On Jan 24, 2023, at 5:00 AM, r-help-requ...@r-project.org wrote:
Send R-help mailing list submissions to r-help@ r-project. org To subscribe or
unsubscribe via the World Wide Web, visit https: //urldefense. proofpoint.
com/v2/url?u=https-3A__stat. ethz.
ch_mailman_listinfo_r-2Dhelp&d=DwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=ug-gw1ia3rShGleyKIdg4GIXRt6aKD3u1CM4odHlsvE&m=FCARkfGgHXcSaTZN1f38_6XCbtZ-Lopl641M4MpApMJf7EuJ7y2Y4873aWz38wiY&s=WyAtmOvZqkJ83zE98hkQxz9o1I6k6gYj7KJzInNKmcQ&e=
ZjQcmQRYFpfptBannerStart
This Message Is From an External Sender
This message came from outside your organization.
ZjQcmQRYFpfptBannerEnd
Send R-help mailing list submissions to
r-help@r-project.org
To subscribe or unsubscribe via the World Wide Web, visit
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dhelp&d=DwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=ug-gw1ia3rShGleyKIdg4GIXRt6aKD3u1CM4odHlsvE&m=FCARkfGgHXcSaTZN1f38_6XCbtZ-Lopl641M4MpApMJf7EuJ7y2Y4873aWz38wiY&s=WyAtmOvZqkJ83zE98hkQxz9o1I6k6gYj7KJzInNKmcQ&e=
or, via email, send a message with subject or body 'help' to
r-help-requ...@r-project.org
You can reach the person managing the list at
r-help-ow...@r-project.org
When replying, please edit your Subject line so it is more specific
than "Re: Contents of R-help digest..."
Today's Topics:
1. Re: Info files in Windows and Mac distributions (Duncan Murdoch)
2. Re: [EXTERNAL] Re: function doesn't exists but still
runs..... (akshay kulkarni) (Jorgen Harmse)
3. Re: [EXTERNAL] Re: function doesn't exists but still
runs..... (akshay kulkarni) (akshay kulkarni)
4. package FactoMineR (varin sacha)
5. Re: package FactoMineR (Rui Barradas)
6. Re: Flickering when scrolling in R graphics windows
(Martin Maechler)
7. Re: package FactoMineR (PIKAL Petr)
----------------------------------------------------------------------
Message: 1
Date: Sun, 22 Jan 2023 12:38:13 -0500
From: Duncan Murdoch <murdoch.dun...@gmail.com>
To: Naresh Gurbuxani <naresh_gurbux...@hotmail.com>, R Help
<r-help@r-project.org>
Subject: Re: [R] Info files in Windows and Mac distributions
Message-ID: <6a1cb904-fd30-7686-9f7f-3d28e9b63...@gmail.com>
Content-Type: text/plain; charset="utf-8"; Format="flowed"
On 22/01/2023 12:09 p.m., Naresh Gurbuxani wrote:
> Recently I installed Linux on my desktop. I discovered that R for Linux
> ships with info files of manuals. R for Windows and Mac only ship with html
> and pdf files of manuals.
>
> Why not include info files in R distributions for Windows and Mac? These are
> very convenient with emacs. Using pandoc , I tried converting from html to
> info. The results were nowhere near as good as the originals.
I think the answer to the question is just that there isn't much demand
for them: emacs is mainly used by Linux users these days.
But the source to the manuals is available, so presumably you could
produce these pretty easily yourself. The R-devel versions are here:
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_r-2Ddevel_r-2Dsvn_tree_master_doc_manual&d=DwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=ug-gw1ia3rShGleyKIdg4GIXRt6aKD3u1CM4odHlsvE&m=FCARkfGgHXcSaTZN1f38_6XCbtZ-Lopl641M4MpApMJf7EuJ7y2Y4873aWz38wiY&s=XnWhnshtwyINVkabbrzkIYLCxHOxWnBrO3Jemc-Mqcw&e=
I don't know whether the .texi files are sufficient for emacs or whether
you need to process them first; I'm not an emacs user.
Duncan Murdoch
------------------------------
Message: 2
Date: Mon, 23 Jan 2023 16:01:15 +0000
From: Jorgen Harmse <jhar...@roku.com>
To: "r-help@r-project.org" <r-help@r-project.org>, akshay kulkarni
<akshay...@hotmail.com>
Subject: Re: [R] [EXTERNAL] Re: function doesn't exists but still
runs..... (akshay kulkarni)
Message-ID:
<mw4pr01mb6465aab90079281b2151d808dc...@mw4pr01mb6465.prod.exchangelabs.com>
Content-Type: text/plain; charset="utf-8"
Hi Akshay,
I usually use debug (a function provided by R). When you are stepping through a
function your environment is the one in which function code is being executed,
so you can easily see everything that is visible to the function. If you single
step into a function that the first function calls then you also see everything
that is available to that function. Moreover, you don't see anything that is
not visible to the function you are debugging, so you can really determine what
any piece of code would do if called inside the function.
Note 1: Code in R is always executed in an environment. I show in the example
below that in the empty environment (the ultimate ancestor of all other
environments) R can't even add. Usually the current environment (e.g.
