Re: [Rd] typos in src/main/gram.y (PR#8780)
* On Wed 07:19AM, 19 Apr 2006, Prof Brian Ripley ([EMAIL PROTECTED]) wrote: > By `documentation' do you mean `comments in the file'? If so, this is too > minor to change whilst R 2.3.0 is in code freeze, but has been changed for > R-devel. Yes, I am referring to the comments in the file src/main/gram.y. I agree that these are very minor errors. I have checked out R-devel and I see that the changes have been made (as you said). Thank you! > [ snipped ] Best, Hsiu-Khuern Tang HP Labs __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] commercial software selling a R module - question about GPL license rights
Hello all, Sorry for this email not directly related to R developement. I just come from a nice demonstration session from Scitegic about their Pipeline Pilot (PP) software, and especially their 'R collection' which brings R calculations into the software (http://www.scitegic.com/documents/RStats_Collection.pdf). I looked carefully on the way they do it: they pass data from PP to R using text files, they call R.exe using a R script and input - output files, like: R.exe --nosave --no-environ --no-resore-data < script.R > output.txt And in the script, you have: read.table(...) which imports the data just exported from PP in an CVS file by the component. I don't want to discuss here the ugly and extremely inefficient solution they use to call R on their data, but anyway... So far, so good, they respect the GPL license since R is not embedded into PP, and you have to download and install it separately. But they also provide a series of "R component" ready to use like 'R ANOVA', 'R PCA', R Neural Net', etc... which are basically R scripts with replaceable variables (replacement is done by PP before feeding the script to the R engine). For instance, you will have: parameter <- $(PPvariable) in the R script. In the PP component, you have an option to specify the value of 'PPvariable', let's say: PPvariable = 10, and the replacement done in the R script is: parameter <- 10 before to feed this script to R. So, everything appears transparent to the end-user who parameterizes the scripts from within the PP GUI. That is what they call "each component generates an R script on-the-fly"... (sic!) However, I was suprised to learn that the Pipeline Pilot R Collection is not GPL and is not free (in term of money, i.e., you have to pay 3500$/year to use it). I am not sure, but I think they break the GPL license here since they use a commercial license for, basically, a collection of R scripts embedded in their 'PP components'. Anyone with better expertise than me could look at this, please? Best, Philippe Grosjean -- ..<°}))>< ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Belgium ( ( ( ( ( .. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Probable Numeric Bugs in svd function (PR#8781)
Hello,=0D =0D I just noticed that the "svd" function does not work properly for some=0D sparse matrices.=0D When I replace the 0 by very small noises (let's say 10^-16), it then=0D works.=0D The test I've performed is to compared the singular values to the eigen=0D values (as I work with squarred matrices).=0D =0D Here is the code (I may be wrong!):=0D =0D usHigh<-(Sp5>=3D300 & Region=3D=3D1)=0D usLow<-(Sp5<300 & Region=3D=3D1)=0D euHigh<-(Sp5>=3D200 & Region=3D=3D2)=0D euLow<-(Sp5<200 & Region=3D=3D2)=0D sigmas<-c(13.71,162.71,8.78,103.83,5.29,77.08,3.42,41.04)=0D temp1<-sigmas[1]*usLow+sigmas[2]*usHigh+sigmas[5]*euLow+sigmas[6]*euHigh=0D temp10<-sigmas[3]*usLow+sigmas[4]*usHigh+sigmas[7]*euLow+sigmas[8]*euHig=0D h=0D CorrEU<-0.89=0D CorrUS<-0.82=0D =0D CorrR<-matrix(0,2*SN.nb,2*SN.nb)=0D diag(CorrR)<-c(temp1^2,temp10^2)=0D =0D temp<-ifelse(Region=3D=3D1,CorrUS,CorrEU)=0D tempMat<-matrix(0,SN.nb,SN.nb)=0D diag(tempMat)<-temp*temp1*temp10=0D CorrR[(SN.nb+1):(2*SN.nb),1:SN.nb]<-tempMat=0D CorrR[1:SN.nb,(SN.nb+1):(2*SN.nb)]<-tempMat=0D =0D CorrR is positive definite but "svd" returns negative singular values!=0D When replacing 0s by very week noises, the error disppears.=0D =0D Hope I'm not saying stupid things.=0D =0D Rgds,=0D =0D Mehdi=0D =0D =0D =0D =0D =0D =0D -=0D The information contained in this e-mail message, and any=0D attachment thereto, is confidential and may not be disclosed=0D without our express permission. If you are not the intended=0D recipient or an employee or agent responsible for delivering this=0D message to the intended recipient, you are hereby notified that you=0D have received this message in error and that any review,=0D dissemination, distribution or copying of this message, or any=0D attachment thereto, in whole or in part, is strictly prohibited. If=0D you have received this message in error, please immediately notify=0D us by telephone, fax or e-mail and delete the message and all of=0D its attachments. Thank you. Every effort is made to keep our=0D network free from viruses. You should, however, review this e-mail=0D message, as well as any attachment thereto, for viruses. We take no=0D responsibility and have no liability for any computer virus which=0D may be transferred via this e-mail message.=0D [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] commercial software selling a R module - question about GPL license rights
