library="C:/Users/bpoling/Documents/R/R-3.4.4/library" --install-tests
> >
> > ERROR: dependency 'mice' is not available for package 'finalfit'
> > * removing 'C:/Users/bpoling/Documents/R/R-3.4.4/library/finalfit'
> > In R CMD INSTALL
> > Installation failed: Command failed (1)
> >
> > I believe I had a similar problem last week and was advised to install the package library(Matrix) which was evidently necessary for sessionInfo() and for lazy load DB -- *source* package 'psycho' etc... which I now load at the beginning of every session.
> >
> > So my hunch is that maybe I need 3.5.5 for all this to work?
> >
> > Also I have this error with the mice package:
> >
> >
> >> install.packages("mice")
> >
> > trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/mice_3.0.0.zip<https://cran.rstudio.com/bin/windows/contrib/3.4/mice_3.0.0.zip>'
> >
> > Content type 'application/zip' length 1490726 bytes (1.4 MB)
> >
> > downloaded 1.4 MB
> >
> >
> >
> > package 'mice' successfully unpacked and MD5 sums checked
> >
> > Warning in install.packages :
> >
> > cannot remove prior installation of package 'mice'
> >
> >
> >
> > The downloaded binary packages are in
> >
> > C:\Users\bpoling\AppData\Local\Temp\RtmpWYkyVd\downloaded_packages
> >
> >> library(mice)
> >
> > Error in library(mice) : there is no package called 'mice'
> >
> >
> > I would appreciate any suggestion please.
> >
> > Thank you
> >
> > WHP
> >
> > Confidentiality Notice This message is sent from Zelis. ...{{dropped:15}}
> >
> > ______________________________________________
> > R-help using r-project.org<mailto:R-help using r-project.org> mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help<https://stat.ethz.ch/mailman/listinfo/r-help>
> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html<http://www.R-project.org/posting-guide.html>
> > and provide commented, minimal, self-contained, reproducible code.
>
> David Winsemius
> Alameda, CA, USA
>
> 'Any technology distinguishable from magic is insufficiently advanced.' -Gehm's Corollary to Clarke's Third Law
>
>
>
>
>
> Confidentiality Notice This message is sent from Zelis. This transmission may contain information which is privileged and confidential and is intended for the personal and confidential use of the named recipient only. Such information may be protected by applicable State and Federal laws from this disclosure or unauthorized use. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any disclosure, review, discussion, copying, or taking any action in reliance on the contents of this transmission is strictly prohibited. If you have received this transmission in error, please contact the sender immediately. Zelis, 2018.

David Winsemius
Alameda, CA, USA

'Any technology distinguishable from magic is insufficiently advanced.' -Gehm's Corollary to Clarke's Third Law




Confidentiality Notice This message is sent from Zelis. ...{{dropped:15}}




More information about the R-help mailing list