.GlobalEnv at the command line or a fresh environment created by a function
call) has the right contents and the right parent to do what you expect, but in
some special cases you need to understand how environments work. Even evalq &
with are functions (unavailable for example in the empty environment), and the
environment argument has to be evaluated in the current environment before the
main expression can be evaluated in the environment that you want.
> E[1]
[[1]]
<environment: R_EmptyEnv>
> evalq(2+2, E[[1L]])
Error in 2 + 2 : could not find function "+"
> evalq(2L+2L, E[[1L]])
Error in 2L + 2L : could not find function "+"
Note 2: Besides automatically showing what a function sees, using debug
(instead of hand-executing lines of code from the function) gives you the
correct call stack. Suppose that you run some code at the debug command line to
make a sub-sub-…-function do what you want, and you create in that environment
what you hope is the correct return value. You can then use parent.frame() to
put that value into the environment of the caller and run the caller's
remaining code in the correct environment to see what happens. If there are no
other problems then you can work your way up to top level and confirm that your
patch has the right effect before you even modify the actual code of the
offending function. (Saving all environments in .GlobalEnv forces R to keep
them even if you quit the debugger. Combining eval & parse is sometimes more
convenient than using evalq.)
Regards,
Jorgen.
------------------------------
Message: 2
Date: Sun, 22 Jan 2023 14:25:59 +0000
From: akshay kulkarni <akshay...@hotmail.com>
To: Jorgen Harmse <jhar...@roku.com>, "r-help@r-project.org"
<r-help@r-project.org>, "williamwdun...@gmail.com"
<williamwdun...@gmail.com>
Subject: Re: [R] [EXTERNAL] Re: function doesn't exists but still
runs..... (akshay kulkarni)
Message-ID:
<pu4p216mb1568bde0e4929806e096cc11c8...@pu4p216mb1568.korp216.prod.outlook.com>
Content-Type: text/plain; charset="utf-8"
Dear Jorgen,
regrets to reply this late....
I got into this issue because it threw an error, and it took more than 4 days
to fix this. I learnt a lot, and one things I learnt is to debug the
function, even when that is a public package function....instead of googling
the error message...Any ideas on how to do this more efficiently?
THanking you,
Yours sincerely,
AKSHAY M KULKARNI
________________________________
From: Jorgen Harmse <jhar...@roku.com>
Sent: Friday, January 20, 2023 11:35 PM
To: akshay kulkarni <akshay...@hotmail.com>; r-help@r-project.org
<r-help@r-project.org>; williamwdun...@gmail.com <williamwdun...@gmail.com>
Subject: Re: [EXTERNAL] Re: function doesn't exists but still runs..... (akshay
kulkarni)
Hi Akshay,
Lexical scoping and environments are closely tied. (I think Bill even cited the
documentation.) I guess it's arcane in the sense that scoping usually does what
you expect, but the way that works is related to what we discussed.
What led you to discover the issue? Were you debugging the public package
function because it didn't do what you expected, or were you just curious how
it worked?
Regards,
Jorgen.
From: akshay kulkarni <akshay...@hotmail.com>
Date: Friday, January 20, 2023 at 11:19
To: Jorgen Harmse <jhar...@roku.com>, r-help@r-project.org
<r-help@r-project.org>, williamwdun...@gmail.com <williamwdun...@gmail.com>
Subject: [EXTERNAL] Re: function doesn't exists but still runs..... (akshay
kulkarni)
Dear Jorgen,
thanks for the reply.....so according to you one can
pegion hole the problem as concerning R's lexical scoping rules,am I right? Or
some arcane concept regarding environments....?
THanking you,
Yours sincerely,
AKSHAY M KULKARNI
________________________________
From: Jorgen Harmse <jhar...@roku.com>
Sent: Friday, January 20, 2023 9:34 PM
To: r-help@r-project.org <r-help@r-project.org>; akshay...@hotmail.com
<akshay...@hotmail.com>; williamwdun...@gmail.com <williamwdun...@gmail.com>
Subject: Re: function doesn't exists but still runs..... (akshay kulkarni)
It may help to expand a bit on Bill Dunlap's answer. I think that library does
something like this:
Create a new environment for all the package objects. This environment will not
be directly visible from .GlobalEnv, and ancestor environments may not be
directly visible either. It may contain functions & other objects that are not
exported, and it may use objects in ancestor environments that .GlobalEnv
doesn't see directly. On the other hand, functions in the package will still
see external functions in the way the package author intended instead of seeing
functions with the same name that are visible to .GlobalEnv.
Run the source code in the private environment (using source(local=private
environment, ....)?). Most package source code just defines functions, but the
source code could build other objects that the package needs for some reason,
or it could use delayedAssign to build the objects lazily. By default, the
environment of any function defined by the source code is the private
environment, so the function has access to private objects and to anything in
ancestor environments.
Create a second new environment whose parent is parent.env(.GlobalEnv). For
every export, assign the corresponding object from the private environment into
the corresponding name in the public environment. Note that the environment of
any function is still the private environment in which it was created. (I think
that a function is mostly determined by its environment, its formals, and its
body. A function call creates a new environment whose parent is the environment
of the function. Thus whoever wrote the function can control the search for
anything that isn�t passed in or created by the function itself.)
