[Rd] Project suggestion: Interface between R and graphic devices
Hi to all developer, sure that I will not be the first one with this idea but I did not found treads about this. I realized that there are some user interfaces like Brodgar and SciViews. There was used a lot of manpower to develop those programs. On the other side I realized that it could be very helpful to have such programs if somebody would like to change the statistical software from SPSS or other commercial software to R-Statistic. The first steps would be more easy and the acceptance of R would be much more than with the command line interpreter. It would be a great help to introduce R in the institutes, which does not use R just now. One of the features of R is that it is state of the art all the time. If anybody would use R version 1.?? because of any graphic devise it would not be helpful. So my suggestion: Is it possible to define any interface between the R-system and the Gui applications, so that the GUIs, but only the interface does need to rebuild if the R-system is changed. I am out of order with programming since ten years, but it seems (but it not sure just now) that I have more time to oversee such a project. But I will need a lot of advice the first time. I was developing the software for medical systems and this would be a complete new subject for me. with regards Knut Krueger http://www.biostatistic.de __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Project suggestion: Interface between R and graphic devices
Prof Brian Ripley schrieb: > I think you do not mean `graphics devices' as used by R (pdf, > postscript, X11, windows, quartz etc). Sorry no I do not mean such "devices" I thought about the Graphic User Interfaces, to use the R-System with a windows like surface http://www.sciviews.org/. I see the difficulties for the user which want to change from SPSS or Statistica or ? to R just inside my family. I am using R to reproduce the SPSS results (just for fun because I want my to learn R) my wife is using SPSS for her research program. But it takes a long time for scientist to learn the command line syntax. There is not time for this if the scientist is just inside a any research ... and the scientist is mostly inside any research. for example http://www.sciviews.org/. was broken since the new version 2.?? (I think so). But if there would be a defined interface between the GUIs and R the developer of this interface must only change one interface instead all developer of the GUIs must change their GUIs If i remember then I it was a great improvement of Linux in the past after there was a GUI available which was like windows. This was a great step for the acceptance of LINUX. I think this would be the same for R. but there must be a stable interface for GUI programmers available before. Hope this could clarify my suggestion :-) Regards Knut __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Project suggestion: Interface between R and graphic devices
> > > Prof Brian Ripley wrote: > Please so read the part of my message that you have silently deleted > here. > > There IS A STABLE API, as I said there. What could be the problem for the developer of the GUIs. One of the Gui is only working with a 1.4? version, one of the GUI is only working with the lower than 2.0. and so on. Don't they use the API or is the API not suitable for them? Regards Knut __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Project suggestion: Interface between R and graphic devices
Philippe Grosjean schrieb:
>
> This is not true. Version 0.8-8 of SciViews-R
> (http://www.sciviews.org/SciViews-R) is compatible with R 2.1.1. There
> were several months of delay between R 2.1.X and the compatible
> SciViews-R version... There were a lot of changes required in my code,
> because of the internationalization of R. I though translating R in
> French was a priority, so, I have been working on "R French" first.
> Also, I took a little time with my baby that was born in April... life
> is not limited to programming R!
Congratulations I know the time when my boy was born.
>
> Remember that Open Source is a collaborative and voluntary approach of
> developing software.
Please don't misunderstand my question.
We developed a couple of (commercial) programs for medical university use.
On of the required things were compatible interfaces between different
hardware and software parts.
for example:
There was a definition of a function call:
function (Var1, Var2, ., Version)
begin
case version of
version1: ...
version2 ...
end {case}
end {function}
This functions and procedures did the communication between different
versions of hard an software.
And the open source community is the best development environment to
develop and take care for such API.
So back to my suggestion.
You told me that you must do a lot of changes in your GUI. If there
would be one API which is serving a couple of old R Versions, then all
running systems of GUIs would be running even the code for the latest
R-version is changed. And only one part of the code must be changed not
all available GUIs.
> If you want to use all the time the latest R version, just learn to
> use its standard command line interface.
Some of the user want to use the newest command line interface some of
(the newbies) want to use GUIs
> If you prefer SciViews, JGR, R Commander, etc., then you should expect
> some delay before R releases and compatible GUI releases. Indeed, one
> must say that R Commander has always been released on time with the
> latest R version, as fart as I know, and JGR is very close to.
and this is the point that I thought maybe there could be some
improvement with an universal API for GUIs
> Latest SciViews version was very, very late. I apologize for that.
