Change in behavior of update.views()?

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Change in behavior of update.views()?

Michael Kubovy
I haven't seen this cryptic warning before:
> update.views('Robust')
Warning message:
In update.views("Robust") :
  The following packages are not available: covRobust, distr, FRB, MASS, mblm, multinomRob, mvoutlier, quantreg, RandVar, rgam, RobAStBase, robfilter, RobLox, RobRex, robust, RobustAFT, robustbase, ROptEst, ROptRegTS, rrcov, sandwich, wle
> library(covRobust)
>

It is puzzling because — as the second command shows — the package covRobust is installed.

Here is my
> sessionInfo()
R version 2.14.2 (2012-02-29)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] datasets  splines   utils     stats     graphics  grDevices methods   base    

other attached packages:
[1] covRobust_1.0       ade4_1.4-17         BiocInstaller_1.2.1 ctv_0.7-4           sos_1.3-1           brew_1.0-6          Hmisc_3.9-2         survival_2.36-12  
[9] MASS_7.3-17        

loaded via a namespace (and not attached):
[1] cluster_1.14.2 grid_2.14.2    lattice_0.20-0 tools_2.14.2  


______________________________________________
Professor Michael Kubovy
University of Virginia
Department of Psychology
for mail add: for FedEx or UPS add:
P.O.Box 400400 Gilmer Hall, Room 102
Charlottesville, VA 22904-4400 485 McCormick Road
USA Charlottesville, VA 22903
                room phone
Office:    B011 +1-434-982-4729
Lab:        B019 +1-434-982-4751
WWW:    http://www.people.virginia.edu/~mk9y/


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Re: Change in behavior of update.views()?

Achim Zeileis-4
On Fri, 16 Mar 2012, Michael Kubovy wrote:

> I haven't seen this cryptic warning before:
>> update.views('Robust')
> Warning message:
> In update.views("Robust") :
>  The following packages are not available: covRobust, distr, FRB, MASS,
> mblm, multinomRob, mvoutlier, quantreg, RandVar, rgam, RobAStBase,
> robfilter, RobLox, RobRex, robust, RobustAFT, robustbase, ROptEst,
> ROptRegTS, rrcov, sandwich, wle
>> library(covRobust)
>>
>
> It is puzzling because ? as the second command shows ? the package
> covRobust is installed.

Even though it is installed, update.views() tries to find out whether the
installed version is the most current version.

Essentially, it does the following:
(1) Query names of packages in the task view.
(2) Query names/versions of all available.packages() in the repository.
(3) Query names/versions of all installed.packages() on the local machine.
(4) install.packages() that are either not yet installed or not current.

The error message above occurs in step (2). The available.packages() found
with your setup include _none_ of the packages in the task view. Possibly
this is due to the repos used or the getOption("pkgType") requested.

On my machine:

R> getOption("repos")
[1] "http://CRAN.R-project.org/"
R> getOption("pkgType")
[1] "source"

And then the following works:

Step (1)

R> pkgs <- ctv:::.get_pkgs_from_ctv_or_repos("Robust")
R> pkgs
$`http://CRAN.R-project.org/`
  [1] "covRobust"   "distr"       "FRB"         "MASS"        "mblm"
  [6] "multinomRob" "mvoutlier"   "quantreg"    "RandVar"     "rgam"
[11] "RobAStBase"  "robfilter"   "RobLox"      "RobRex"      "robust"
[16] "RobustAFT"   "robustbase"  "ROptEst"     "ROptRegTS"   "rrcov"
[21] "sandwich"    "wle"

Step (2)

R> apkgs <- available.packages(contriburl = contrib.url(names(pkgs)))
R> dim(apkgs)
[1] 3661   13

And for the error message ctv looks essentially at

R> pkgs[[1]][ !(pkgs[[1]] %in% apkgs[,1]) ]
character(0)

I suspect that with your settings the apkgs object does not include all
CRAN packages yet. Setting a different repos and/or a different pkgType
should solve the problem.

hth,
Z

> Here is my
>> sessionInfo()
> R version 2.14.2 (2012-02-29)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] datasets  splines   utils     stats     graphics  grDevices methods   base
>
> other attached packages:
> [1] covRobust_1.0       ade4_1.4-17         BiocInstaller_1.2.1 ctv_0.7-4           sos_1.3-1           brew_1.0-6          Hmisc_3.9-2         survival_2.36-12
> [9] MASS_7.3-17
>
> loaded via a namespace (and not attached):
> [1] cluster_1.14.2 grid_2.14.2    lattice_0.20-0 tools_2.14.2
>
>
> ______________________________________________
> Professor Michael Kubovy
> University of Virginia
> Department of Psychology
> for mail add: for FedEx or UPS add:
> P.O.Box 400400 Gilmer Hall, Room 102
> Charlottesville, VA 22904-4400 485 McCormick Road
> USA Charlottesville, VA 22903
> room phone
> Office:    B011 +1-434-982-4729
> Lab:        B019 +1-434-982-4751
> WWW:    http://www.people.virginia.edu/~mk9y/
>
>
> [[alternative HTML version deleted]]
>
>

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