I was under the impression that PP communicates with R via SOAP, but what do I know... If I didn't read your description wrong, the "R Collection" contains PP code (PilotScript?) for generating R code to be run by R, but does not include R itself. If that's the case, I don't think it has any licensing problem. If I write some R code that generates SAS code (God forbid), I doubt that constitute violation of SAS license. Just my $0.02... Andy From: Philippe Grosjean > > Hello all, > > Sorry for this email not directly related to R developement. > I just come > from a nice demonstration session from Scitegic about their Pipeline > Pilot (PP) software, and especially their 'R collection' > which brings R > calculations into the software > (http://www.scitegic.com/documents/RStats_Collection.pdf). > > I looked carefully on the way they do it: they pass data from PP to R > using text files, they call R.exe using a R script and input - output > files, like: > > R.exe --nosave --no-environ --no-resore-data < script.R > output.txt > > And in the script, you have: > > read.table(...) > > which imports the data just exported from PP in an CVS file by the > component. I don't want to discuss here the ugly and extremely > inefficient solution they use to call R on their data, but anyway... > > So far, so good, they respect the GPL license since R is not embedded > into PP, and you have to download and install it separately. > > But they also provide a series of "R component" ready to use like 'R > ANOVA', 'R PCA', R Neural Net', etc... which are basically R scripts > with replaceable variables (replacement is done by PP before > feeding the > script to the R engine). For instance, you will have: > > parameter <- $(PPvariable) > > in the R script. In the PP component, you have an option to > specify the > value of 'PPvariable', let's say: PPvariable = 10, and the > replacement > done in the R script is: > > parameter <- 10 > > before to feed this script to R. So, everything appears > transparent to > the end-user who parameterizes the scripts from within the PP > GUI. That > is what they call "each component generates an R script > on-the-fly"... > (sic!) > > However, I was suprised to learn that the Pipeline Pilot R > Collection is > not GPL and is not free (in term of money, i.e., you have to pay > 3500$/year to use it). I am not sure, but I think they break the GPL > license here since they use a commercial license for, basically, a > collection of R scripts embedded in their 'PP components'. > > Anyone with better expertise than me could look at this, please? > > Best, > > Philippe Grosjean > > -- > ..<°}))>< > ) ) ) ) ) > ( ( ( ( (Prof. Philippe Grosjean > ) ) ) ) ) > ( ( ( ( (Numerical Ecology of Aquatic Systems > ) ) ) ) ) Mons-Hainaut University, Belgium > ( ( ( ( ( > .. > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > > __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Wishlist for promptPackage / index
On 4/19/2006 1:49 AM, Duncan Murdoch wrote: >On 4/18/2006 7:02 PM, Peter Ruckdeschel wrote: >> would it be possible to enhance either promptPackage() >> or the default indexing mechanism for packages >> so that -- if it exists -- (the contents of) file >> -package.Rd is sorted first in >> >> * the .dvi / .pdf documentation file >> * the .chm documentation file >> * the package 00index.html documentation file >They already sort first in the last of those. I don't think it is >really possible in the index of a .chm file; they are alphabetical >sorting only, as far as I know. (The package topic does sort first in >the main contents page, which is the same as the 00index.html file.) Yes, you are right: the first two cases are already settled in a completely satisfying way [even with "+","-"-type methods!]. Sorry to have stirred you up --- I should have tried first. >It probably makes sense in a .dvi/.pdf, I tried out with an example now: at least for this case my request still applies ... >but as far as I recall, at the time I thought those were produced >by the shell script for Rd2dvi, and it just seemed like too much trouble >to change the collation order there. >In fact, now I look closer I see they are produced by the Perl >script tools/pkg2tex.pl so it shouldn't be hard to port the changes I >made to Rdlists.pm over. I'll take a look. would be very nice; thank you very much Peter __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] commercial software selling a R module - question about GPL license rights
