[Rd] problem with 'install.packages'
Hi, All:
Is there a way to identify whether any users are using a
particular package in a shared network R installation?
I ask, because we have such a multiple-user installation and when
I tried to install a package using Rgui that was in use by Rterm on a
single-user installation, 'install.packages' deleted the existing
package but failed to install the new version; see below.
I'm concerned especially about the following multiple user
scenario: User A on terminalServer1 tries "install.packages('mvtnorm')"
when user B on terminalServer2 was using 'mvtnorm'; both are using the
same network installation. If the results match my experience on a
single-user installation, the existing version will be deleted but the
new version will NOT be installed. Any subsequent new attempt to access
'mvtnorm' will fail until all current users of 'mvtnorm' quit those
sessions and someone subsequently invokes
"install.packages('mvtnorm')". In fact, user B could have disconnected
from that session a month ago, and may have long forgotten the R session
that is still officially active, though perhaps consuming 0 CPU seconds
in the past month!
Thanks,
Spencer
###
##
## Rgui
##
###
R version 2.6.2 (2008-02-08)
> utils:::menuInstallPkgs()
trying URL
'http://cran.cnr.berkeley.edu/bin/windows/contrib/2.6/mvtnorm_0.8-3.zip'
Content type 'application/zip' length 214769 bytes (209 Kb)
opened URL
downloaded 209 Kb
package 'mvtnorm' successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package 'mvtnorm'
The downloaded packages are in
C:\Documents and Settings\spencerg\Local
Settings\Temp\RtmpghgskA\downloaded_packages
updating HTML package descriptions
> library(mvtnorm)
Error in library(mvtnorm) : there is no package called 'mvtnorm'
> sessionInfo()
R version 2.6.2 (2008-02-08)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
Error in x[["Version"]] : subscript out of bounds
In addition: Warning message:
In FUN(c("mvtnorm", "tools")[[2L]], ...) :
DESCRIPTION file of package 'mvtnorm' is missing or broken
>
###
##
## Concurrent Rterm session
##
###
R version 2.6.2 (2008-02-08)
> dmvnorm(1:2)
[1] 0.01306423
[1] ".GlobalEnv""package:mvtnorm" "package:stats"
[4] "package:graphics" "package:grDevices" "package:utils"
[7] "package:datasets" "package:methods" "Autoloads"
[10] "package:base"
> detach()
> dmvnorm(1:2)
Error: could not find function "dmvnorm"
> library(mvtnorm)
Error in library(mvtnorm) : there is no package called 'mvtnorm'
> sessionInfo()
R version 2.6.2 (2008-02-08)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
Error in x[["Version"]] : subscript out of bounds
In addition: Warning message:
In FUN(c("mvtnorm", "stepAICc")[[2L]], ...) :
DESCRIPTION file of package 'mvtnorm' is missing or broken
>
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Re: [Rd] problem with 'install.packages'
Spencer Graves wrote:
> Hi, All:
>
> Is there a way to identify whether any users are using a
> particular package in a shared network R installation?
>
> I ask, because we have such a multiple-user installation and when
> I tried to install a package using Rgui that was in use by Rterm on a
> single-user installation, 'install.packages' deleted the existing
> package but failed to install the new version; see below.
>
> I'm concerned especially about the following multiple user
> scenario: User A on terminalServer1 tries "install.packages('mvtnorm')"
> when user B on terminalServer2 was using 'mvtnorm'; both are using the
> same network installation. If the results match my experience on a
> single-user installation, the existing version will be deleted but the
> new version will NOT be installed. Any subsequent new attempt to access
> 'mvtnorm' will fail until all current users of 'mvtnorm' quit those
> sessions and someone subsequently invokes
Spencer,
I am using a script that asks Windows if a file is opened in a
subdirectory of the R library I am going to install or update packages
in, which basically uses the Windows shell command
net file
Then simply grep for the package name you want to install...
> "install.packages('mvtnorm')". In fact, user B could have disconnected
> from that session a month ago, and may have long forgotten the R session
> that is still officially active, though perhaps consuming 0 CPU seconds
> in the past month!
That's worse and really hard to deal with, I fear.
Best wishes,
Uwe
> Thanks,
> Spencer
> ###
> ##
> ## Rgui
> ##
> ###
> R version 2.6.2 (2008-02-08)
>
> > utils:::menuInstallPkgs()
> trying URL
> 'http://cran.cnr.berkeley.edu/bin/windows/contrib/2.6/mvtnorm_0.8-3.zip'
> Content type 'application/zip' length 214769 bytes (209 Kb)
> opened URL
> downloaded 209 Kb
>
> package 'mvtnorm' successfully unpacked and MD5 sums checked
> Warning: cannot remove prior installation of package 'mvtnorm'
>
> The downloaded packages are in
> C:\Documents and Settings\spencerg\Local
> Settings\Temp\RtmpghgskA\downloaded_packages
> updating HTML package descriptions
> > library(mvtnorm)
> Error in library(mvtnorm) : there is no package called 'mvtnorm'
>
> > sessionInfo()
> R version 2.6.2 (2008-02-08)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> loaded via a namespace (and not attached):
> Error in x[["Version"]] : subscript out of bounds
> In addition: Warning message:
> In FUN(c("mvtnorm", "tools")[[2L]], ...) :
> DESCRIPTION file of package 'mvtnorm' is missing or broken
> >
> ###
> ##
> ## Concurrent Rterm session
> ##
> ###
> R version 2.6.2 (2008-02-08)
>
>
>
> > dmvnorm(1:2)
> [1] 0.01306423
> [1] ".GlobalEnv""package:mvtnorm" "package:stats"
> [4] "package:graphics" "package:grDevices" "package:utils"
> [7] "package:datasets" "package:methods" "Autoloads"
> [10] "package:base"
> > detach()
> > dmvnorm(1:2)
> Error: could not find function "dmvnorm"
> > library(mvtnorm)
> Error in library(mvtnorm) : there is no package called 'mvtnorm'
> > sessionInfo()
> R version 2.6.2 (2008-02-08)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> loaded via a namespace (and not attached):
> Error in x[["Version"]] : subscript out of bounds
> In addition: Warning message:
> In FUN(c("mvtnorm", "stepAICc")[[2L]], ...) :
> DESCRIPTION file of package 'mvtnorm' is missing or broken
> >
>
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> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
__
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Re: [Rd] idea for GSoC: an R package for fitting Bayesian Hierarchical Models
Antonio, Fabio Di Narzo gmail.com> writes: > > I've put online a temp web page with some more info (and sources): > > http://antonio.fabio.googlepages.com/rgs%3Athergibbssampler > > Bests, > Antonio. > Have you seen Jouni Kerman's Umacs package? It sounds similar in spirit. Something I would love to see done (not that I have the time and energy to supervise someone to do it right now) would be an R (or Python/etc.: R wouldn't necessarily be the best tool) to translate lmer/nlme syntax (Wilkinson-Rogers with extensions for specifying random factors, correlation structures, etc.) into a BUGS file. It strikes me that it would be a really nice way to bridge the gap between what mixed-model code can do and what requires BUGS/MCMC. Such models could also serve as (1) a way to cross-check the results of mixed model code; (2) a way to get started in relaxing the assumptions of mixed models (e.g. allowing for non-normal random effects distributions). Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
