R/Calc - 0.1.6

Hi everyone,

>From an administrative point of view, I am supposed to
stop working as a
Google Summer of Code student today at 3 pm EST. As such,
I've leased a new
version of the package: 0.1.6, with links at
h
ttp://wiki.services.openoffice.org/wiki/R_and_Calc

First, I should say that I will continue working on this
package and won't
stop just because the Summer of Code period is over.  However, I
would be
grateful for any advice about this new release prior to 3
pm, so I can make
any changes before submitting this work for evaluation.

Below are some comments to specific people, based on advice
they gave last
week.

Eike -- this new version uses "make" rather than
sh scripts... Please have a
look at the makefile, because this was the first time I've
actually coded in
make. To make life easy for people using the package and
those coding in it,
I moved the Rserve clients (licensed under LGPL) into the
package itself,
giving appropriate credit and information where necessary. I
also
reorganized the code a bit to make life easy for anyone else
working on the
project.

With regards to the bulky image embedding code, my
apologies! I didn't
realize there was a Calc tutorial for this already.

Leo -- I implemented the Chi Square, Fisher Exact, Wilcox
tests, and also
the Kaplan-Meier curve. The other two (from the survival
analysis package)
will be harder to implement because there is currently no
easy way to accept
an unlimited amount of formula variables as inputs using the
GUI windows. I
will work on this, as well as dynamically setting array
sizes (e.g.
{$A1:A(length+1)} -- this is a pretty big change, so I
wanted to fix some of
the bugs and problems from version 0.1.5 before addressing
this.

I also created an "About" button in the
"Advanced" sub menu which gives all
sorts of diagnostic information. Please let me know if this
works.

Also, I think the problem with plotting had to do with where
I stored the
temporary image file... I changed this, so please let me
know if it works
for you! I tested the tool on Ubuntu, Fedora Core, and
Windows XP and it
worked in all cases, so I hope Windows 2K will also
cooperate now.

Again, comments are welcome! Thank you to all who have
already sent them.

Thanks,
Wojciech

Hi Wojciech,

nice work. I am happy to see the "About"-Dialog.

Now, I still have some issues / proposals. I don't think
they will be solved until 3 o'clock (it would be great), but
rather should be kept on the radar.

A. STRINGS

It is currently not possible to read strings from the
spreadsheet (or am I making something wrong?).

IF indeed strings are not imported (because of coding
issues), BUT only numerical values, then I have the
following proposal:

 1. simple input: {#cell_range} as currently implemented
 2. strings: {s#cell_range} or {string#cell_range}
          or {(s)#cell_range), whatever fits the code best
 3. factors: {factor#cell_range} => read as
'as.factor(...)'
 4. data frame:
             {frame#cell_range} => read as 
'data.frame(...}'
     - that is: use the strings stored in the column-header
       as the variable names (R takes usually care of
invalid names)
     - this is especially useful to read large data-sets
 
B. I still have some issues with the PLOT command, i.e it
crashes RServe. Though I haven't had time yet, to test if
the 2nd method (importing the image-file) works.

Keep the good work,

Leonard

x86, Win Xp SP 2 (with all updates)
R 2.4.1


> Hi everyone,
> 
> >From an administrative point of view, I am supposed
to stop working as a
> Google Summer of Code student today at 3 pm EST. As
such, I've leased a
> new
> version of the package: 0.1.6, with links at
> h
ttp://wiki.services.openoffice.org/wiki/R_and_Calc
> 
> First, I should say that I will continue working on
this package and won't
> stop just because the Summer of Code period is over.

