Has anyone come across any alternatives to rJava and JRI? Are they any good? Better perhaps? Please give your reasons. Thanks, Danish - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This message is intended only for the personal and confidential use of the designated recipient(s) named above. If you are not the intended recipient of this message you are hereby notified that any review, dissemination, distribution or copying of this message is strictly prohibited. This communication is for information purposes only and should not be regarded as an offer to sell or as a solicitation of an offer to buy any financial product, an official confirmation of any transaction, or as an official statement of Lehman Brothers. Email transmission cannot be guaranteed to be secure or error-free. Therefore, we do not represent that this information is complete or accurate and it should not be relied upon as such. All information is subject to change without notice. -------- IRS Circular 230 Disclosure: Please be advised that any discussion of U.S. tax matters contained within this communication (including any attachments) is not intended or written to be used and cannot be used for the purpose of (i) avoiding U.S. tax related penalties or (ii) promoting, marketing or recommending to another party any transaction or matter addressed herein.
I do not know if this is "better" as we are just starting to look into it (and "better" is in the eye of the beholder) but look at: http://tolstoy.newcastle.edu.au/R/e3/help/07/11/4253.html in the archives. The link to the software is http://www.ebi.ac.uk/ microarray-srv/frontendapp/ HTH, -Roy M. On May 22, 2008, at 12:50 PM, Munir, Danish wrote:> > Has anyone come across any alternatives to rJava and JRI? Are they any > good? Better perhaps? > > Please give your reasons. > > Thanks, > Danish > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > - - - - - - - - - - > > This message is intended only for the personal and confidential use > of the designated recipient(s) named above. If you are not the > intended recipient of this message you are hereby notified that any > review, dissemination, distribution or copying of this message is > strictly prohibited. This communication is for information > purposes only and should not be regarded as an offer to sell or as > a solicitation of an offer to buy any financial product, an > official confirmation of any transaction, or as an official > statement of Lehman Brothers. Email transmission cannot be > guaranteed to be secure or error-free. Therefore, we do not > represent that this information is complete or accurate and it > should not be relied upon as such. All information is subject to > change without notice. > > -------- > IRS Circular 230 Disclosure: > Please be advised that any discussion of U.S. tax matters contained > within this communication (including any attachments) is not > intended or written to be used and cannot be used for the purpose > of (i) avoiding U.S. tax related penalties or (ii) promoting, > marketing or recommending to another party any transaction or > matter addressed herein. > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting- > guide.html > and provide commented, minimal, self-contained, reproducible code.********************** "The contents of this message do not reflect any position of the U.S. Government or NOAA." ********************** Roy Mendelssohn Supervisory Operations Research Analyst NOAA/NMFS Environmental Research Division Southwest Fisheries Science Center 1352 Lighthouse Avenue Pacific Grove, CA 93950-2097 e-mail: Roy.Mendelssohn at noaa.gov (Note new e-mail address) voice: (831)-648-9029 fax: (831)-648-8440 www: http://www.pfeg.noaa.gov/ "Old age and treachery will overcome youth and skill."