Philippe Grosjean <[EMAIL PROTECTED]> writes: > Hello all, > > Sorry for this email not directly related to R developement. I just come > from a nice demonstration session from Scitegic about their Pipeline > Pilot (PP) software, and especially their 'R collection' which brings R > calculations into the software > (http://www.scitegic.com/documents/RStats_Collection.pdf). > > I looked carefully on the way they do it: they pass data from PP to R > using text files, they call R.exe using a R script and input - output > files, like: > > R.exe --nosave --no-environ --no-resore-data < script.R > output.txt > > And in the script, you have: > > read.table(...) > > which imports the data just exported from PP in an CVS file by the > component. I don't want to discuss here the ugly and extremely > inefficient solution they use to call R on their data, but anyway... > > So far, so good, they respect the GPL license since R is not embedded > into PP, and you have to download and install it separately. > > But they also provide a series of "R component" ready to use like 'R > ANOVA', 'R PCA', R Neural Net', etc... which are basically R scripts > with replaceable variables (replacement is done by PP before feeding the > script to the R engine). For instance, you will have: > > parameter <- $(PPvariable) > > in the R script. In the PP component, you have an option to specify the > value of 'PPvariable', let's say: PPvariable = 10, and the replacement > done in the R script is: > > parameter <- 10 > > before to feed this script to R. So, everything appears transparent to > the end-user who parameterizes the scripts from within the PP GUI. That > is what they call "each component generates an R script on-the-fly"... > (sic!) > > However, I was suprised to learn that the Pipeline Pilot R Collection is > not GPL and is not free (in term of money, i.e., you have to pay > 3500$/year to use it). I am not sure, but I think they break the GPL > license here since they use a commercial license for, basically, a > collection of R scripts embedded in their 'PP components'. > > Anyone with better expertise than me could look at this, please? Offhand, I don't think this is a problem. We've discussed a few similar cases. Things are sometimes slightly murky due to the FSF's unclear (or undecided) definition of the relation between "linking" and "derived work". However, it was never the intention that GPL code could not be _used_ by non-free software. That point might get clearer if you substitute mySql or a similar database instead of R. There are some limitations though. In particular if the connection is so tight that R has become an integrated part of the application, then the rules for derived works may apply. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] commercial software selling a R module - question about GPL license rights
Oh, yes! There is also a RSoap interface. I did not mention it.
Best,
Philippe Grosjean
Liaw, Andy wrote:
> I was under the impression that PP communicates with R via SOAP, but
> what do I know...
>
> If I didn't read your description wrong, the "R Collection" contains
> PP code (PilotScript?) for generating R code to be run by R, but does
> not include R itself. If that's the case, I don't think it has any
> licensing problem. If I write some R code that generates SAS code
> (God forbid), I doubt that constitute violation of SAS license.
>
> Just my $0.02...
>
> Andy
>
> From: Philippe Grosjean
>
>>Hello all,
>>
>>Sorry for this email not directly related to R developement.
>>I just come
>>from a nice demonstration session from Scitegic about their Pipeline
>>Pilot (PP) software, and especially their 'R collection'
>>which brings R
>>calculations into the software
>>(http://www.scitegic.com/documents/RStats_Collection.pdf).
>>
>>I looked carefully on the way they do it: they pass data from PP to R
>>using text files, they call R.exe using a R script and input - output
>>files, like:
>>
>>R.exe --nosave --no-environ --no-resore-data < script.R > output.txt
>>
>>And in the script, you have:
>>
>>read.table(...)
>>
>>which imports the data just exported from PP in an CVS file by the
>>component. I don't want to discuss here the ugly and extremely
>>inefficient solution they use to call R on their data, but anyway...
>>
>>So far, so good, they respect the GPL license since R is not embedded
>>into PP, and you have to download and install it separately.
>>
>>But they also provide a series of "R component" ready to use like 'R
>>ANOVA', 'R PCA', R Neural Net', etc... which are basically R scripts
>>with replaceable variables (replacement is done by PP before
>>feeding the
>>script to the R engine). For instance, you will have:
>>
>>parameter <- $(PPvariable)
>>
>>in the R script. In the PP component, you have an option to
>>specify the
>>value of 'PPvariable', let's say: PPvariable = 10, and the
>>replacement
>>done in the R script is:
>>
>>parameter <- 10
>>
>>before to feed this script to R. So, everything appears
>>transparent to
>>the end-user who parameterizes the scripts from within the PP
>>GUI. That
>>is what they call "each component generates an R script
>>on-the-fly"...
>>(sic!)
>>
>>However, I was suprised to learn that the Pipeline Pilot R
>>Collection is
>>not GPL and is not free (in term of money, i.e., you have to pay
>>3500$/year to use it). I am not sure, but I think they break the GPL
>>license here since they use a commercial license for, basically, a
>>collection of R scripts embedded in their 'PP components'.
>>
>>Anyone with better expertise than me could look at this, please?
>>
>>Best,
>>
>>Philippe Grosjean
>>
>>--
>>..<°}))><
>> ) ) ) ) )
>>( ( ( ( (Prof. Philippe Grosjean
>> ) ) ) ) )
>>( ( ( ( (Numerical Ecology of Aquatic Systems
>> ) ) ) ) ) Mons-Hainaut University, Belgium
>>( ( ( ( (
>>..