Reset parent.env(.GlobalEnv) to be the public environment. This makes all the
exported objects (usually functions) available at the command line and allows
the user to see everything that was available before (usually by name only, but
by scope-resolved name if necessary). As noted by Bill Dunlap and in more
detail above, package functions can use functions & other objects that are not
directly visible to the user. As he also showed, you can (usually) pierce the
privacy as long at least one function is exported.
environment(package_function) is the private environment, so you can use it to
see all the private objects and everything in the ancestor environments. You
can repeat the trick to see private environments of packages you didn't
directly pull in. I think you can even unlock bindings and do ghastly things to
the package's private environment.
Regards,
Jorgen Harmse.
------------------------------
Message: 17
Date: Thu, 19 Jan 2023 16:02:31 -0800
From: Bill Dunlap <williamwdun...@gmail.com>
To: akshay kulkarni <akshay...@hotmail.com>
Cc: R help Mailing list <r-help@r-project.org>
Subject: Re: [R] function doesn't exists but still runs.....
Message-ID:
<CAHqSRuTCBqh84FHg7=xmd9qhxuian3y4zbjbkar3drwhggu...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Look into R's scoping rules. E.g.,
https://urldefense.proofpoint.com/v2/url?u=https-3A__bookdown.org_rdpeng_rprogdatascience_scoping-2Drules-2Dof-2Dr.html&d=DwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=ug-gw1ia3rShGleyKIdg4GIXRt6aKD3u1CM4odHlsvE&m=FCARkfGgHXcSaTZN1f38_6XCbtZ-Lopl641M4MpApMJf7EuJ7y2Y4873aWz38wiY&s=Mb3F4Yi_5e0mAkovoM8_Dai8vSPPDK3hbOWblRvh4Yo&e=.
* When a function looks up a name, it looks it up in the environment in
which the function was defined.
* Functions in a package are generally defined in the package's environment
(although sometimes they are in a descendent of the parent's environment).
* When one searches an environment for a name, if it is not found in the
environment the search continues in the parent environment of that
environment, recursively until the parent environment is the empty
environment.
> with(environment(wdman::selenium), java_check)
function ()
{
javapath <- Sys.which("java")
if (identical(unname(javapath), "")) {
stop("PATH to JAVA not found. Please check JAVA is installed.")
}
javapath
}
<bytecode: 0x000001fd0ab826a8>
<environment: namespace:wdman>
-Bill
On Thu, Jan 19, 2023 at 2:28 PM akshay kulkarni <akshay...@hotmail.com>
wrote:
> dear members,
> I am using the RSelenium package which uses
> the function selenium() from the wdman package. The selenium function
> contains the function java_check at line 12. If I try to run it, it throws
> an error:
>
> > javapath <- java_check()
> Error in java_check() : could not find function "java_check"
>
> Also:
>
> > exists("java_check")
> [1] FALSE
>
> But when I run selenium(), it works fine....
>
> How do you explain this conundrum? You can refer to this link:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ropensci_wdman_issues_15&d=DwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=ug-gw1ia3rShGleyKIdg4GIXRt6aKD3u1CM4odHlsvE&m=FCARkfGgHXcSaTZN1f38_6XCbtZ-Lopl641M4MpApMJf7EuJ7y2Y4873aWz38wiY&s=XolZgwav8rnGPXeiF55H6PWDBFufTzdVohRiF_1uj7g&e=
>
> Specifically what concept of R explains this weird behaviour?
>
> Thanking you,
> Yours sincerely,
> AKSHAY M KULKARNI
>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dhelp&d=DwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=ug-gw1ia3rShGleyKIdg4GIXRt6aKD3u1CM4odHlsvE&m=FCARkfGgHXcSaTZN1f38_6XCbtZ-Lopl641M4MpApMJf7EuJ7y2Y4873aWz38wiY&s=WyAtmOvZqkJ83zE98hkQxz9o1I6k6gYj7KJzInNKmcQ&e=
> PLEASE do read the posting guide
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.R-2Dproject.org_posting-2Dguide.html&d=DwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=ug-gw1ia3rShGleyKIdg4GIXRt6aKD3u1CM4odHlsvE&m=FCARkfGgHXcSaTZN1f38_6XCbtZ-Lopl641M4MpApMJf7EuJ7y2Y4873aWz38wiY&s=LvYxgn0N8iyJd6E3RK9ecZ0STO1_BIgO6gtE_zSJv-g&e=
> and provide commented, minimal, self-contained, reproducible code.
>
[[alternative HTML version deleted]]
------------------------------
Subject: Digest Footer
_______________________________________________
R-help@r-project.org mailing list
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dhelp&d=DwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=ug-gw1ia3rShGleyKIdg4GIXRt6aKD3u1CM4odHlsvE&m=FCARkfGgHXcSaTZN1f38_6XCbtZ-Lopl641M4MpApMJf7EuJ7y2Y4873aWz38wiY&s=WyAtmOvZqkJ83zE98hkQxz9o1I6k6gYj7KJzInNKmcQ&e=
PLEASE do read the posting guide
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.R-2Dproject.org_posting-2Dguide.html&d=DwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=ug-gw1ia3rShGleyKIdg4GIXRt6aKD3u1CM4odHlsvE&m=FCARkfGgHXcSaTZN1f38_6XCbtZ-Lopl641M4MpApMJf7EuJ7y2Y4873aWz38wiY&s=LvYxgn0N8iyJd6E3RK9ecZ0STO1_BIgO6gtE_zSJv-g&e=
and provide commented, minimal, self-contained, reproducible code.