Please don't think that this was my intention - it was just the other
side. I realized that there was a long time especially for your nice GUI
and I thought:
It seems to be wasted time if Mr Grosjean must always do such a lot work
after there is a new version of R. And therefor I tough about something
to do for the R-Community.
But dear community please see this suggestion in a manner that I do not
have any knowledge about the work of the core team but that I am
fascinated about the work, but that I am not able to win user for R
because of problems with missing or not working GUIs.
Missing:
I do not know whether you know Wordperfect Office. They want the user to
change from MS-Office.
They build in a function: Switch to Word Mode, or switch to Powerpoint
Mode. and this is the point to get Statistica user and SPSS user away
from their programs.
medium universities in Germany have between 500 and 1000 licences for
SPSS. What a lot of money which is not available for the researchers
Conclusion.
I did not want a just ready solution, but I thought about some steps for
the next years.
There is an API available if I understand Prof. Ripley right, but then I
do not understand the problems of the GUI developer.
And please again I do not want to blame anybody of any development team
I want to understand the project.
>
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Re: [Rd] Project suggestion: Interface between R and graphic devices
Simon Urbanek schrieb: >Knut, > >On Oct 9, 2005, at 1:19 PM, Knut Krueger wrote: > > > >>>If you prefer SciViews, JGR, R Commander, etc., then you should >>>expect >>>some delay before R releases and compatible GUI releases. Indeed, one >>>must say that R Commander has always been released on time with the >>>latest R version, as fart as I know, and JGR is very close to. >>> >>> >>> >>and this is the point that I thought maybe there could be some >>improvement with an universal API for GUIs >> >> > > >As Brian was pointing out there is such an API and as with all APIs >it is allowed to improve between releases. ... > Ok all your answers are clarifying the points of discussion about GUIs. I think I could say that I should not recommend a GUI which is not updated since the 1.4 Version. It seems to be that it was a "Mc Murphy" problem that I recommended SCIviews in the institute just a week before the compatibility was broken with the newest version. > From my point of view I can say that building and testing of >installers and binaries takes far more time than fixing the code for >API changes. If you are willing to build and test binaries during the >R beta phase, you're encouraged to do so - that would make the GUI >available right on time for the R release. > OK as I wrote, I am out of order with programming technique about 10 years now. A very long time for technical solutions. And I was working in a different language. I have small experience in C but lot in Assembler and Pascal (my biggest program of my own was about 65.000 lines). Pascal was required because it was very save for experimental and often changing programs. If you think I could start testing first and if this would be helpful I could start,. but I will have more time after January. But I am still a Newbie in R maybe there might be some problems and needless questions the first time. and maybe you are able to find tasks for the first steps in the community. Regards Knut [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] 8 char labels in read.spss
I was wondering why it is possible to read long labels from the CVS files but not from the SPSS files. I did not have much time to search for the code but I found: in foreign_0.8-10 source file var.h.in > /* Definition of the max length of a short string value, generally >eight characters. */ > #define MAX_SHORT_STRING ((SIZEOF_DOUBLE)>=8 ? ((SIZEOF_DOUBLE)+1)/2*2 > : 8) > #define MIN_LONG_STRING (MAX_SHORT_STRING+1) > > /* FYI: It is a bad situation if sizeof(R_flt64) < MAX_SHORT_STRING: >then short string missing values can be truncated in system files >because there's only room for as many characters as can fit in a >R_flt64. */ > #if MAX_SHORT_STRING > 8 > #error MAX_SHORT_STRING must be less than 8. > #endif I am am right then there was a restriction in the year 2000 because the files are from the year 2000. Now there are some questions: Did I found the right code? is it possible that anybody could recompile this with long value names or where is the best manual for a quick start in compiling packages. I found a couple of weeks before a tread where anybody wrote a complete way for building packages. He described all problems of him and there were a lot of hints for the first steps, but I am not able to find it again - I don't know the search terms which I used before :-( with regards Knut __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] 8 char labels in read.spss