>>
>>__
>>R-devel@r-project.org mailing list
>>https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>
>
>
>
> --
> Notice: This e-mail message, together with any attachment...{{dropped}}
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] `as.vector' documentation
Hi, people. This is R 2.2.1 under i686 Linux: > attributes(as.vector(data.frame(a=1))) $names [1] "a" $row.names [1] "1" $class [1] "data.frame" ?attribute says: 'as.vector', a generic, attempts to coerce its argument into a vector of mode 'mode' (the default is to coerce to whichever mode is most convenient). The attributes of 'x' are removed. The last sentence could be amended to say that the attributes of 'x' are removed "if the coercion succeeds". As currently written, it may be interpreted as meaning that the attributes are removed unconditionally. -- François Pinard http://pinard.progiciels-bpi.ca __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] commercial software selling a R module - question about GPL license rights
I understand that it is difficult to make the distinction between "linking" and "derived work". Whatever the conclusion, I always feel a little bit abused when someone wants to "sell" me R somehow (here, you have to pay 3500$/year to use R inside of Pipeline Pilot). I would accept to pay this money if I was in front of R experts that sell me their expertise, indeed. But this is not the case: they don't know much about R, and they made a really ugly and inefficient interface between PP and R that is not worth those 3500$/year. Best, Philippe Grosjean Peter Dalgaard wrote: > Philippe Grosjean <[EMAIL PROTECTED]> writes: > > >>Hello all, >> >>Sorry for this email not directly related to R developement. I just come >>from a nice demonstration session from Scitegic about their Pipeline >>Pilot (PP) software, and especially their 'R collection' which brings R >>calculations into the software >>(http://www.scitegic.com/documents/RStats_Collection.pdf). >> >>I looked carefully on the way they do it: they pass data from PP to R >>using text files, they call R.exe using a R script and input - output >>files, like: >> >>R.exe --nosave --no-environ --no-resore-data < script.R > output.txt >> >>And in the script, you have: >> >>read.table(...) >> >>which imports the data just exported from PP in an CVS file by the >>component. I don't want to discuss here the ugly and extremely >>inefficient solution they use to call R on their data, but anyway... >> >>So far, so good, they respect the GPL license since R is not embedded >>into PP, and you have to download and install it separately. >> >>But they also provide a series of "R component" ready to use like 'R >>ANOVA', 'R PCA', R Neural Net', etc... which are basically R scripts >>with replaceable variables (replacement is done by PP before feeding the >>script to the R engine). For instance, you will have: >> >>parameter <- $(PPvariable) >> >>in the R script. In the PP component, you have an option to specify the >>value of 'PPvariable', let's say: PPvariable = 10, and the replacement >>done in the R script is: >> >>parameter <- 10 >> >>before to feed this script to R. So, everything appears transparent to >>the end-user who parameterizes the scripts from within the PP GUI. That >>is what they call "each component generates an R script on-the-fly"... >>(sic!) >> >>However, I was suprised to learn that the Pipeline Pilot R Collection is >>not GPL and is not free (in term of money, i.e., you have to pay >>3500$/year to use it). I am not sure, but I think they break the GPL >>license here since they use a commercial license for, basically, a >>collection of R scripts embedded in their 'PP components'. >> >>Anyone with better expertise than me could look at this, please? > > > Offhand, I don't think this is a problem. > > We've discussed a few similar cases. Things are sometimes slightly > murky due to the FSF's unclear (or undecided) definition of the > relation between "linking" and "derived work". However, it was never > the intention that GPL code could not be _used_ by non-free software. > That point might get clearer if you substitute mySql or a similar > database instead of R. > > There are some limitations though. In particular if the connection is > so tight that R has become an integrated part of the application, then > the rules for derived works may apply. > __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Wishlist: 'quietly' argument for .onAttach() / .First.lib()
Dear Seth, thank you very much for your helpful comments: >I had a quick look and for what it's worth, a few comments... > >* Seems a bit more code than I would expect. Arguable, yes... > I think you have some use cases that I don't have ;-). hopefully I'm not the only one to have these cases :-) > In terms of general use, I would suggest making a stab at a > simplified version. I have tried to do something in that direction: * files startUpMessage.R / StartupUtilities.Rd now gather the code addressing a more general audience; (?"startupmsg") * files illustration.R / myStartupUtilities.Rd [ with mySMHandler, mystartupMessage, buildStartupMessage ] (?"mySMHandler") may be thought of an illustration of the concept (and hence should not enter general packages, I suppose) the revised code is available again under http://www.uni-bayreuth.de/departments/math/org/mathe7/R-devel/startupmsg_0.2.tar.gz > For example, what's the difference between startupMessage and > startupVersionMessage; are both needed? I guessed so: the idea is to have more than one type of StartupMessage, and suppressing should be done according to the type; I have rethought this now: instead of two (or more) subclasses of StartupMessage, I now have endowed class StartupMessage with an extra slot type, which currently is supposed to take one of the tree values + "version": version and title information from the DESCRIPTION file + "notabene": "nota bene"s on the package to be given at this prominent place + "information": (starting) pointers for more information on the package: -howto call the package help file, -howto inspect the NEWS file, -additional manuals/vignettes -URLs (but the code already supports arbitrarily