Re: [Rd] Problem with accessibility in R 4.2.0 and 4.2.1.

[Tomas Kalibera]

On 9/22/22 23:15, Andrew Hart via R-devel wrote:

On 22/09/2022 16:42, Toby Hocking wrote:
Another option is to use https://emacspeak.sourceforge.net/ 
 (version of emacs editor/ide 
which can speak letters/words/lines -- has a blind maintainer) with 
https://ess.r-project.org/  (interface 
for editing and running R code from within emacs)


Thanks everyone for all the suggestions. Of course, the optimal 
solution would be to figure out what is going on in Rgui, but, as is 
always the case, the blind user use case is a fairly niche one. I 
appreciate all the suggestions for finding an immediate solution to my 
problem.


Hi Andrew,

I am glad to hear that Rterm seems to be working for you, but I would 
still like to see if Rgui could be improved to work as well.


I am completely new to screen readers, but I learned that NVDA is free 
and open-source and doesn't need any special hardware. So I installed it 
on my system.


When I enter something to the current line in Rterm console and navigate 
over the typed letters using left/right arrow, NVDA reads the character 
at the cursor.


When I enter something to the current line in Rgui console (executed in 
the default way), NVDA either doesn't read anything when I navigate over 
the typed characters or it reads incorrect characters. Is this a 
reproduction of the problem you are reporting? Or, how could I reproduce 
the problem you are seeing with NVDA?


Now, for me, even Rgui from R 4.0.5 and R 4.1.3 has the problem: the 
characters read are either wrong (usually space and newline), or no 
characters are read at all.


Also, I tried building R-devel modified so that Rgui doesn't use UTF-8 
as the system/R native encoding. It didn't change anything: NVDA still 
can't read the characters when navigating.


Best
Tomas



I don't use any kind of IDE for working with R since I simply haven't 
found one that is accessible or that i understand how to use. There is 
a plug-in for the Eclipse IDE I installed a few years ago, but I 
didn't understand the first thing about how it was to be used. So I've 
just always worked with an editor open in one Window and R in another,
working interactively in R or bouncing over to the editor for more 
complex things and sourcing code into R as necessary. However, I only 
use the R console in Rgui. I went and had a look at Rterm, which I 
have never used on Windows; I've only ever used it when ssh-ing into 
Linux systems to use R. However, I've just found out that Rterm does a 
number of fairly important things that probably mean I can just use it 
instead of Rgui:

1. You can paste from the clipboard into the Rterm prompt;
2. It has a command history;
3. If you plot something, it opens a Window to draw the plot (I never 
realised it could do this and had always assumed Rgui was needed for 
this); and
4. It opens the HTML help if you ask for help on windows. I only ever 
saw it display text help on Linux, but I was logged in remotely. 
Text-based help is fine when ssh-ing into a machine, but HTML help is 
much nicer to read and navigate.


I think I'll just switch over to Rterm for a while, but I can also 
check out ess, which I wasn't aware of.


Thanks a lot,
Andrew.

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Re: [Rd] Better 'undefined columns' error for data.frame

[GILLIBERT, Andre]

Duncan Murdoch  wrote:
> On 24/09/2022 9:56 a.m., GILLIBERT, Andre wrote:
> > Dear R developers,
> >
> >
> > One of the error messages that make me loose the most time is the 
> > "undefined columns selected" of `[.data.frame`.
> >
> > It ought to specify the list of bad column names, but currently does not.
> >
> > Fortunately, this can easily be fixed by a small patch I can write.
> >
> >
> > Are you interested in that patch?
>
> I doubt if you'll get an answer to this without showing it to us.
>
> > Is there a standard way to transfer patches for feature requests?
>
> The standard instructions are here:  https://www.r-project.org/bugs.html .
> You're offering an enhancement rather than a bug fix, but the process is
> the same.  But since your change is probably quite small, you might not
> need to go through the whole process:  proposing it on this mailing list
> might be sufficient.
>
> Duncan Murdoch

Please, find the patch attached, based on the latest R SVN trunk code.
In order to avoid any accidental modification of the behavior of 
`[.data.frame`, I only inserted code at positions where the "undefined columns 
selected" error was generated.
In order to test all code paths, I wrote a small test script (code attached), 
but did not insert clean & standardized tests to the R build.

I added a new base::.undefined_columns_msg closure. I am not sure that adding 
such new internal symbols to the base package is smart because it pollutes the 
base environment, but looking at the base-internal documentation page, it seems 
to be standard practice.

For message translations, I tried to use tools::xgettext() to re-generate the 
R-base.pot file, but this file seems to be out of sync for a few messages. So, 
I manually added the new messages to R-base.pot.
As I am a native french speaker, I added appropriate translations to R-fr.po.
The make command did not regenerate .mo files, and I did not find any 
appropriate make target to rebuild them, so, for testing purposes, I manually 
generated them.  The R installation & administration manual did not help 
(https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Localization-of-messages).

When compiling the source code on a x86_64 Ubuntu 16.04 system, I got a problem 
with position independent code in the internal R LAPACK module. The -fPIC 
option was not properly passed to the gfortran command line. I fixed that by 
replacing $(ALL_FCFLAGS) by $(ALL_FFLAGS) on line 16 of 
src/modules/lapack/Makefile.in
That looks like a bug to me (misspelling of FFLAGS), but I did not fix that in 
my patch, since it is a very different issue.