Thomas Lumley schrieb: > On Tue, 11 Oct 2005, Knut Krueger wrote: > >> I was wondering why it is possible to read long labels from the CVS >> files but not from the SPSS files. > > > The SPSS file formats are not documented, and so we rely on the code > from PSPP. At the time, PSPP did not read long variable names. It > now does, so it would be possible for someone update the SPSS-reading > code to handle long variable names. This is much more complicated > than just changing a #define; the long variable names are stored in a > different part of the file. > > I don't expect anyone on R-core to get around to this any time soon. > If you want to try, the current PSPP code is at >http://savannah.gnu.org/projects/pspp Thanks for your reply, unfortunatlley the link is broken and gnu.org is linking to the same page http://www.gnu.org/software/pspp/pspp.html ... Knut __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] 8 char labels in read.spss
Thomas Lumley schrieb: > On Tue, 11 Oct 2005, Knut Krueger wrote: > >> I was wondering why it is possible to read long labels from the CVS >> files but not from the SPSS files. > > > The SPSS file formats are not documented, and so we rely on the code > from PSPP. I found a definition of the SPSS files. http://www.wotsit.org/download.asp?f=spssdata but they recommend to use the spss input/output dll to ensure upward compatbility Regards Knut __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] 8 char labels in read.spss
Thomas Lumley schrieb: > On Tue, 11 Oct 2005, Knut Krueger wrote: > >> Thanks for your reply, >> unfortunatlley the link is broken >> and gnu.org is linking to the same page >> http://www.gnu.org/software/pspp/pspp.html ... >> > > It works for me now (as it did then) Mc Murpey was working ... seems that the server did not answer just in the 5 minutes I tried it Regards Knut > > > -thomas > > -- with regards Knut Krueger http://www.biostatistic.de __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] SPSS I/O dll was: 8 char labels in read.spss
Thomas Lumley schrieb: >On Tue, 11 Oct 2005, Knut Krueger wrote: > > >>I found a definition of the SPSS files. >>http://www.wotsit.org/download.asp?f=spssdata >>but they recommend to use the spss input/output dll to ensure upward >>compatbility >> >> >> > >"Well, they would say that, wouldn't they" (Rice-Davis 1963) > >Unfortunately, that document is an old file format. It doesn't describe >record 7 subtype 13, which is where the long variable names live. > What about using the SPSS input dll for those R users which would like to use their old SPSS files. Most universities here have SPSS licences and therefor the dll is available. I did not found yet any copyright notice on the developer part of the SPSS CD. Maybe the DLL is usable with the own program without the SPSS Licence. I will look for that if using the I/O dll is possible with R. All necessary C codes are delivered with the developer kit on the SPSS CD. Regards Knut [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] SPSS I/O dll was: 8 char labels in read.spss
Thomas Lumley schrieb: >Yes, but it can't be incorporated in the "foreign" package, which has a >GPL license, and in any case wouldn't work off Windows. It's not clear >that it would be much easier than using the PSPP code in any case. > > > Seems that it is easier to save as Excel files and using read.xls and if active pearl is not available open Excel and save as .csv file ... or using 8 character variable identifier Knut __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Authors@R: and Author field
Hi to all
Authors@R: c(person("fooa","foob", role = c("aut","cre"),
email = "fooa.f...@fooc.de"),
person("foo1","foo2", role = c("ctb"),
email = "foo1.f...@foo3.de"))
Author: fooa foob, with contributions from foo1 foo2
using r CMD check --as-cran .. (R 3.1 and Windows) I get an error
Author field differs from that derived from Authors@R
Author:'fooa foob, with contributions from foo1 foo2
Authors@R: 'fooa foob [aut, cre], foo1 foo2 [ctb]'
as I can see it is the same as in
http://cran.r-project.org/doc/manuals/R-exts.html#The-DESCRIPTION-file
and additionally
> Both 'Author' and 'Maintainer' fields can be omitted if a suitable
'Authors@R' field is given.