many type values) > And linestarter? I agree: this should better be dealt with in a more general/flexible way by allowing + the developper using 'startupMessages' to use his own SMHandler (for /S/tartup/M/essage/Handler/) as illustrated in 'mystartupMessages' + the user of a package with 'startupMessages' to specify a suitable custom restart (see examples in ?"startupmsg") --- is achieved using your code example >* Consider adding a customizable restart. As it stands, startupmsg > doesn't give a user more control than message(). Now it does; I admit, I should have integrated your proposed elegant code right from the beginning. > That is, you can either muffle the messages or not. If I want to write > them to a file or prefix them with funny characters, doing so by grabbing > hold of the message before it is emitted via the restart seems like a > nice approach (although one could argue for a more general system > logging system that probably would not need the fancy condition > system use). Thank you again Peter __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] commercial software selling a R module - question about GPL license rights
But its value to you and whether or not you would pay for it is a completely separate matter from whether or not they are violating the R license by selling their R collection. I imagine a discussion of the latter is on-topic for this list, less so for the former, I'd imagine. Cyrus On Apr 19, 2006, at 11:45 AM, Philippe Grosjean wrote: > I understand that it is difficult to make the distinction between > "linking" and "derived work". Whatever the conclusion, I always feel a > little bit abused when someone wants to "sell" me R somehow (here, you > have to pay 3500$/year to use R inside of Pipeline Pilot). I would > accept to pay this money if I was in front of R experts that sell me > their expertise, indeed. But this is not the case: they don't know > much > about R, and they made a really ugly and inefficient interface between > PP and R that is not worth those 3500$/year. > > Best, > > Philippe Grosjean > > Peter Dalgaard wrote: >> Philippe Grosjean <[EMAIL PROTECTED]> writes: >> >> >>> Hello all, >>> >>> Sorry for this email not directly related to R developement. I >>> just come >>> from a nice demonstration session from Scitegic about their Pipeline >>> Pilot (PP) software, and especially their 'R collection' which >>> brings R >>> calculations into the software >>> (http://www.scitegic.com/documents/RStats_Collection.pdf). >>> >>> I looked carefully on the way they do it: they pass data from PP >>> to R >>> using text files, they call R.exe using a R script and input - >>> output >>> files, like: >>> >>> R.exe --nosave --no-environ --no-resore-data < script.R > output.txt >>> >>> And in the script, you have: >>> >>> read.table(...) >>> >>> which imports the data just exported from PP in an CVS file by the >>> component. I don't want to discuss here the ugly and extremely >>> inefficient solution they use to call R on their data, but anyway... >>> >>> So far, so good, they respect the GPL license since R is not >>> embedded >>> into PP, and you have to download and install it separately. >>> >>> But they also provide a series of "R component" ready to use like 'R >>> ANOVA', 'R PCA', R Neural Net', etc... which are basically R scripts >>> with replaceable variables (replacement is done by PP before >>> feeding the >>> script to the R engine). For instance, you will have: >>> >>> parameter <- $(PPvariable) >>> >>> in the R script. In the PP component, you have an option to >>> specify the >>> value of 'PPvariable', let's say: PPvariable = 10, and the >>> replacement >>> done in the R script is: >>> >>> parameter <- 10 >>> >>> before to feed this script to R. So, everything appears >>> transparent to >>> the end-user who parameterizes the scripts from within the PP >>> GUI. That >>> is what they call "each component generates an R script on-the- >>> fly"... >>> (sic!) >>> >>> However, I was suprised to learn that the Pipeline Pilot R >>> Collection is >>> not GPL and is not free (in term of money, i.e., you have to pay >>> 3500$/year to use it). I am not sure, but I think they break the GPL >>> license here since they use a commercial license for, basically, a >>> collection of R scripts embedded in their 'PP components'. >>> >>> Anyone with better expertise than me could look at this, please? >> >> >> Offhand, I don't think this is a problem. >> >> We've discussed a few similar cases. Things are sometimes slightly >> murky due to the FSF's unclear (or undecided) definition of the >> relation between "linking" and "derived work". However, it was never >> the intention that GPL code could not be _used_ by non-free software. >> That point might get clearer if you substitute mySql or a similar >> database instead of R. >> >> There are some limitations though. In particular if the connection is >> so tight that R has become an integrated part of the application, >> then >> the rules for derived works may apply. >> > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] gsummary function (nlme library) (PR#8782)
Full_Name: Ben Saville Version: 2.1 OS: Windows XP Submission from: (NULL) (152.2.94.145) I'm using the gsummary function to calculate a sum of V1 (column one) from my data 'mytest' by group (V2,or column 2). If V1 (the variable of interest) is all the same value (in this case all 2's), I do not get back the correct summation. If there is at least one difference in V1 (all 2's except for one 1), it gives me correct values. So either I am doing something wrong or there is a bug in the gsummary function. # Incorrect sums mytest <- as.data.frame(matrix(c(2,rep(2,8),1,1,2,2,2,3,3,3,3),ncol=2)) mytest gsummary(mytest,form=V1~1|V2, FUN=sum)[,1] # Correct sums mytest <- as.data.frame(matrix(c(1,rep(2,8),1,1,2,2,2,3,3,3,3),ncol=2)) mytest gsummary(mytest,form=V1~1|V2, FUN=sum)[,1] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] AIX libjpeg still looms
Simon,
Did you get a chance to review your AIX configuration? I'd be
curious to know the differences with my own as while I have R installed,
I still get the error related to libjpeg.a.
