Re: [R] Help installing the finalfit package
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:dwinsem...@comcast.net]
Sent: Wednesday, June 13, 2018 11:33 AM
To: Bill Poling
Cc: r-help (r-help@r-project.org)
Subject: Re: [R] Help installing the finalfit package
> On Jun 13, 2018, at 3:20 AM, Bill Poling
> mailto:bill.pol...@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:dwinsem...@comcast.net]
> Sent: Wednesday, June 13, 2018 12:48 AM
> To: Bill Poling mailto:bill.pol...@zelis.com>>
> Cc: r-help (r-help@r-project.org<mailto:r-help@r-project.org>)
> mailto:r-help@r-project.org>>
> Subject: Re: [R] Help installing the finalfit package
>
>
> > On Jun 12, 2018, at 5:00 AM, Bill Poling
> > mailto:bill.pol...@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@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&
Re: [R] Help installing the finalfit package
> On Jun 13, 2018, at 3:20 AM, Bill Poling 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:dwinsem...@comcast.net]
> Sent: Wednesday, June 13, 2018 12:48 AM
> To: Bill Poling
> Cc: r-help (r-help@r-project.org)
> Subject: Re: [R] Help installing the finalfit package
>
>
> > On Jun 12, 2018, at 5:00 AM, Bill Poling 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@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
> >
> >
> >
Re: [R] Help installing the finalfit package
Good morning David, thank you for your reply.
However, I am not sure what you mean regarding the windows error? Where or what
is the windows error? And how would I remedy this issue please?
Thanks
WHP
From: David Winsemius [mailto:dwinsem...@comcast.net]
Sent: Wednesday, June 13, 2018 12:48 AM
To: Bill Poling
Cc: r-help (r-help@r-project.org)
Subject: Re: [R] Help installing the finalfit package
> On Jun 12, 2018, at 5:00 AM, Bill Poling
> mailto:bill.pol...@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@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@r-project.org<mailto:R-help@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. ...{{dropped:15}}
__
R-help@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.
Re: [R] Help installing the finalfit package
> On Jun 12, 2018, at 5:00 AM, Bill Poling 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@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
>
> Confidentiality Notice This message is sent from Zelis. ...{{dropped:15}}
>
> __
> R-help@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.
David Winsemius
Alameda, CA, USA
'Any technology distinguishable from magic is insufficiently advanced.'
-Gehm's Corollary to Clarke's Third Law
__
R-help@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.
[R] Help installing the finalfit package
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@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'
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
Confidentiality Notice This message is sent from Zelis. ...{{dropped:15}}
__
R-help@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.