is not working if the Author field is empty or missing it will give an
error
Kind regards Knut
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[Rd] checking dependencies in R code ... WARNING
I am trying to update an unsupported package and got the warning: * checking dependencies in R code ... WARNING 'library' or 'require' calls not declared from: 'Hmisc' 'R2HTML' 'tcltk' Missing or unexported object: 'utils::.win32consoleCompletion' See the information on DESCRIPTION files in the chapter 'Creating R packages' of the 'Writing R Extensions' manual. Is it only an error in the description file or in the code? Regards Knut __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] checking dependencies in R code ... WARNING
Am 08.05.2014 08:35, schrieb Tobias Verbeke: Hi Knut, The code will contain library or require statements, which do not belong there, but need to replaced by specifying the dependencies on these packages in the DESCRIPTION file (Depends / Imports field). For imports you also need to make sure the NAMESPACE file contains the intended statements. See http://cran.r-project.org/doc/manuals/R-exts.html#Package-Dependencies Best, Tobias Hi Tobias, if I am right it should be a code from the utils package # Use the internal win32consoleCompletion function in utils package res <- utils:::.win32consoleCompletion(code, nchar(code)) IMPORT field ... Namespaces accessed by the ‘::’ and ‘:::’ operators must be listed here, DESCRIPTION Imports: utils, foo, ... it is included NAMESAPCE: import(utils, foo, ) could it be another problem? I found: Using foo:::f instead of foo::f allows access to unexported objects. This is generally not recommended, as the semantics of unexported objects may be changed by the package author in routine maintenance. Best Knut __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] checking dependencies in R code ... WARNING
Am 08.05.2014 09:34, schrieb Tobias Verbeke: Hi Knut, I was primarily referring to the issues reported on the line Hi Tobias, ok the warning is a little bit misleading, it was an additional use of require(foo) of the import packages in NAMESPACE and DESCRIPTION do you have a hint for this to change the line res <- utils:::.win32consoleCompletion(code, nchar(code)) so that the issue of the warning will be solved? * checking dependencies in R code ... WARNING Unexported object imported by a ':::' call: 'utils:::.win32consoleCompletion' See the note in ?`:::` about the use of this operator. Including base/recommended package(s): 'utils' Best Knut __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] legitimate use of :::
Is there another new solution for this issue?
especially I would like to use:
utils:::.win32consoleCompletion
the use of this is suggested in the completion.r file of utils:
## test some typical completion attempts
library(utils)
testLine <- function(line, cursor = nchar(line))
{
str(utils:::.win32consoleCompletion(line, cursor))
}
testLine("")
(full quote because of the age of the tread)
Kind regards Knut
Am 22.08.2013 20:57, schrieb Michael Friendly:
On 8/22/2013 7:45 AM, Uwe Ligges wrote:
On 22.08.2013 07:45, Yihui Xie wrote:
Hi,
So now R CMD check starts to warn against :::, but I believe sometimes
it is legitimate to use it when developing R packages. For example, I
have some utils functions that are not exported but I want to share
them across the packages that I maintain. I do not need to coordinate
with other authors about these internal functions since I'm the only
author and I know clearly what I'm doing, and I want to avoid copying
and pasting the code across packages just to avoid the NOTE in R CMD
check. What should I do in this case?
Nothing. The way you describe above seems to be a reasonable usage, iff
you are the same maintainer who knows what is going on. Other
maintainers should not use one of your not exported (hence non API)
functions, of course.
Uwe Ligges
Related to this is the use of other-package unexported utility functions
that don't pass Uwe's iff test, but I, as maintainer,
want to use in my package.
Cases in point: in heplots, I had used stats:::Pillai, stats:::Wilks,
stats:::Roy and stats:::LH for calculation in one of my functions.
Similarly, I had a need to use car:::df.terms, also unexported, but
don't want to ask John Fox to export it just for my use. Uwe's
reply suggests that I should not be using car:::df.terms, however.
To avoid the NOTEs (which often triggers a 'pls fix' upon submission to
CRAN), I simply copied/pasted these functions to my package, but this
seems wasteful.