Error in get(getOption("device"))() : X11 module cannot be loaded
In addition: Warning message:
unable to load shared library '/usr/local/R/lib/R/modules/R_X11.so':
Could not load module /usr/local/R/lib/R/modules/R_X11.so.
Dependent module /usr/java14/jre/bin/libjpeg.a(libjpeg.so.62)
could not be loaded.
File /usr/java14/jre/bin/libjpeg.a is not an
archive or the file could not be read properly.
System error: Exec format error
System error: Exec format error
Could not load module /usr/java14/jre/bin/libjpeg.a.
Dependent module /usr/java14/jre/bin/libjpeg.a could not be
loaded.
Another user had suggested re-compiling the jpeg library based
on the "Running Linux Applications on AIX" redbook. However, I haven't
had any luck with that as of yet.
Matthew Beason
Analyst - Capacity Planning
Harrah's Entertainment, Inc.
One Harrah's Court, Las Vegas, NV 89119-4312
Office: 702-494-4097
Mobile: 702-622-6902
[EMAIL PROTECTED]
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Re: [Rd] AIX libjpeg still looms
Hi.
If I remove a java-related pass from PATH before configure and build
it, I am successful.
try
# Cut Java Path . java library(libjpeg...etc.) probrem.
export PATH=`echo $PATH|tr ':' '\n'|sed -e '/^.*java.*$/d'|tr '\n' ':'`
./configure options...
make
For a point to confirm.
dump -H modules/R_X11.so
JAVA-related PATH should not be included in here.
my environment `/opt/freeware/lib/libjpeg.a' used.
2006/4/20, Matthew Beason <[EMAIL PROTECTED]>:
> Simon,
>
> Did you get a chance to review your AIX configuration? I'd be
> curious to know the differences with my own as while I have R installed,
> I still get the error related to libjpeg.a.
>
> Error in get(getOption("device"))() : X11 module cannot be loaded
> In addition: Warning message:
> unable to load shared library '/usr/local/R/lib/R/modules/R_X11.so':
> Could not load module /usr/local/R/lib/R/modules/R_X11.so.
> Dependent module /usr/java14/jre/bin/libjpeg.a(libjpeg.so.62)
> could not be loaded.
> File /usr/java14/jre/bin/libjpeg.a is not an
> archive or the file could not be read properly.
> System error: Exec format error
> System error: Exec format error
> Could not load module /usr/java14/jre/bin/libjpeg.a.
> Dependent module /usr/java14/jre/bin/libjpeg.a could not be
> loaded.
>
> Another user had suggested re-compiling the jpeg library based
> on the "Running Linux Applications on AIX" redbook. However, I haven't
> had any luck with that as of yet.
>
> Matthew Beason
> Analyst - Capacity Planning
> Harrah's Entertainment, Inc.
> One Harrah's Court, Las Vegas, NV 89119-4312
> Office: 702-494-4097
> Mobile: 702-622-6902
> [EMAIL PROTECTED]
> The information contained in this email may be legally privileged and
> confidential. It is intended to be read only by the person to whom it is
> addressed. If you have received this in error or are not the intended
> recipient, please immediately notify the sender and delete all copies of
> this message. Thank you.