However, I would
> be
> grateful for any advice about this new release prior to
3 pm, so I can
> make
> any changes before submitting this work for
evaluation.
> 
> Below are some comments to specific people, based on
advice they gave last
> week.
> 
> Eike -- this new version uses "make" rather
than sh scripts... Please have
> a
> look at the makefile, because this was the first time
I've actually coded
> in
> make. To make life easy for people using the package
and those coding in
> it,
> I moved the Rserve clients (licensed under LGPL) into
the package itself,
> giving appropriate credit and information where
necessary. I also
> reorganized the code a bit to make life easy for anyone
else working on
> the
> project.
> 
> With regards to the bulky image embedding code, my
apologies! I didn't
> realize there was a Calc tutorial for this already.
> 
> Leo -- I implemented the Chi Square, Fisher Exact,
Wilcox tests, and also
> the Kaplan-Meier curve. The other two (from the
survival analysis package)
> will be harder to implement because there is currently
no easy way to
> accept
> an unlimited amount of formula variables as inputs
using the GUI windows.
> I
> will work on this, as well as dynamically setting array
sizes (e.g.
> {$A1:A(length+1)} -- this is a pretty big change, so I
wanted to fix some
> of
> the bugs and problems from version 0.1.5 before
addressing this.
> 
> I also created an "About" button in the
"Advanced" sub menu which gives
> all
> sorts of diagnostic information. Please let me know if
this works.
> 
> Also, I think the problem with plotting had to do with
where I stored the
> temporary image file... I changed this, so please let
me know if it works
> for you! I tested the tool on Ubuntu, Fedora Core, and
Windows XP and it
> worked in all cases, so I hope Windows 2K will also
cooperate now.
> 
> Again, comments are welcome! Thank you to all who have
already sent them.
> 
> Thanks,
> Wojciech

-- 
Psssst! Schon vom neuen GMX MultiMessenger gehört?
Der kanns mit allen: http://www.gm
x.net/de/go/multimessenger

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Hi  Wojciech ,

I did some further tests this  afternoon. The results are
encouraging, 
though I found additional errors:

1.) spaces before {$OUT:...} prevent any output, e.g.
_{$OUT}<-...something...
where '_' is a space won't work.

2.) I still have problems with the PLOT. Both with Win XP
SP2 and Win2k SP4.
Where is the temporary file stored? Both machines I tested
on do not use 
standard MS Win directories, so this may be an issue.

Here, I have:
   OOo 2.3 dev installed in "L:ProgramsTextOOo-dev
2.3", and
   Rserve in
"L:ProgramsScienceStatisticsRR-2.5.0libraryRserv
e".
Needless to say, R is in:
  "L:ProgramsScienceStatisticsRR-2.5.0"

Maybe there is an issue with the program-path. (The Win
%PROGRAMS% path 
is also set to "L:Programs".) This is the Win 2k
machine.

The Win Xp machine has also some special settings, though I 
don't 
recall exactly what they were. (Though the Win %PROGRAMS%
should be the 
standard one. However, I installed R on a different path.)

3.) This brings me to the 3rd issue: the R-Addon Menus do
NOT work. They 
actually never worked on my machine. Not even the GUI is
displayed.

When I manually insert the path to the GUI *.txt-file 
downloaded from 
the source zip-file, the GUI shows up (and the non-graphical
commands do 
work - at least some of them).

Should the  user download separately these GUI-files? Or
should they 
have worked when installing the uno-package?

Hope this information will allow pinpointing the problem.

Sincerely,

Leonard


Wojciech Gryc wrote:
> Hi everyone,
>
> >From an administrative point of view, I am supposed
to stop working as a
> Google Summer of Code student today at 3 pm EST. As
such, I've leased a new
> version of the package: 0.1.6, with links at
> h
ttp://wiki.services.openoffice.org/wiki/R_and_Calc
>
> First, I should say that I will continue working on
this package and won't
> stop just because the Summer of Code period is over.