------------------------------
End of R-help Digest, Vol 239, Issue 20
***************************************
[[alternative HTML version deleted]]
[[alternative HTML version deleted]]
------------------------------
Message: 3
Date: Mon, 23 Jan 2023 17:54:47 +0000
From: akshay kulkarni <akshay...@hotmail.com>
To: Jorgen Harmse <jhar...@roku.com>, "r-help@r-project.org"
<r-help@r-project.org>
Subject: Re: [R] [EXTERNAL] Re: function doesn't exists but still
runs..... (akshay kulkarni)
Message-ID:
<pu4p216mb15683a4fa52903d059493eb3c8...@pu4p216mb1568.korp216.prod.outlook.com>
Content-Type: text/plain; charset="utf-8"
Dear Jorgen,
thanks a lot....
Thanking you,
Yours sincerely
Akshay M Kulkarni
________________________________
From: Jorgen Harmse <jhar...@roku.com>
Sent: Monday, January 23, 2023 9:31 PM
To: r-help@r-project.org <r-help@r-project.org>; akshay kulkarni
<akshay...@hotmail.com>
Subject: Re: [R] [EXTERNAL] Re: function doesn't exists but still runs.....
(akshay kulkarni)
Hi Akshay,
I usually use debug (a function provided by R). When you are stepping through a
function your environment is the one in which function code is being executed,
so you can easily see everything that is visible to the function. If you single
step into a function that the first function calls then you also see everything
that is available to that function. Moreover, you don't see anything that is
not visible to the function you are debugging, so you can really determine what
any piece of code would do if called inside the function.
Note 1: Code in R is always executed in an environment. I show in the example
below that in the empty environment (the ultimate ancestor of all other
environments) R can't even add. Usually the current environment (e.g.
.GlobalEnv at the command line or a fresh environment created by a function
call) has the right contents and the right parent to do what you expect, but in
some special cases you need to understand how environments work. Even evalq &
with are functions (unavailable for example in the empty environment), and the
environment argument has to be evaluated in the current environment before the
main expression can be evaluated in the environment that you want.
> E[1]
[[1]]
<environment: R_EmptyEnv>
> evalq(2+2, E[[1L]])
Error in 2 + 2 : could not find function "+"
> evalq(2L+2L, E[[1L]])
Error in 2L + 2L : could not find function "+"
Note 2: Besides automatically showing what a function sees, using debug
(instead of hand-executing lines of code from the function) gives you the
correct call stack. Suppose that you run some code at the debug command line to
make a sub-sub-…-function do what you want, and you create in that environment
what you hope is the correct return value. You can then use parent.frame() to
put that value into the environment of the caller and run the caller's
remaining code in the correct environment to see what happens. If there are no
other problems then you can work your way up to top level and confirm that your
patch has the right effect before you even modify the actual code of the
offending function. (Saving all environments in .GlobalEnv forces R to keep
them even if you quit the debugger. Combining eval & parse is sometimes more
convenient than using evalq.)
Regards,
Jorgen.
------------------------------
Message: 2
Date: Sun, 22 Jan 2023 14:25:59 +0000
From: akshay kulkarni <akshay...@hotmail.com>
To: Jorgen Harmse <jhar...@roku.com>, "r-help@r-project.org"
<r-help@r-project.org>, "williamwdun...@gmail.com"
<williamwdun...@gmail.com>
Subject: Re: [R] [EXTERNAL] Re: function doesn't exists but still
runs..... (akshay kulkarni)
Message-ID:
<pu4p216mb1568bde0e4929806e096cc11c8...@pu4p216mb1568.korp216.prod.outlook.com>
Content-Type: text/plain; charset="utf-8"
Dear Jorgen,
regrets to reply this late....
I got into this issue because it threw an error, and it took more than 4 days
to fix this. I learnt a lot, and one things I learnt is to debug the
function, even when that is a public package function....instead of googling
the error message...Any ideas on how to do this more efficiently?
THanking you,
Yours sincerely,
AKSHAY M KULKARNI
________________________________
From: Jorgen Harmse <jhar...@roku.com>
Sent: Friday, January 20, 2023 11:35 PM
To: akshay kulkarni <akshay...@hotmail.com>; r-help@r-project.org
<r-help@r-project.org>; williamwdun...@gmail.com <williamwdun...@gmail.com>
Subject: Re: [EXTERNAL] Re: function doesn't exists but still runs..... (akshay
kulkarni)
Hi Akshay,
Lexical scoping and environments are closely tied. (I think Bill even cited the
documentation.) I guess it's arcane in the sense that scoping usually does what
you expect, but the way that works is related to what we discussed.
What led you to discover the issue? Were you debugging the public package
function because it didn't do what you expected, or were you just curious how
it worked?