>
>
>
> [[alternative HTML version deleted]]
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
--
EI-JI Nakama <[EMAIL PROTECTED]>
"\u4e2d\u9593\u6804\u6cbb" <[EMAIL PROTECTED]>
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Re: [Rd] UTF8 letters are imaged incorrectly (PR#8770)
Thanks to Ei-ji Nakama's hints, I was able to confirm that on FC3 Linux: 1) in locale ru_RU.koi8r Russian letters are rendered correctly if I use "-cronyx-helvetica-%s-%s-*--%d-*-*-*-*-*-*-*" as the first element of option "X11fonts". 2) This does not work in locale ru_RU.utf8, and the reason is that there is no XLC_LOCALE locale directory. Adding a suitably configured directory made this work. 3) There _is_ an XLC_LOCALE locale directory ja_JA.utf8, and I was able to get Japanese text to display by using "-*-mincho-%s-%s-*--%d-*-*-*-*-*-*-*" as the first element of option "X11fonts". Systems which have suitable .ttf fonts installed may work with the default setting. I've added some notes on 1) and 3) to ?X11. Thanks Ei-ji! Brian Ripley On Sat, 15 Apr 2006, Ei-ji Nakama wrote: > This was not a bug. > > 2006/4/15, Mike Bocharov <[EMAIL PROTECTED]>: >> It work, thanks for your help! >> >>> If an error is not given by a locale command, I think that local >>> setting of glibc does not have any problem. >>> I think that there is not problem if add encoding of koi8-r to >>> XLC_LOCALE file. >>> >>> I am not readable, but probably the following URL is useful. >>> http://ru.gentoo-wiki.com/HOWTO_ru_RU.utf8_Gentoo_way >> > > > -- > EI-JI Nakama <[EMAIL PROTECTED]> > "\u4e2d\u9593\u6804\u6cbb" <[EMAIL PROTECTED]> > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > > -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Probable Numeric Bugs in svd function (PR#8781)
This is unreadable, but getting as far as the first couple of lines it seems to be unreproducible (what are Sp5 and Region?). You have also not told us the version of R, platform, and crucial details such as what BLAS was used. Can you please use the web interface to R-bugs to add (use this PR in the subject line) a complete, readable and reproducible example? On Wed, 19 Apr 2006, [EMAIL PROTECTED] wrote: > Hello,=0D > =0D > I just noticed that the "svd" function does not work properly for some=0D > sparse matrices.=0D > When I replace the 0 by very small noises (let's say 10^-16), it then=0D > works.=0D > The test I've performed is to compared the singular values to the eigen=0D > values (as I work with squarred matrices).=0D > =0D > Here is the code (I may be wrong!):=0D > =0D > usHigh<-(Sp5>=3D300 & Region=3D=3D1)=0D > usLow<-(Sp5<300 & Region=3D=3D1)=0D > euHigh<-(Sp5>=3D200 & Region=3D=3D2)=0D > euLow<-(Sp5<200 & Region=3D=3D2)=0D > sigmas<-c(13.71,162.71,8.78,103.83,5.29,77.08,3.42,41.04)=0D > temp1<-sigmas[1]*usLow+sigmas[2]*usHigh+sigmas[5]*euLow+sigmas[6]*euHigh=0D > temp10<-sigmas[3]*usLow+sigmas[4]*usHigh+sigmas[7]*euLow+sigmas[8]*euHig=0D > h=0D > CorrEU<-0.89=0D > CorrUS<-0.82=0D > =0D > CorrR<-matrix(0,2*SN.nb,2*SN.nb)=0D > diag(CorrR)<-c(temp1^2,temp10^2)=0D > =0D > temp<-ifelse(Region=3D=3D1,CorrUS,CorrEU)=0D > tempMat<-matrix(0,SN.nb,SN.nb)=0D > diag(tempMat)<-temp*temp1*temp10=0D > CorrR[(SN.nb+1):(2*SN.nb),1:SN.nb]<-tempMat=0D > CorrR[1:SN.nb,(SN.nb+1):(2*SN.nb)]<-tempMat=0D > =0D > CorrR is positive definite but "svd" returns negative singular values!=0D > When replacing 0s by very week noises, the error disppears.=0D > =0D > Hope I'm not saying stupid things.=0D > =0D > Rgds,=0D > =0D > Mehdi=0D > =0D > =0D > =0D > =0D > =0D > =0D > -=0D > The information contained in this e-mail message, and any=0D > attachment thereto, is confidential and may not be disclosed=0D > without our express permission. If you are not the intended=0D > recipient or an employee or agent responsible for delivering this=0D > message to the intended recipient, you are hereby notified that you=0D > have received this message in error and that any review,=0D > dissemination, distribution or copying of this message, or any=0D > attachment thereto, in whole or in part, is strictly prohibited. If=0D > you have received this message in error, please immediately notify=0D > us by telephone, fax or e-mail and delete the message and all of=0D > its attachments. Thank you. Every effort is made to keep our=0D > network free from viruses. You should, however, review this e-mail=0D > message, as well as any attachment thereto, for viruses. We take no=0D > responsibility and have no liability for any computer virus which=0D > may be transferred via this e-mail message.=0D > > [[alternative HTML version deleted]] > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > > -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R CMD check: non source files in src on (2.3.0 RC (2006-04-19 r37860))
