Re: [Rd] Searching R Packages
Dear Spencer, Nice initiative! I discover a lot of packages not by explicit search, but by running into them. I find cranberries really helpful there, especially the twitter feed (@CRANberries) and also r-bloggers, especially through Joseph Rickert's monthly roundup of new packages. And then of course there is the R journal and JSS, but those speak for themselves. So maybe a 'keeping up to date' section would be nice in the article? Best, Mark Op ma 29 jan. 2018 om 00:25 schreef Ravi Varadhan : > Hi Spencer, > Thank you for this wonderful service to the R community. > > A suggestion: it would be great to discuss how to search github and > Bioconductor repositories. > > Thanks, > Ravi > > > From: R-devel on behalf of Spencer Graves > > Sent: Saturday, January 27, 2018 11:17 AM > To: R-Devel > Subject: [Rd] Searching R Packages > > Hello, All: > > > Might you have time to review the article I recently posted to > Wikiversity on "Searching R Packages" > (https://en.wikiversity.org/wiki/Searching_R_Packages)? > > > Please edit this yourself or propose changes in the associated > "Discuss" page or in an email to this list or to me. > > > My goal in this is to invite readers to turn that article into a > proposal for improving the search capabilities in R that would > ultimately be funded by, e.g., The R Foundation. > > > What do you think? > > > Please forward this to anyone you think might be interested. > > > Thanks for your contributions to improving the lot of humanity > through better statistical software. > > >Best Wishes, >Spencer Graves, PhD >Founder >EffectiveDefense.org >7300 W. 107th St. # 506 >Overland Park, KS 66212 > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Searching R Packages
On 29 January 2018 at 11:02, Mark van der Loo wrote: | I discover a lot of packages not by explicit search, but by running into | them. I find cranberries really helpful there, especially the twitter feed | (@CRANberries) and also r-bloggers, especially through Joseph Rickert's | monthly roundup of new packages. And then of course there is the R journal | and JSS, but those speak for themselves. | | So maybe a 'keeping up to date' section would be nice in the article? Yes. But it is @CRANberriesFeed --- the handle for @cranberries was already taken by either fans of the Irish band, or the fruit ... Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] bug [methods]: double execution of `insertSource` within the same session does not work
Hello everyone,
I hope this reaches someone at all. It's my first bug report to the R-core,
and, apparently, bugzilla is locked from new reports for now.
I was using `methods::insertSource` to debug and successfully fix another
package, until it suddenly stopped working. I figured out, that it is
because I am using it on the same function multiple times within one
session. It also produces warnings even during the first call, but somehow
still works. Below I provide a reproducible example:
SETUP:
```bash
demetrio@laptop:[folder_structure]/Bugreports/methods_insertSource$ ls -a
. .. gmapsdistance_fix.R methods_insertSource.R
```
file `gmapsdistance_fix.R`
```R
gmapsdistance = function(param) {
print('I am a bug report, my params are:')
print(param)
}
```
file `methods_insertSource.R`
```R
library(gmapsdistance) # works with any package
methods::insertSource('gmapsdistance_fix.R',
package = 'gmapsdistance',
functions = 'gmapsdistance',
force = T
)
buggy = gmapsdistance('Works?')
```
TO REPRODUCE:
in that directory `R --vanilla` then
```R
> source('methods_insertSource.R')
Modified functions inserted through trace(): gmapsdistance
[1] "I am a bug report, my params are:"
[1] "Works?"
Warning message:
In methods::insertSource("gmapsdistance_fix.R", package = "gmapsdistance",
:
cannot insert these (not found in source): "gmapsdistance"
# Works, but gives the warning that it does not
# repeat:
> source('methods_insertSource.R')
Error in assign(this, thisObj, envir = envwhere) :
cannot change value of locked binding for 'gmapsdistance'
In addition: Warning message:
In methods::insertSource("gmapsdistance_fix.R", package = "gmapsdistance",
:
cannot insert these (not found in source): "gmapsdistance"
# does not work, and gets even more confusing: so is it that the object is
not find, or is it about a locked object?
```
I think it's a bug.
- BUG REPORT END
I looked into it a bit myself, in case you are interested:
```R
# lines 20-22
if (is(source, "environment"))
env <- source
else env <- evalSource(source, package, FALSE)
# We're in the second case I guess
# Browse[2]> env
# Object of class "sourceEnvironment"
# Source environment created 2017-12-01 05:19:51
# For package "gmapsdistance"
# From source file "gmapsdistancefix.R"
# later, before line 52:
x = env
Browse[2]> package
[1] "gmapsdistance"
# evaluate 52
packageSlot(env) <- package
# objects x and env are still identical
# Browse[2]> class(env)
# [1] "sourceEnvironment"
# attr(,"package")
# [1] "methods"
# Browse[2]> class(x)
# [1] "sourceEnvironment"
# attr(,"package")
# [1] "methods"
# Browse[2]> env
# Object of class "sourceEnvironment"
# Source environment created 2017-12-01 05:19:51
# For package "gmapsdistance"
# From source file "gmapsdistancefix.R"
# Browse[2]> x
# Object of class "sourceEnvironment"
# Source environment created 2017-12-01 05:19:51
# For package "gmapsdistance"
# From source file "gmapsdistancefix.R"
# so:
Browse[2]> names(env)
NULL
# which is why 53-60 do not work:
allObjects <- names(env)
if (!missing(functions)) {
notThere <- is.na(match(functions, allObjects))
if (any(notThere)) {
warning(gettextf("cannot insert these (not found in source): %s",
paste("\"", functions[notThere], "\"", sep = "",
collapse = ", ")), domain = NA)
}
}
```
Looking forward to your feedback!