--
Sincerely
André GILLIBERT
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Re: [Rd] Better 'undefined columns' error for data.frame

[Dirk Eddelbuettel]

Andre,

On 25 September 2022 at 18:09, GILLIBERT, Andre wrote:
| Please, find the patch attached, based on the latest R SVN trunk code.

Well the mailing list software tends to drop attachments.  There is a reason
all these emails suggest to use bugs.r-project.org.

Dirk

-- 
dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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Re: [Rd] Better 'undefined columns' error for data.frame

[Duncan Murdoch]

Hi.  That change is much more ambitious than I would have guessed.  R 
Core might prefer it to arrive via bugzilla.


A couple of small comments:

1.  Your last test, "dfa[,cols]" produces a really long message:

> dfa[,cols]
Error in `[.data.frame`(dfa, , cols) :
  undefined columns selected:   4,   5,   6,   7,   8,   9,  10,  11, 
12,  13,  14,  15,  16,  17,  18,  19,  20,  21,  22,  23,  24,  25, 
26,  27,  28,  29,  30,  31,  32,  33,  34,  35,  36,  37,  38,  39, 
40,  41,  42,  43,  44,  45,  46,  47,  48,  49,  50,  51,  52,  53, 
54,  55,  56,  57,  58,  59,  60,  61,  62,  63,  64,  65,  66,  67, 
68,  69,  70,  71,  72,  73,  74,  75,  76,  77,  78,  79,  80,  81, 
82,  83,  84,  85,  86,  87,  88,  89,  90,  91,  92,  93,  94,  95, 
96,  97,  98,  99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 
110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 
124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 
138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 
152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 
166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 
180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 
194, 195, 196


but it is still incomplete, because cols is 1:1e6.  It might be 
preferable to use ellipsis when the number of columns is too large, e.g.


> dfa[,cols]
Error in `[.data.frame`(dfa, , cols) :
  undefined columns selected:   4,   5,   6,   7,   8,   9,  10,  ...

(I think it's not worth the trouble to give the count of missing 
columns, but you might choose to do that.)


2.  Your patch file should be produced by "svn diff", which would have 
included the revision number.


I think your code is an improvement over the current code; let's hope it 
gets accepted.


Duncan Murdoch


On 25/09/2022 2:09 p.m., GILLIBERT, Andre wrote:


Duncan Murdoch  wrote:
 > On 24/09/2022 9:56 a.m., GILLIBERT, Andre wrote:
 > > Dear R developers,
 > >
 > >
 > > One of the error messages that make me loose the most time is the 
"undefined columns selected" of `[.data.frame`.

 > >
 > > It ought to specify the list of bad column names, but currently 
does not.

 > >
 > > Fortunately, this can easily be fixed by a small patch I can write.
 > >
 > >
 > > Are you interested in that patch?
 >
 > I doubt if you'll get an answer to this without showing it to us.
 >
 > > Is there a standard way to transfer patches for feature requests?
 >
 > The standard instructions are here: 
https://www.r-project.org/bugs.html  .

 > You're offering an enhancement rather than a bug fix, but the process is
 > the same.  But since your change is probably quite small, you might not
 > need to go through the whole process:  proposing it on this mailing list
 > might be sufficient.
 >
 > Duncan Murdoch

Please, find the patch attached, based on the latest R SVN trunk code.
In order to avoid any accidental modification of the behavior of 
`[.data.frame`, I only inserted code at positions where the "undefined 
columns selected" error was generated.
In order to test all code paths, I wrote a small test script (code 
attached), but did not insert clean & standardized tests to the R build.


I added a new base::.undefined_columns_msg closure. I am not sure that 
adding such new internal symbols to the base package is smart because it 
pollutes the base environment, but looking at the base-internal 
documentation page, it seems to be standard practice.


For message translations, I tried to use tools::xgettext() to 
re-generate the R-base.pot file, but this file seems to be out of sync 
for a few messages. So, I manually added the new messages to R-base.pot.
As I am a native french speaker, I added appropriate translations to 
R-fr.po.
The make command did not regenerate .mo files, and I did not find any 
appropriate make target to rebuild them, so, for testing purposes, I 
manually generated them.  The R installation & administration manual did 
not help 
(https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Localization-of-messages 
).


When compiling the source code on a x86_64 Ubuntu 16.04 system, I got a 
problem with position independent code in the internal R LAPACK module. 
The -fPIC option was not properly passed to the gfortran command line. I 
fixed that by replacing $(ALL_FCFLAGS) by $(ALL_FFLAGS) on line 16 of 
src/modules/lapack/Makefile.in
That looks like a bug to me (misspelling of FFLAGS), but I did not fix 
that in my patch, since it is a very different issue.


--
Sincerely
André GILLIBERT


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Re: [Rd] Better 'undefined columns' error for data.frame

[Duncan Murdoch]

On 25/09/2022 2:48 p.m., Dirk Eddelbuettel wrote:


Andre,

On 25 September 2022 at 18:09, GILLIBERT, Andre wrote:
| Please, find the patch attached, based on the latest R SVN trunk code.

Well the mailing list software tends to drop attachments.  There is a reason
all these emails suggest to use bugs.r-project.org.



I was named in the posting, so I saw the patch file, my copy didn't come 
via the list.  It's a good patch, I hope Andre does post there.


Duncan Murdoch

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