However, I would be
> grateful for any advice about this new release prior to
3 pm, so I can make
> any changes before submitting this work for
evaluation.
>
> Below are some comments to specific people, based on
advice they gave last
> week.
>
> Eike -- this new version uses "make" rather
than sh scripts... Please have a
> look at the makefile, because this was the first time
I've actually coded in
> make. To make life easy for people using the package
and those coding in it,
> I moved the Rserve clients (licensed under LGPL) into
the package itself,
> giving appropriate credit and information where
necessary. I also
> reorganized the code a bit to make life easy for anyone
else working on the
> project.
>
> With regards to the bulky image embedding code, my
apologies! I didn't
> realize there was a Calc tutorial for this already.
>
> Leo -- I implemented the Chi Square, Fisher Exact,
Wilcox tests, and also
> the Kaplan-Meier curve. The other two (from the
survival analysis package)
> will be harder to implement because there is currently
no easy way to accept
> an unlimited amount of formula variables as inputs
using the GUI windows. I
> will work on this, as well as dynamically setting array
sizes (e.g.
> {$A1:A(length+1)} -- this is a pretty big change, so I
wanted to fix some of
> the bugs and problems from version 0.1.5 before
addressing this.
>
> I also created an "About" button in the
"Advanced" sub menu which gives all
> sorts of diagnostic information. Please let me know if
this works.
>
> Also, I think the problem with plotting had to do with
where I stored the
> temporary image file... I changed this, so please let
me know if it works
> for you! I tested the tool on Ubuntu, Fedora Core, and
Windows XP and it
> worked in all cases, so I hope Windows 2K will also
cooperate now.
>
> Again, comments are welcome! Thank you to all who have
already sent them.
>
> Thanks,
> Wojciech
>
>   

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Wojciech Gryc wrote:
> From an administrative point of view, I am supposed to
stop working as a
> Google Summer of Code student today at 3 pm EST. As
such, I've leased a new
> version of the package: 0.1.6, with links at
> h
ttp://wiki.services.openoffice.org/wiki/R_and_Calc

Great to see graphics from R. Someone might want come up
with a more 
colorful, shiny example, for the "wow" effect.

> First, I should say that I will continue working on
this package and won't
> stop just because the Summer of Code period is over.

However, I would be
> grateful for any advice about this new release prior to
3 pm, so I can make
> any changes before submitting this work for
evaluation.

Some comments (the first two seem to be the same problems
that Leonard had):
- The dialog txt files aren't found without strange
CLASSPATH settings.
- On Windows, R doesn't seem to like the backslashes in the
path to the 
jpeg file. Replacing them with forward slashes seems to
work, I didn't 
check if it's supposed to be that way.
- Compiling is still a bit painful. SDK sets environment
variables for 
its own and office's path. Why don't you use those?
- I also had to add "." to CLASSPATH do get it to
compile.
- I'm not sure if the RServe client sources should be in the
source package.

Niklas

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Hi, Wojciech,

Niklas Nebel wrote:
> Wojciech Gryc wrote:
>> From an administrative point of view, I am supposed
to stop working as a
>> Google Summer of Code student today at 3 pm EST. As
such, I've leased 
>> a new
>> version of the package: 0.1.6, with links at
>> h
ttp://wiki.services.openoffice.org/wiki/R_and_Calc
>
> Great to see graphics from R. Someone might want come
up with a more 
> colorful, shiny example, for the "wow"
effect.
>
>> First, I should say that I will continue working on
this package and 
>> won't
>> stop just because the Summer of Code period is
over. 
However, I 
>> would be
>> grateful for any advice about this new release
prior to 3 pm, so I 
>> can make
>> any changes before submitting this work for
evaluation.
>
> Some comments (the first two seem to be the same
problems that Leonard 
> had):
> - The dialog txt files aren't found without strange
CLASSPATH settings.
> - On Windows, R doesn't seem to like the backslashes in
the path to 
> the jpeg file. Replacing them with forward slashes
seems to work, I 
> didn't check if it's supposed to be that way.

Well, now that the culprit is found, I hope in a fast
solution. One 
small note with R:
 - on Windows, IF you want to use a path with ''-slashes in
R, you need 
to escape the slashes, like: '\'
 - R accepts the '/'-slashes on windows, too
 - I don't know IF one needs to additionally escape the
''-slashes in 
Rserve, too (like in some regexp's, having to write '\\'
for a single 
literal '')

Hope this helps to solve the Windows problems.

