[R] [bug] spdep package?

[Henrik Bengtsson]

This is intended/expected because the spdep package *depends* on the
spData package (see https://cran.r-project.org/web/packages/spdep/),
which means that the maintainer of spdep intends also spData to be
*attached* whenever spdep is attached.    If they would have only
imported it, then spData would only be *loaded* (but not attached),
and you would not get 'spData' on your search() path and therefore not
see 'x' either.

Example:

## Loading spData
> loadNamespace("spData")
<environment: namespace:spData>

> loadedNamespaces()
[1] "compiler"  "graphics"  "utils"     "grDevices" "stats"     "datasets"
[7] "methods"   "spData"    "base"

## The search path used to find objects
> search()
[1] ".GlobalEnv"        "package:stats"     "package:graphics"
[4] "package:grDevices" "package:utils"     "package:datasets"
[7] "package:methods"   "Autoloads"         "package:base"

## So, spData::x is not found
> x
Error: object 'x' not found

## But is still there
> spData::x
 [1]   0  30  60  90 120 150 180 210 240 270 300 330 360 390 420 450


## Attaching spData, which also happens when you do library(spdat)
> library(spData)
To access larger datasets in this package, install the spDataLarge
package with: `install.packages('spDataLarge',
repos='https://nowosad.github.io/drat/', type='source'))

> loadedNamespaces()
[1] "compiler"  "graphics"  "utils"     "grDevices" "stats"     "datasets"
[7] "methods"   "spData"    "base"

## Now, spData is on the search path
> search()
 [1] ".GlobalEnv"        "package:spData"    "package:stats"
 [4] "package:graphics"  "package:grDevices" "package:utils"
 [7] "package:datasets"  "package:methods"   "Autoloads"
[10] "package:base

> x
 [1]   0  30  60  90 120 150 180 210 240 270 300 330 360 390 420 450

> find("x")
[1] "package:spData"

/Henrik
On Mon, Jul 23, 2018 at 2:01 PM Jeremie Juste <jeremiejuste using gmail.com> wrote:
>
>
> Helllo,
>
> Thanks for the info. I still think these variables should not be loaded
> when library(spdep) is called.
>
> But I'll handle it following your suggestion.
>
> Thanks,
>
> Jeremie
>
>
>
>
>
>
> > It turns out that that 'x' comes from the spData package and lives
> > inside that package (part of its namespace).
> >
> >> spData::x
> >  [1]   0  30  60  90 120 150 180 210 240 270 300 330 360 390 420 450
> >
> > This is conceptually no different from other objects in package
> > namespace, although we are more used to seeing functions and not data
> > object.  Another well-known example of this is:
> >
> >> base::pi
> > [1] 3.141593
> >
> > So, this 'x' is *not* in your global workspace and you cannot remove
> > it without unloading the package.
> >
> > /Henrik
>
>
> >>
> >>
> >> I found a dangerous issue in the library spdep. I get variables x and y
> >> that cannot be removed by rm() and I don't don't how they show up. Can
> >> anyone reproduce this?
> >>
> >> ~$ R --vanilla
> >> > rm(list=ls())
> >> > library(spdep)
> >> > x
> >> [1]   0  30  60  90 120 150 180 210 240 270 300 330 360 390 420 450
> >> > rm(list=ls())
> >> > x
> >> [1]   0  30  60  90 120 150 180 210 240 270 300 330 360 390 420 450
> >>
> >>
> >>
> >> > Sys.info()
> >>
> >> sysname        "Linux"
> >> release        "4.9.0-6-amd64"
> >> version        "#1 SMP Debian 4.9.88-1+deb9u1 (2018-05-07)"
> >> nodename       "freegnu"
> >> machine        "x86_64"
> >>
> >>
> >> > Session
> >>
> >>
> >> > sessionInfo()
> >>
> >> R version 3.4.1 (2017-06-30)
> >> Platform: x86_64-pc-linux-gnu (64-bit)
> >> Running under: Debian GNU/Linux 9 (stretch)
> >>
> >> Matrix products: default
> >> BLAS: /usr/local/lib/R/lib/libRblas.so
> >> LAPACK: /usr/local/lib/R/lib/libRlapack.so
> >>
> >> locale:
> >>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> >>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> >>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
> >>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
> >>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> >>
> >> attached base packages:
> >> [1] stats     graphics  grDevices utils     datasets  methods   base
> >>
> >> loaded via a namespace (and not attached):
> >> [1] compiler_3.4.1
> >>
> >> ______________________________________________
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> >> and provide commented, minimal, self-contained, reproducible code.