Regards,
Jorgen.
From: akshay kulkarni <akshay...@hotmail.com>
Date: Friday, January 20, 2023 at 11:19
To: Jorgen Harmse <jhar...@roku.com>, r-help@r-project.org
<r-help@r-project.org>, williamwdun...@gmail.com <williamwdun...@gmail.com>
Subject: [EXTERNAL] Re: function doesn't exists but still runs..... (akshay
kulkarni)
Dear Jorgen,
thanks for the reply.....so according to you one can
pegion hole the problem as concerning R's lexical scoping rules,am I right? Or
some arcane concept regarding environments....?
THanking you,
Yours sincerely,
AKSHAY M KULKARNI
________________________________
From: Jorgen Harmse <jhar...@roku.com>
Sent: Friday, January 20, 2023 9:34 PM
To: r-help@r-project.org <r-help@r-project.org>; akshay...@hotmail.com
<akshay...@hotmail.com>; williamwdun...@gmail.com <williamwdun...@gmail.com>
Subject: Re: function doesn't exists but still runs..... (akshay kulkarni)
It may help to expand a bit on Bill Dunlap's answer. I think that library does
something like this:
Create a new environment for all the package objects. This environment will not
be directly visible from .GlobalEnv, and ancestor environments may not be
directly visible either. It may contain functions & other objects that are not
exported, and it may use objects in ancestor environments that .GlobalEnv
doesn't see directly. On the other hand, functions in the package will still
see external functions in the way the package author intended instead of seeing
functions with the same name that are visible to .GlobalEnv.
Run the source code in the private environment (using source(local=private
environment, ....)?). Most package source code just defines functions, but the
source code could build other objects that the package needs for some reason,
or it could use delayedAssign to build the objects lazily. By default, the
environment of any function defined by the source code is the private
environment, so the function has access to private objects and to anything in
ancestor environments.
Create a second new environment whose parent is parent.env(.GlobalEnv). For
every export, assign the corresponding object from the private environment into
the corresponding name in the public environment. Note that the environment of
any function is still the private environment in which it was created. (I think
that a function is mostly determined by its environment, its formals, and its
body. A function call creates a new environment whose parent is the environment
of the function. Thus whoever wrote the function can control the search for
anything that isn�t passed in or created by the function itself.)
Reset parent.env(.GlobalEnv) to be the public environment. This makes all the
exported objects (usually functions) available at the command line and allows
the user to see everything that was available before (usually by name only, but
by scope-resolved name if necessary). As noted by Bill Dunlap and in more
detail above, package functions can use functions & other objects that are not
directly visible to the user. As he also showed, you can (usually) pierce the
privacy as long at least one function is exported.
environment(package_function) is the private environment, so you can use it to
see all the private objects and everything in the ancestor environments. You
can repeat the trick to see private environments of packages you didn't
directly pull in. I think you can even unlock bindings and do ghastly things to
the package's private environment.
Regards,
Jorgen Harmse.
------------------------------
Message: 17
Date: Thu, 19 Jan 2023 16:02:31 -0800
From: Bill Dunlap <williamwdun...@gmail.com>
To: akshay kulkarni <akshay...@hotmail.com>
Cc: R help Mailing list <r-help@r-project.org>
Subject: Re: [R] function doesn't exists but still runs.....
Message-ID:
<CAHqSRuTCBqh84FHg7=xmd9qhxuian3y4zbjbkar3drwhggu...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Look into R's scoping rules. E.g.,
https://urldefense.proofpoint.com/v2/url?u=https-3A__bookdown.org_rdpeng_rprogdatascience_scoping-2Drules-2Dof-2Dr.html&d=DwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=ug-gw1ia3rShGleyKIdg4GIXRt6aKD3u1CM4odHlsvE&m=FCARkfGgHXcSaTZN1f38_6XCbtZ-Lopl641M4MpApMJf7EuJ7y2Y4873aWz38wiY&s=Mb3F4Yi_5e0mAkovoM8_Dai8vSPPDK3hbOWblRvh4Yo&e=.
* When a function looks up a name, it looks it up in the environment in
which the function was defined.
* Functions in a package are generally defined in the package's environment
(although sometimes they are in a descendent of the parent's environment).
* When one searches an environment for a name, if it is not found in the
environment the search continues in the parent environment of that
environment, recursively until the parent environment is the empty
environment.
> with(environment(wdman::selenium), java_check)
function ()
{
javapath <- Sys.which("java")
if (identical(unname(javapath), "")) {
stop("PATH to JAVA not found. Please check JAVA is installed.")
}
javapath
}
<bytecode: 0x000001fd0ab826a8>
<environment: namespace:wdman>
-Bill
On Thu, Jan 19, 2023 at 2:28 PM akshay kulkarni <akshay...@hotmail.com>
wrote:
> dear members,
> I am using the RSelenium package which uses
> the function selenium() from the wdman package. The selenium function
> contains the function java_check at line 12. If I try to run it, it throws
> an error:
>
> > javapath <- java_check()
> Error in java_check() : could not find function "java_check"
>
> Also:
>
> > exists("java_check")
> [1] FALSE
>
> But when I run selenium(), it works fine....