-Michael
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Re: [Rd] legitimate use of :::
Am 14.05.2014 08:56, schrieb Deepayan Sarkar: On Wed, May 14, 2014 at 12:29 AM, Duncan Murdoch wrote: I think you are misunderstanding the comments in that file. It's an internal set of tests for the package, so "test some typical completion attempts" is a description of the tests that follow, it's not a suggestion that you should be able to run those lines from your package. If you do want access to the completion mechanism from a package, you should write to its author (Deepayan Sarkar) and explain the kinds of things you need to do. If you can convince him that giving you access is worth the trouble of exposing some of it to user-level code, then he'll export a function for you. (I think it's unlikely to be .win32consoleCompletion, but who knows.) Yes, .win32consoleCompletion() was meant for use by the Windows GUI, but I can see a use-case for something similar elsewhere (for example, ESS defines something analogous). But I don't immediately see why another R package should need this. If you have a legitimate use, we can discuss off-list and come up with a solution. As TinnR was used at the University I tried to update the TinnR package because it was removed from cran http://cran.rstudio.com/web/packages/TinnR/index.html I think they used the win32consoleCompletion to connect Tinnr (Windows) with R - I do not really know the reason. Actually I found that R-Studio is much better for R-beginner and available for all platforms. Thanks for your hints - but I will not solve this problem anymore Knut __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Line breaks in rd files
How can I add a new line in an rd file f.e between references? Knut __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] install.packages from own rpository - depencies
I am trying to setup a respository for students with a own package.
Its working fine when the depended packages are already installed with:
install.packages("mypackage",
type="source",repos="http://myrepository.example.com";)
but if the the dependencies are not already installed I get the
following error:
ERROR: dependencies 'igraph', 'chron', 'gdata' are not available for
package 'mypackage'
* removing 'C:/.../mypackage'
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[Rd] Latex errors (build on windows)
Where can I found hepl about latex errors:
the R CMD check tells me less, but:
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
* checking PDF version of manual without hyperrefs or index ... ERROR
Re-running with no redirection of stdout/stderr.
Hmm ... looks like a package
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
pdflatex is not available
Error in running tools::texi2pdf()
The http://win-builder.r-project.org tells me more details but I am
comlpetely lost
especially.:
LaTeX errors found:
! Paragraph ended before \hyper@n@rmalise was complete.
\par
l.575 \end
{ExampleCode}
! You can't use `macro parameter character #' in horizontal mode.
...1,1,1,-1),stringsAsFactors=FALSE) ##
## comment text in the
examples ...
l.575 \end
{ExampleCode}
! Missing $ inserted.
$
l.575 \end
Knut
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Re: [Rd] Latex errors (build on windows)
Am 03.05.2013 09:58, schrieb R. Michael Weylandt: Can you post the offending package? http://rrepository.konstanze-krueger.de/src/contrib/Dominance_0.9.5.tar.gz Knut __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Latex errors (build on windows)
Am 03.05.2013 13:03, schrieb Duncan Murdoch: You should install MikTeX, from www.miktex.org. I think it will put itself on your path, but if it does not, you need to make sure the miktex/bin directory is on your path. Thank you, it worked first with a strange error message: File ended while scanning use of \Rhref. there was a % in the DOI path of an URL Knut __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Latex errors (build on windows)
Am 03.05.2013 09:58, schrieb R. Michael Weylandt: Can you post the offending package? I solved the problem all is fine now, thanks __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Latex errors (build on windows)
Percent signs are comment markers in .Rd files, so if you want to keep one, you need to escape it by preceding it with a backslash. I know but it was a copy and paste error ... I fixed it just in this way. Duncan Murdoch by the way, what's the next step to get the files on an mirror .. if anybody is interested in that stuff? Knut __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] submiting a package [was]Latex errors (build on windows)
Am 03.05.2013 16:05, schrieb Duncan Murdoch: On 03/05/2013 9:35 AM, Knut Krueger wrote: > Percent signs are comment markers in .Rd files, so if you want to keep > one, you need to escape it by preceding it with a backslash. > I know but it was a copy and paste error ... I fixed it just in this way. > Duncan Murdoch > by the way, what's the next step to get the files on an mirror .. if anybody is interested in that stuff? There are several different systems that distribute packages. The main one is CRAN. Their policies and upload instructions are here: http://cran.r-project.org/web/packages/policies.html You might instead want to submit to Bioconductor, R-forge, Rforge, etc. I don't know where is the best for that the package is building an ADI (Average Dominance index) building a special sociogramm with igraph, and building a Musicnotation graph http://dx.doi.org/10.1186%2F1742-9994-3-18 all three things are for calculating dominance hierarchies in animals. Knut __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