And keep the good work.

Sincerely,

Leonard

> - Compiling is still a bit painful. SDK sets
environment variables for 
> its own and office's path. Why don't you use those?
> - I also had to add "." to CLASSPATH do get
it to compile.
> - I'm not sure if the RServe client sources should be
in the source 
> package.
>
> Niklas
>
>
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Hi Leonard,

On Wednesday, 2007-08-22 21:20:49 +0300, Leonard Mada
wrote:

> >- The dialog txt files aren't found without strange
CLASSPATH settings.
> >- On Windows, R doesn't seem to like the
backslashes in the path to 
> >the jpeg file. Replacing them with forward slashes
seems to work, I 
> >didn't check if it's supposed to be that way.
> 
> Well, now that the culprit is found, I hope in a fast
solution. One 
> small note with R:
> - on Windows, IF you want to use a path with
''-slashes in R, you need 
> to escape the slashes, like: '\'
> - R accepts the '/'-slashes on windows, too
> - I don't know IF one needs to additionally escape the
''-slashes in 
> Rserve, too (like in some regexp's, having to write
'\\' for a single 
> literal '')

Usually path munging library functions on Windows consume
'/' instead of
'', even the ones shipped with MSVC. It's only command line
arguments
that may confuse applications with '/' (e.g. dir c:/windows
) because
they take it for an option switch. IMHO, in a programmatical
context
there shouldn't be need to use '' in paths on Windows, so
they can be
written transparently on all platforms.

  Eike

-- 
 OOo/SO Calc core developer. Number formatter stricken i18n
transpositionizer.
 SunSign   0x87F8D412 : 2F58 5236 DB02 F335 8304  7D6C 65C9
F9B5 87F8 D412
 OpenOffice.org Engineering at Sun: http://blogs.sun.com/Gu
llFOSS
 Please don't send personal mail to this erlsun.com
account, which I use for
 mailing lists only and don't read from outside Sun. Use
eracksun.com Thanks.

Hi Eike, Hi Wojciech,

Eike Rathke wrote:
> Hi Leonard,
>
> On Wednesday, 2007-08-22 21:20:49 +0300, Leonard Mada
wrote:
>
>   
>>> - The dialog txt files aren't found without
strange CLASSPATH settings.
>>> - On Windows, R doesn't seem to like the
backslashes in the path to 
>>> the jpeg file. Replacing them with forward
slashes seems to work, I 
>>> didn't check if it's supposed to be that way.
>>>       
>> Well, now that the culprit is found, I hope in a
fast solution. One 
>> small note with R:
>> - on Windows, IF you want to use a path with
''-slashes in R, you need 
>> to escape the slashes, like: '\'
>> - R accepts the '/'-slashes on windows, too
>> - I don't know IF one needs to additionally escape
the ''-slashes in 
>> Rserve, too (like in some regexp's, having to write
'\\' for a single 
>> literal '')
>>     
>
> Usually path munging library functions on Windows
consume '/' instead of
> '', even the ones shipped with MSVC. It's only command
line arguments
> that may confuse applications with '/' (e.g. dir
c:/windows ) because
> they take it for an option switch. IMHO, in a
programmatical context
> there shouldn't be need to use '' in paths on Windows,
so they can be
> written transparently on all platforms.
>
>   Eike
>   

Indeed, forward-slashes ('/') are the preferred way to write
a file path 
in R (even under Windows).

Now to serious things: when will I see a new version of the
RCalc 
plugin? (maybe it's time for 0.2)
I am eagerly awaiting to see image-import working.

Sincerely,

Leonard

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Hi everyone,

Posted 0.1.7 up at h
ttp://wiki.services.openoffice.org/wiki/R_and_Calc

Leonard -- sorry for being so modest with the version
system! But please
don't worry, we're actually going to jump to "1.0"
as soon as enough bugs
are fixed. I won't be adding new features until the current
bugs are worked
out.