>
> How do you explain this conundrum? You can refer to this link:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ropensci_wdman_issues_15&d=DwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=ug-gw1ia3rShGleyKIdg4GIXRt6aKD3u1CM4odHlsvE&m=FCARkfGgHXcSaTZN1f38_6XCbtZ-Lopl641M4MpApMJf7EuJ7y2Y4873aWz38wiY&s=XolZgwav8rnGPXeiF55H6PWDBFufTzdVohRiF_1uj7g&e=
>
> Specifically what concept of R explains this weird behaviour?
>
> Thanking you,
> Yours sincerely,
> AKSHAY M KULKARNI
>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dhelp&d=DwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=ug-gw1ia3rShGleyKIdg4GIXRt6aKD3u1CM4odHlsvE&m=FCARkfGgHXcSaTZN1f38_6XCbtZ-Lopl641M4MpApMJf7EuJ7y2Y4873aWz38wiY&s=WyAtmOvZqkJ83zE98hkQxz9o1I6k6gYj7KJzInNKmcQ&e=
> PLEASE do read the posting guide
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.R-2Dproject.org_posting-2Dguide.html&d=DwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=ug-gw1ia3rShGleyKIdg4GIXRt6aKD3u1CM4odHlsvE&m=FCARkfGgHXcSaTZN1f38_6XCbtZ-Lopl641M4MpApMJf7EuJ7y2Y4873aWz38wiY&s=LvYxgn0N8iyJd6E3RK9ecZ0STO1_BIgO6gtE_zSJv-g&e=
> and provide commented, minimal, self-contained, reproducible code.
>
[[alternative HTML version deleted]]
------------------------------
Subject: Digest Footer
_______________________________________________
R-help@r-project.org mailing list
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dhelp&d=DwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=ug-gw1ia3rShGleyKIdg4GIXRt6aKD3u1CM4odHlsvE&m=FCARkfGgHXcSaTZN1f38_6XCbtZ-Lopl641M4MpApMJf7EuJ7y2Y4873aWz38wiY&s=WyAtmOvZqkJ83zE98hkQxz9o1I6k6gYj7KJzInNKmcQ&e=
PLEASE do read the posting guide
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.R-2Dproject.org_posting-2Dguide.html&d=DwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=ug-gw1ia3rShGleyKIdg4GIXRt6aKD3u1CM4odHlsvE&m=FCARkfGgHXcSaTZN1f38_6XCbtZ-Lopl641M4MpApMJf7EuJ7y2Y4873aWz38wiY&s=LvYxgn0N8iyJd6E3RK9ecZ0STO1_BIgO6gtE_zSJv-g&e=
and provide commented, minimal, self-contained, reproducible code.
------------------------------
End of R-help Digest, Vol 239, Issue 20
***************************************
[[alternative HTML version deleted]]
[[alternative HTML version deleted]]
------------------------------
Message: 4
Date: Mon, 23 Jan 2023 18:38:23 +0000 (UTC)
From: varin sacha <varinsa...@yahoo.fr>
To: "r-help@r-project.org" <r-help@r-project.org>
Subject: [R] package FactoMineR
Message-ID: <830985149.1604446.1674499103...@mail.yahoo.com>
Content-Type: text/plain; charset="utf-8"
Dear R-experts,
Here below the R code working (page 8
https://urldefense.proofpoint.com/v2/url?u=http-3A__www2.uaem.mx_r-2Dmirror_web_packages_FactoMineR_FactoMineR.pdf&d=DwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=ug-gw1ia3rShGleyKIdg4GIXRt6aKD3u1CM4odHlsvE&m=FCARkfGgHXcSaTZN1f38_6XCbtZ-Lopl641M4MpApMJf7EuJ7y2Y4873aWz38wiY&s=YSmLvNnRQ7MWmcgbyifplmgAMBL22w7f9xufQdUzwyQ&e=).
But I am trying to get all the labels (the writes) : comfort, university,
economic, world, ... smaller.
How could I do that ?
Many thanks.
library(FactoMineR)
data(children)
res.ca <- CA (children, row.sup = 15:18, col.sup = 6:8)
------------------------------
Message: 5
Date: Mon, 23 Jan 2023 19:16:42 +0000
From: Rui Barradas <ruipbarra...@sapo.pt>
To: varin sacha <varinsa...@yahoo.fr>, "r-help@r-project.org"
<r-help@r-project.org>
Subject: Re: [R] package FactoMineR
Message-ID: <1fc08bf7-1a52-cabc-f8e9-4dabc1586...@sapo.pt>
Content-Type: text/plain; charset="utf-8"; Format="flowed"
Às 18:38 de 23/01/2023, varin sacha via R-help escreveu:
> Dear R-experts,
>
> Here below the R code working (page 8
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www2.uaem.mx_r-2Dmirror_web_packages_FactoMineR_FactoMineR.pdf&d=DwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=ug-gw1ia3rShGleyKIdg4GIXRt6aKD3u1CM4odHlsvE&m=FCARkfGgHXcSaTZN1f38_6XCbtZ-Lopl641M4MpApMJf7EuJ7y2Y4873aWz38wiY&s=YSmLvNnRQ7MWmcgbyifplmgAMBL22w7f9xufQdUzwyQ&e=).
