[R] Help installing the finalfit package

[David Winsemius]

> On Jun 13, 2018, at 3:20 AM, Bill Poling <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/


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>
> 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 12, 2018, at 5:00 AM, Bill Poling <Bill.Poling using zelis.com> wrote:
> > 
> > Good morning. Over the weekend I worked through this tutorial on 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/
> > 
> > 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
> > Installing finalfit
> > Installing 1 package: mice
> > trying URL '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'
> > 
> > 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
> > 
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> 
> David Winsemius
> Alameda, CA, USA
> 
> 'Any technology distinguishable from magic is insufficiently advanced.' -Gehm's Corollary to Clarke's Third Law
> 
> 
> 
> 
> 
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David Winsemius
Alameda, CA, USA

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