Speaking of bugs, I *think* I fixed the Windows image
problem. Also, I think
I fixed the problem for outputting text and Strings (at
least some of these
problems). You can also output a matrix of labels, though
they have to be
the same text (e.g. {$OUT#A1:C10}<-hello )

Leonard -- one more question... You'll notice the plot
commands use JPG and
PNG files. Do you know if there's any way to send output to
an EPS (or
similar) file without having an R window pop up? i.e.
Sending it to print an
EPS wouldn't be a good idea, but rather using a command
similar to the
jpeg() command.

Niklas -- can you please elaborate on the CLASSPATH settings
you used to get
the GUI menus to work? They worked for me without any
problems, on both
Fedore Core, Ubuntu, and Windows XP, so I'd really
appreciate some more
advice on this bug.

Thank you,
Wojciech

On 8/23/07, Leonard Mada <discoleogmx.net> wrote:
>
> Hi Eike, Hi Wojciech,
>
> Eike Rathke wrote:
> > Hi Leonard,
> >
> > On Wednesday, 2007-08-22 21:20:49 +0300, Leonard
Mada wrote:
> >
> >
> >>> - The dialog txt files aren't found
without strange CLASSPATH
> settings.
> >>> - On Windows, R doesn't seem to like the
backslashes in the path to
> >>> the jpeg file. Replacing them with forward
slashes seems to work, I
> >>> didn't check if it's supposed to be that
way.
> >>>
> >> Well, now that the culprit is found, I hope in
a fast solution. One
> >> small note with R:
> >> - on Windows, IF you want to use a path with
''-slashes in R, you need
> >> to escape the slashes, like: '\'
> >> - R accepts the '/'-slashes on windows, too
> >> - I don't know IF one needs to additionally
escape the ''-slashes in
> >> Rserve, too (like in some regexp's, having to
write '\\' for a single
> >> literal '')
> >>
> >
> > Usually path munging library functions on Windows
consume '/' instead of
> > '', even the ones shipped with MSVC. It's only
command line arguments
> > that may confuse applications with '/' (e.g. dir
c:/windows ) because
> > they take it for an option switch. IMHO, in a
programmatical context
> > there shouldn't be need to use '' in paths on
Windows, so they can be
> > written transparently on all platforms.
> >
> >   Eike
> >
>
> Indeed, forward-slashes ('/') are the preferred way to
write a file path
> in R (even under Windows).
>
> Now to serious things: when will I see a new version of
the RCalc
> plugin? (maybe it's time for 0.2)
> I am eagerly awaiting to see image-import working.
>
> Sincerely,
>
> Leonard
>
>
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>
>


-- 

Five Minutes to Midnight:
Youth on human rights and current affairs
http://www.five
minutestomidnight.org/

Wojciech Gryc wrote:
> Niklas -- can you please elaborate on the CLASSPATH
settings you used to get
> the GUI menus to work? They worked for me without any
problems, on both
> Fedore Core, Ubuntu, and Windows XP, so I'd really
appreciate some more
> advice on this bug.

For me, they didn't work, unless I extended the class path
(in OOo Java 
settings). Note that getSystemClassLoader is supposed to
only look in 
the class path. To load the dialog definition files from the
class JAR 
file, getClass().getResourceAsStream should be used.

Niklas

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Hi Wojciech,


Wojciech Gryc wrote:
 > Hi everyone,
 >
 > Posted 0.1.7 up at h
ttp://wiki.services.openoffice.org/wiki/R_and_Calc

Very nice! Graphics work now, which is great!

What still does not work, are the Menu-Commands (like ANOVA,

Correlation). RServe just silently crashes when calling one
of the 
Menus. However, loading the script by hand works fine, so it
seems that 
the script file is fine.

 > Leonard -- sorry for being so modest with the version
system! But please
 > don't worry, we're actually going to jump to
"1.0" as soon as enough bugs
 > are fixed. I won't be adding new features until the
current bugs are 
worked
 > out.