>
> But I am trying to get all the labels (the writes) : comfort, university,
> economic, world, ... smaller.
> How could I do that ?
>
> Many thanks.
>
> library(FactoMineR)
> data(children)
> res.ca <- CA (children, row.sup = 15:18, col.sup = 6:8)
>
> ______________________________________________
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dhelp&d=DwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=ug-gw1ia3rShGleyKIdg4GIXRt6aKD3u1CM4odHlsvE&m=FCARkfGgHXcSaTZN1f38_6XCbtZ-Lopl641M4MpApMJf7EuJ7y2Y4873aWz38wiY&s=WyAtmOvZqkJ83zE98hkQxz9o1I6k6gYj7KJzInNKmcQ&e=
> PLEASE do read the posting guide
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.R-2Dproject.org_posting-2Dguide.html&d=DwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=ug-gw1ia3rShGleyKIdg4GIXRt6aKD3u1CM4odHlsvE&m=FCARkfGgHXcSaTZN1f38_6XCbtZ-Lopl641M4MpApMJf7EuJ7y2Y4873aWz38wiY&s=LvYxgn0N8iyJd6E3RK9ecZ0STO1_BIgO6gtE_zSJv-g&e=
> and provide commented, minimal, self-contained, reproducible code.
Hello,
I'm not finding "smaller" but are you looking for
rownames(res.ca$row$coord)
rownames(res.ca$row.sup$coord)
?
Hope this helps,
Rui Barradas
------------------------------
Message: 6
Date: Tue, 24 Jan 2023 10:50:26 +0100
From: Martin Maechler <maech...@stat.math.ethz.ch>
To: Ziyun Tang <tziy...@gmail.com>
Cc: <r-help@r-project.org>
Subject: Re: [R] Flickering when scrolling in R graphics windows
Message-ID: <25551.43490.524282.598...@stat.math.ethz.ch>
Content-Type: text/plain; charset="us-ascii"
>>>>> Ziyun Tang
>>>>> on Sat, 21 Jan 2023 15:14:15 -0500 writes:
> Hello, I have been experiencing some issues regarding scrolling with
> the mouse or trackpad in R graphics windows (from the base graphics
> package), which sometimes results in flickering, and wanted to see if
> anyone else had the same issues, or any advice. This happens for R
> version 4.2.2 on Windows 10 x64, and occurs when using Rgui and at the
> command line (whenever graphics windows are invoked). Note that some
> of the example code below can cause flickering and can be an issue for
> those with photosensitive epilepsy.
> Specifically, I have been experiencing three main issues, as follows:
> 1. When viewing a dataset with View(), the graphics window flickers
> when scrolling downwards too quickly, even with the option
> buffered=TRUE. For example:
>> View(iris)
If you use [Page Up] and [Page Down] there is no "flickering",
also using the cursor (up/down "arrows").
Still here, I would not think anything to be "wrong".
If you tell the computer to refresh a screen more quickly than
makes sense I guess you must expect what you see here.
(but yes, more modern GUIs would do 'smooth scrolling' here; I
think that's not available for the graphapp GUI in R for Windows)
By "scrolling", what exactly do you mean?
Is it that you use your mouse "wheel"? ... I assume "yes" in
the following, because in that case I can partly reproduce what
you describe.
> 2. When viewing a graph with plot(), and scrolling down, the graphics
> window flickers between the background and the graph itself. For
> example:
>> plot(iris$Sepal.Length, iris$Sepal.Width)
At first I wrote
I don't understand how you can "scroll down" in this plot
but now that I've guessed you mean "mouse wheel scrolling" I can
indeed see what you describe.
> 3. When viewing a matrix of scatterplots with pairs(), and scrolling
> down, the graphics window flickers between the background and the
> individual scatterplots. In some instances, when scrolling down with
> the trackpad, the window flickers continuously, and subsequently
> closing the window crashes R. For example:
>> pairs(iris[1:4])
That you bring R to crash just by "scrolling" really seems a bad
thing and points to a bug.
OTOH, I have not been able to replicate a crash.
I don't know what mouse-wheel-scrolling should do in a graphics window
in R for Windows.
In our terminal server version of Windows,
using Rterm (via ESS = Emacs Speaks Statistics), I can indeed
see that mouse-scrolling in a graphics window has *very funny*
/ strange effects when using the default interactive graphics
device ( .Device == "windows" ) :
Notably, after say pairs(iris) mouse-wheel-scrolling
"kind of" redraws some of the panel plots mostly in full size
(instead of the size they were as panels and as part of the full
"pairs" i.e., scatter plot matrix.
If instead I use RStudio and their own device "RD<something>"
mouse-wheel-scrolling has no effect, e.g., after pairs(iris).
And "no effect" is clearly better than what we observe with the R
default device "windows" i.e., windows() in the above situation.