Cheers,
Demetrio
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Re: [Rd] bug [methods]: double execution of `insertSource` within the same session does not work
Thanks, I will fix this.
On Mon, Jan 29, 2018 at 8:06 AM, Demetrio Rodriguez T. <
demetrio.rodrigue...@gmail.com> wrote:
> Hello everyone,
>
>
> I hope this reaches someone at all. It's my first bug report to the R-core,
> and, apparently, bugzilla is locked from new reports for now.
>
> I was using `methods::insertSource` to debug and successfully fix another
> package, until it suddenly stopped working. I figured out, that it is
> because I am using it on the same function multiple times within one
> session. It also produces warnings even during the first call, but somehow
> still works. Below I provide a reproducible example:
>
> SETUP:
> ```bash
> demetrio@laptop:[folder_structure]/Bugreports/methods_insertSource$ ls -a
> . .. gmapsdistance_fix.R methods_insertSource.R
> ```
>
> file `gmapsdistance_fix.R`
> ```R
> gmapsdistance = function(param) {
> print('I am a bug report, my params are:')
> print(param)
> }
> ```
>
>
> file `methods_insertSource.R`
> ```R
> library(gmapsdistance) # works with any package
>
> methods::insertSource('gmapsdistance_fix.R',
> package = 'gmapsdistance',
> functions = 'gmapsdistance',
> force = T
> )
> buggy = gmapsdistance('Works?')
> ```
>
>
> TO REPRODUCE:
> in that directory `R --vanilla` then
> ```R
> > source('methods_insertSource.R')
> Modified functions inserted through trace(): gmapsdistance
> [1] "I am a bug report, my params are:"
> [1] "Works?"
> Warning message:
> In methods::insertSource("gmapsdistance_fix.R", package = "gmapsdistance",
> :
> cannot insert these (not found in source): "gmapsdistance"
> # Works, but gives the warning that it does not
>
> # repeat:
> > source('methods_insertSource.R')
> Error in assign(this, thisObj, envir = envwhere) :
> cannot change value of locked binding for 'gmapsdistance'
> In addition: Warning message:
> In methods::insertSource("gmapsdistance_fix.R", package = "gmapsdistance",
> :
> cannot insert these (not found in source): "gmapsdistance"
>
> # does not work, and gets even more confusing: so is it that the object is
> not find, or is it about a locked object?
> ```
>
> I think it's a bug.
>
> - BUG REPORT END
>
>
> I looked into it a bit myself, in case you are interested:
>
> ```R
> # lines 20-22
> if (is(source, "environment"))
> env <- source
> else env <- evalSource(source, package, FALSE)
> # We're in the second case I guess
>
> # Browse[2]> env
> # Object of class "sourceEnvironment"
> # Source environment created 2017-12-01 05:19:51
> # For package "gmapsdistance"
> # From source file "gmapsdistancefix.R"
>
>
> # later, before line 52:
> x = env
> Browse[2]> package
> [1] "gmapsdistance"
>
> # evaluate 52
> packageSlot(env) <- package
>
> # objects x and env are still identical
> # Browse[2]> class(env)
> # [1] "sourceEnvironment"
> # attr(,"package")
> # [1] "methods"
> # Browse[2]> class(x)
> # [1] "sourceEnvironment"
> # attr(,"package")
> # [1] "methods"
>
> # Browse[2]> env
> # Object of class "sourceEnvironment"
> # Source environment created 2017-12-01 05:19:51
> # For package "gmapsdistance"
> # From source file "gmapsdistancefix.R"
> # Browse[2]> x
> # Object of class "sourceEnvironment"
> # Source environment created 2017-12-01 05:19:51
> # For package "gmapsdistance"
> # From source file "gmapsdistancefix.R"
>
> # so:
> Browse[2]> names(env)
> NULL
>
> # which is why 53-60 do not work:
> allObjects <- names(env)
> if (!missing(functions)) {
> notThere <- is.na(match(functions, allObjects))
> if (any(notThere)) {
> warning(gettextf("cannot insert these (not found in source): %s",
> paste("\"", functions[notThere], "\"", sep = "",
> collapse = ", ")), domain = NA)
> }
> }
> ```
>
> Looking forward to your feedback!
>
> Cheers,
> Demetrio
>
> [[alternative HTML version deleted]]
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
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[Rd] help(pac=xxx) get data from CRAN?
Hello, All: A feature request: What about modifying the code for "help(pac=xxx)" so it looks for "xxx" on CRAN as well as locally: If it finds it locally, it uses that version but with an annotation reporting what it found on CRAN: * If it doesn't find CRAN, it doesn't report anything on this. * If it finds CRAN, and the version numbers match, it reports that. * If it finds CRAN, and the local version is behind CRAN, it says, "newer version on CRAN". * If it finds CRAN, and the local version is ahead of CRAN, it says something like, "Local newer than CRAN." This occurred to me, because someone suggested I update the "sos" package to use CRAN to get package information for packages not already installed. It's a great idea, but I'm not ready to do that just yet. Best Wishes, Spencer Graves __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] as.list method for by Objects
Good day, I'd like to suggest the addition of an as.list method for a by object that actually returns a list of class "list". This would make it safer to do type-checking, because is.list also returns TRUE for a data.frame variable and using class(result) == "list" is an alternative that only returns TRUE for lists. It's also confusing initially that > class(x) [1] "by" > is.list(x) [1] TRUE since there's no explicit class definition for "by" and no mention if it has any superclasses. -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