Hello, I am having an issue with R CMD check with the nightly build of RC 2.3.0 (listed in the subject.) The problem is this warning: * checking if this is a source package ... WARNING Subdirectory 'src' contains: README _Makefile These are unlikely file names for src files. In fact, they are not source files, but I do not see any reason why they cannot be there, or why I need to be warned of their presence. Potentially I could be informed of their presence, but that is another matter. Now, I only get this warning when I do: R CMD build affxparser R CMD check -l ~/R-packages/ affxparser_1.3.3.tar.gz If I do: R CMD check -l ~/R-packages affxparser I do not get the warning. Is this inconsistent, or is there rationale behind this? I think the warning is inappropriate, or at the least a little restrictive. It seems as if I should be able to put whatever I want in there, especially the _Makefile as I like to build test programs directly and I want to be able to build exactly what I check out from my source code repository without having to copy files in and out. The output from R CMD check is below. Any insight would be appreciated. As always thanks for your patience. jim Directly on directory * [EMAIL PROTECTED]:~/projects/bioc$ R CMD check -l ~/R-packages affxparser * checking for working latex ... OK * using log directory '/home/bullard/projects/bioc/affxparser.Rcheck' * using Version 2.3.0 RC (2006-04-19 r37860) * checking for file 'affxparser/DESCRIPTION' ... OK * this is package 'affxparser' version '1.3.3' * checking package dependencies ... OK * checking if this is a source package ... OK * checking whether package 'affxparser' can be installed ... OK * checking package directory ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for syntax errors ... OK * checking R files for library.dynam ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking Rd files ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking for CRLF line endings in C/C++/Fortran sources/headers ... OK * checking for portable compilation flags in Makevars ... OK * creating affxparser-Ex.R ... OK * checking examples ... OK * creating affxparser-manual.tex ... OK * checking affxparser-manual.tex ... OK *** On the R CMD build version * [EMAIL PROTECTED]:~/projects/bioc$ R CMD check -l ~/R-packages/ affxparser_1.3.3.tar.gz * checking for working latex ... OK * using log directory '/home/bullard/projects/bioc/affxparser.Rcheck' * using Version 2.3.0 RC (2006-04-19 r37860) * checking for file 'affxparser/DESCRIPTION' ... OK * this is package 'affxparser' version '1.3.3' * checking package dependencies ... OK * checking if this is a source package ... WARNING Subdirectory 'src' contains: README _Makefile These are unlikely file names for src files. * checking whether package 'affxparser' can be installed ... OK * checking package directory ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for syntax errors ... OK * checking R files for library.dynam ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking Rd files ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking for CRLF line endings in C/C++/Fortran sources/headers ... OK * checking for portable compilation flags in Makevars ... OK * creating affxparser-Ex.R ... OK * checking examples ... OK * creating affxparser-manual.tex ... OK * checking affxparser-manual.tex ... OK WARNING: There was 1 warning, see /home/bullard/projects/bioc/affxparser.Rcheck/00check.log for details __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD check: non source files in src on (2.3.0 RC (2006-04-19 r37860))
On Wed, 19 Apr 2006, James Bullard wrote: > Hello, I am having an issue with R CMD check with the nightly build of > RC 2.3.0 (listed in the subject.) This is all explained in TFM, `Writing R Extensions'. > The problem is this warning: > > * checking if this is a source package ... WARNING > Subdirectory 'src' contains: > README _Makefile > These are unlikely file names for src files. > > In fact, they are not source files, but I do not see any reason why they > cannot be there, or why I need to be warned of their presence. > Potentially I could be informed of their presence, but that is another > matter. Having unnecessary files in other people's packages just waste space and download bandwidth for each one of the users. > Now, I only get this warning when I do: > > R CMD build affxparser > R CMD check -l ~/R-packages/ affxparser_1.3.3.tar.gz > > If I do: > > R CMD check -l ~/R-packages affxparser > > I do not get the warning. Is this inconsistent, or is there rationale > behind this? I think the warning is inappropriate, or at the least a > little restrictive. It seems as if I should be able to put whatever I > want in there, especially the _Makefile as I like to build test programs > directly and I want to be able to build exactly what I check out from > my source code repository without having to copy files in and out. All described in TFM, including how to set defaults for what is checked. > The output from R CMD check is below. Any insight would be appreciated. > As always thanks for your patience. [...] -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