> My sessionInfo() is as follows:
> R version 4.2.2 (2022-10-31 ucrt)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 10 x64 (build 19044)
> Matrix products: default
> locale:
> [1] LC_COLLATE=English_United States.utf8
> [2] LC_CTYPE=English_United States.utf8
> [3] LC_MONETARY=English_United States.utf8
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.utf8
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
> loaded via a namespace (and not attached):
> [1] compiler_4.2.2 tools_4.2.2
> Thank you in advance,
> Ziyun
------------------------------
Message: 7
Date: Tue, 24 Jan 2023 10:09:52 +0000
From: PIKAL Petr <petr.pi...@precheza.cz>
To: varin sacha <varinsa...@yahoo.fr>, "r-help@r-project.org"
<r-help@r-project.org>
Subject: Re: [R] package FactoMineR
Message-ID:
<8e2fa4fe9f284e08b236e9b9f1dbd...@srvexchcm1302.precheza.cz>
Content-Type: text/plain; charset="utf-8"
Hallo Sacha
AFAIK the functions in FactoMineR do not enable to manipulate label size. Plot
is performed by this part:
if (graph & (ncp > 1)) {
print(plot(res, axes = axes))
if (!is.null(quanti.sup))
print(plot(res, choix = "quanti.sup", axes = axes,
new.plot = TRUE))
and the function is not designed to accept additional parameters to manipulate
size of labels.
I struggled with it few years ago and I decided to use biplot instead as it
enables more options.
You can contact maintainers if they consider an improvement in future
versions. Probably simple ... in function definition and print(plot(res, axes
= axes, ...)) addition could do the trick, but I am not sure.
Cheers
Petr
> -----Original Message-----
> From: R-help <r-help-boun...@r-project.org> On Behalf Of varin sacha via R-
> help
> Sent: Monday, January 23, 2023 7:38 PM
> To: r-help@r-project.org
> Subject: [R] package FactoMineR
>
> Dear R-experts,
>
> Here below the R code working (page 8
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www2.uaem.mx_r-2D&d=DwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=ug-gw1ia3rShGleyKIdg4GIXRt6aKD3u1CM4odHlsvE&m=FCARkfGgHXcSaTZN1f38_6XCbtZ-Lopl641M4MpApMJf7EuJ7y2Y4873aWz38wiY&s=xKACgL9iNPXeIvE0V5ckPFY1PuPDY-l0gT_UjZwmkr4&e=
> mirror/web/packages/FactoMineR/FactoMineR.pdf).
>
> But I am trying to get all the labels (the writes) : comfort, university,
> economic,
> world, ... smaller. How could I do that ?
>
> Many thanks.
>
> library(FactoMineR)
> data(children)
> res.ca <- CA (children, row.sup = 15:18, col.sup = 6:8)
>
> ______________________________________________
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dhelp&d=DwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=ug-gw1ia3rShGleyKIdg4GIXRt6aKD3u1CM4odHlsvE&m=FCARkfGgHXcSaTZN1f38_6XCbtZ-Lopl641M4MpApMJf7EuJ7y2Y4873aWz38wiY&s=WyAtmOvZqkJ83zE98hkQxz9o1I6k6gYj7KJzInNKmcQ&e=
> PLEASE do read the posting guide
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.R-2Dproject.org_posting-2Dguide.html&d=DwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=ug-gw1ia3rShGleyKIdg4GIXRt6aKD3u1CM4odHlsvE&m=FCARkfGgHXcSaTZN1f38_6XCbtZ-Lopl641M4MpApMJf7EuJ7y2Y4873aWz38wiY&s=LvYxgn0N8iyJd6E3RK9ecZ0STO1_BIgO6gtE_zSJv-g&e=
> and provide commented, minimal, self-contained, reproducible code.
------------------------------
Subject: Digest Footer
_______________________________________________
R-help@r-project.org mailing list
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dhelp&d=DwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=ug-gw1ia3rShGleyKIdg4GIXRt6aKD3u1CM4odHlsvE&m=FCARkfGgHXcSaTZN1f38_6XCbtZ-Lopl641M4MpApMJf7EuJ7y2Y4873aWz38wiY&s=WyAtmOvZqkJ83zE98hkQxz9o1I6k6gYj7KJzInNKmcQ&e=
PLEASE do read the posting guide
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.R-2Dproject.org_posting-2Dguide.html&d=DwIGaQ&c=27AKQ-AFTMvLXtgZ7shZqsfSXu-Fwzpqk4BoASshREk&r=ug-gw1ia3rShGleyKIdg4GIXRt6aKD3u1CM4odHlsvE&m=FCARkfGgHXcSaTZN1f38_6XCbtZ-Lopl641M4MpApMJf7EuJ7y2Y4873aWz38wiY&s=LvYxgn0N8iyJd6E3RK9ecZ0STO1_BIgO6gtE_zSJv-g&e=
and provide commented, minimal, self-contained, reproducible code.
------------------------------
End of R-help Digest, Vol 239, Issue 24
***************************************
----------------------------------------------------------------------
Confidentiality Notice: This e-mail message, including any attachments, is for
the sole use of the intended recipient(s) and may contain confidential and
privileged information. Any unauthorized review, use, disclosure or
distribution is prohibited. If you are not the intended recipient, please
contact the sender by reply e-mail and destroy all copies of the original
message.
[[alternative HTML version deleted]]
______________________________________________
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.