It's OK. Fixing bugs has surely top priority.

 > Speaking of bugs, I *think* I fixed the Windows image
problem. Also, 
I think
 > I fixed the problem for outputting text and Strings
(at least some of 
these
 > problems). You can also output a matrix of labels,
though they have to be
 > the same text (e.g. {$OUT#A1:C10}<-hello )

Yes, seems OK. [Though importing strings seems not
implemented, yet.]

There are still some errors. Try the following script inside
the coding 
window:
y<-data.frame(c("my text"))
names(y)<-"test"

my.class<-class(y)
{$OUT#F1}<-{$BASE}
// CORRECT

my.name<-names(y)
{$OUT#F2}<-{$BASE}
// CORRECT

x<-y["test"]
{$OUT#F3}<-{$BASE}
// DID NOT PRODUCE CORRECT OUTPUT

x<-y
{$OUT#F4}<-test
// DOES NOT WORK
// SHOULD PRODUCE my text

The actual output is:

data.frame
test
BASE
           <- EMPTY


 > Leonard -- one more question... You'll notice the plot
commands use 
JPG and
 > PNG files. Do you know if there's any way to send
output to an EPS (or
 > similar) file without having an R window pop up? i.e.
Sending it to 
print an
 > EPS wouldn't be a good idea, but rather using a
command similar to the
 > jpeg() command.

Graphics output is not my specialty. Though you could try:
   help("dev.copy2eps")
Unfortuantely dev.copy2eps() crashes RServe. I will look
further into 
possible solutions, but I just haven't worked at all with
eps files. 
[COPY/PASTE just worked, so I had no need to experiment with
anything 
more complex.]

 > Niklas -- can you please elaborate on the CLASSPATH
settings you used 
to get
 > the GUI menus to work? They worked for me without any
problems, on both
 > Fedore Core, Ubuntu, and Windows XP, so I'd really
appreciate some more
 > advice on this bug.
 >
 > Thank you,
 > Wojciech
 >
 > On 8/23/07, Leonard Mada <discoleogmx.net> wrote:
 >> Hi Eike, Hi Wojciech,
 >>
 >> Eike Rathke wrote:
 >>> Hi Leonard,
 >>>
 >>> On Wednesday, 2007-08-22 21:20:49 +0300,
Leonard Mada wrote:
 >>>
 >>>
 >>>>> - The dialog txt files aren't found
without strange CLASSPATH
 >> settings.
 >>>>> - On Windows, R doesn't seem to like
the backslashes in the path to
 >>>>> the jpeg file. Replacing them with
forward slashes seems to work, I
 >>>>> didn't check if it's supposed to be
that way.
 >>>>>
 >>>> Well, now that the culprit is found, I
hope in a fast solution. One
 >>>> small note with R:
 >>>> - on Windows, IF you want to use a path
with ''-slashes in R, you 
need
 >>>> to escape the slashes, like: '\'
 >>>> - R accepts the '/'-slashes on windows,
too
 >>>> - I don't know IF one needs to
additionally escape the ''-slashes in
 >>>> Rserve, too (like in some regexp's, having
to write '\\' for a 
single
 >>>> literal '')
 >>>>
 >>> Usually path munging library functions on
Windows consume '/' 
instead of
 >>> '', even the ones shipped with MSVC. It's
only command line arguments
 >>> that may confuse applications with '/' (e.g.
dir c:/windows ) because
 >>> they take it for an option switch. IMHO, in a
programmatical context
 >>> there shouldn't be need to use '' in paths on
Windows, so they can be
 >>> written transparently on all platforms.
 >>>
 >>>   Eike
 >>>
 >> Indeed, forward-slashes ('/') are the preferred
way to write a file path
 >> in R (even under Windows).
 >>
 >> Now to serious things: when will I see a new
version of the RCalc
 >> plugin? (maybe it's time for 0.2)
 >> I am eagerly awaiting to see image-import
working.
 >>
 >> Sincerely,
 >>
 >> Leonard

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