There's SJava, http://www.omegahat.org/RSJava. On Thu, May 22, 2008 at 12:50 PM, Munir, Danish <danish.munir@lehman.com> wrote:> > Has anyone come across any alternatives to rJava and JRI? Are they any > good? Better perhaps? > > Please give your reasons. > > Thanks, > Danish > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > - - - - - - > > This message is intended only for the personal and confidential use of the > designated recipient(s) named above. If you are not the intended recipient > of this message you are hereby notified that any review, dissemination, > distribution or copying of this message is strictly prohibited. This > communication is for information purposes only and should not be regarded as > an offer to sell or as a solicitation of an offer to buy any financial > product, an official confirmation of any transaction, or as an official > statement of Lehman Brothers. Email transmission cannot be guaranteed to be > secure or error-free. Therefore, we do not represent that this information > is complete or accurate and it should not be relied upon as such. All > information is subject to change without notice. > > -------- > IRS Circular 230 Disclosure: > Please be advised that any discussion of U.S. tax matters contained within > this communication (including any attachments) is not intended or written to > be used and cannot be used for the purpose of (i) avoiding U.S. tax related > penalties or (ii) promoting, marketing or recommending to another party any > transaction or matter addressed herein. > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >[[alternative HTML version deleted]]
Although this is an update of the same code base, RServe is nice and has newer objects that one may use. For example, the exception handling has been improved and now there is a external server ability. Before you give up on JRI look into the newer code, it might be more useful. http://www.rforge.net/Rserve/ On Thu, May 22, 2008 at 3:50 PM, Munir, Danish <danish.munir@lehman.com> wrote:> > Has anyone come across any alternatives to rJava and JRI? Are they any > good? Better perhaps? > > Please give your reasons. > > Thanks, > Danish > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > - - - - - - > > This message is intended only for the personal and confidential use of the > designated recipient(s) named above. If you are not the intended recipient > of this message you are hereby notified that any review, dissemination, > distribution or copying of this message is strictly prohibited. This > communication is for information purposes only and should not be regarded as > an offer to sell or as a solicitation of an offer to buy any financial > product, an official confirmation of any transaction, or as an official > statement of Lehman Brothers. Email transmission cannot be guaranteed to be > secure or error-free. Therefore, we do not represent that this information > is complete or accurate and it should not be relied upon as such. All > information is subject to change without notice. > > -------- > IRS Circular 230 Disclosure: > Please be advised that any discussion of U.S. tax matters contained within > this communication (including any attachments) is not intended or written to > be used and cannot be used for the purpose of (i) avoiding U.S. tax related > penalties or (ii) promoting, marketing or recommending to another party any > transaction or matter addressed herein. > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >[[alternative HTML version deleted]]
Roy Mendelssohn wrote:> I do not know if this is "better" as we are just starting to look into > it (and "better" is in the eye of the beholder) but look at: > > http://tolstoy.newcastle.edu.au/R/e3/help/07/11/4253.html > > in the archives. The link to the software is > http://www.ebi.ac.uk/microarray-srv/frontendapp/The new website (with all current information) is at http://www.biocep.net It is still very actively developed and there will be a tutorial at useR!2008 as well as a presentation. Cf. http://www.statistik.uni-dortmund.de/useR-2008//tutorials/chine.html HTH, Tobias> > HTH, > > -Roy M. > > On May 22, 2008, at 12:50 PM, Munir, Danish wrote: > >> >> Has anyone come across any alternatives to rJava and JRI? Are they any >> good? Better perhaps? >> >> Please give your reasons. >> >> Thanks, >> Danish >> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - >> - - - - - - - - - >> >> This message is intended only for the personal and confidential use of >> the designated recipient(s) named above. If you are not the intended >> recipient of this message you are hereby notified that any review, >> dissemination, distribution or copying of this message is strictly >> prohibited. This communication is for information purposes only and >> should not be regarded as an offer to sell or as a solicitation of an >> offer to buy any financial product, an official confirmation of any >> transaction, or as an official statement of Lehman Brothers. Email >> transmission cannot be guaranteed to be secure or error-free. >> Therefore, we do not represent that this information is complete or >> accurate and it should not be relied upon as such. All information is >> subject to change without notice. >> >> -------- >> IRS Circular 230 Disclosure: >> Please be advised that any discussion of U.S. tax matters contained >> within this communication (including any attachments) is not intended >> or written to be used and cannot be used for the purpose of (i) >> avoiding U.S. tax related penalties or (ii) promoting, marketing or >> recommending to another party any transaction or matter addressed herein. >> >> ______________________________________________ >> R-help at r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. > > ********************** > "The contents of this message do not reflect any position of the U.S. > Government or NOAA." > ********************** > Roy Mendelssohn > Supervisory Operations Research Analyst > NOAA/NMFS > Environmental Research Division > Southwest Fisheries Science Center > 1352 Lighthouse Avenue > Pacific Grove, CA 93950-2097 > > e-mail: Roy.Mendelssohn at noaa.gov (Note new e-mail address) > voice: (831)-648-9029 > fax: (831)-648-8440 > www: http://www.pfeg.noaa.gov/ > > "Old age and treachery will overcome youth and skill." > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > >
Thanks a lot everyone. These seem like very useful resources. I will check all of these out, and hopefully provide feedback so others can benefit too. -----Original Message----- From: Tobias Verbeke [mailto:tobias.verbeke at telenet.be] Sent: Friday, May 23, 2008 1:03 PM To: Roy Mendelssohn Cc: Munir, Danish; r-help at r-project.org Subject: Re: [R] Alternatives to rJava and JRI Roy Mendelssohn wrote:> I do not know if this is "better" as we are just starting to look into> it (and "better" is in the eye of the beholder) but look at: > > http://tolstoy.newcastle.edu.au/R/e3/help/07/11/4253.html > > in the archives. The link to the software is > http://www.ebi.ac.uk/microarray-srv/frontendapp/The new website (with all current information) is at http://www.biocep.net It is still very actively developed and there will be a tutorial at useR!2008 as well as a presentation. Cf. http://www.statistik.uni-dortmund.de/useR-2008//tutorials/chine.html HTH, Tobias> > HTH, > > -Roy M. > > On May 22, 2008, at 12:50 PM, Munir, Danish wrote: > >> >> Has anyone come across any alternatives to rJava and JRI? Are theyany>> good? Better perhaps? >> >> Please give your reasons. >> >> Thanks, >> Danish >> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ->> - - - - - - - - - >> >> This message is intended only for the personal and confidential useof>> the designated recipient(s) named above. If you are not the intended>> recipient of this message you are hereby notified that any review, >> dissemination, distribution or copying of this message is strictly >> prohibited. This communication is for information purposes only and >> should not be regarded as an offer to sell or as a solicitation of an>> offer to buy any financial product, an official confirmation of any >> transaction, or as an official statement of Lehman Brothers. Email >> transmission cannot be guaranteed to be secure or error-free. >> Therefore, we do not represent that this information is complete or >> accurate and it should not be relied upon as such. All informationis>> subject to change without notice. >> >> -------- >> IRS Circular 230 Disclosure: >> Please be advised that any discussion of U.S. tax matters contained >> within this communication (including any attachments) is not intended>> or written to be used and cannot be used for the purpose of (i) >> avoiding U.S. tax related penalties or (ii) promoting, marketing or >> recommending to another party any transaction or matter addressedherein.>> >> ______________________________________________ >> R-help at r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. > > ********************** > "The contents of this message do not reflect any position of the U.S. > Government or NOAA." > ********************** > Roy Mendelssohn > Supervisory Operations Research Analyst > NOAA/NMFS > Environmental Research Division > Southwest Fisheries Science Center > 1352 Lighthouse Avenue > Pacific Grove, CA 93950-2097 > > e-mail: Roy.Mendelssohn at noaa.gov (Note new e-mail address) > voice: (831)-648-9029 > fax: (831)-648-8440 > www: http://www.pfeg.noaa.gov/ > > "Old age and treachery will overcome youth and skill." > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > >- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This message is intended only for the personal and confidential use of the designated recipient(s) named above. If you are not the intended recipient of this message you are hereby notified that any review, dissemination, distribution or copying of this message is strictly prohibited. This communication is for information purposes only and should not be regarded as an offer to sell or as a solicitation of an offer to buy any financial product, an official confirmation of any transaction, or as an official statement of Lehman Brothers. Email transmission cannot be guaranteed to be secure or error-free. Therefore, we do not represent that this information is complete or accurate and it should not be relied upon as such. All information is subject to change without notice. -------- IRS Circular 230 Disclosure: Please be advised that any discussion of U.S. tax matters contained within this communication (including any attachments) is not intended or written to be used and cannot be used for the purpose of (i) avoiding U.S. tax related penalties or (ii) promoting, marketing or recommending to another party any transaction or matter addressed herein.
I'm having some issues with getting my own jars to work properly with rJava. Bear with me as I explain my scenario: I have a java package called rjbridge, with the following classes: RJBridge.class ObjectInfo.class .... .... Each of the classes has the following line on top: package com.rjbridge My directory structure is: /home/Danish/java/com/rjbridge All the class files lie in the above directory I use the following commands to compile and jar: cd /home/Danish/java javac -d . ./com/rjbridge/*.java jar -cvf rjbridge.jar ./com/rjbridge So far, so good. Everything works as it should, and I can use the RJBridge class as follows: java -cp /home/Danish/java/rjbridge.jar RJBridge [args] and it runs fine. Now in R, when I try the following:>library(rJava) >.jinit() >.jaddClassPath("/home/Danish/java/rjbridge.jar") > r<-.jnew("ObjectInfo")I get, Exception in thread "main" java.lang.ClassNotFoundException at RJavaClassLoader.findClass(RJavaClassLoader.java:195) at java.lang.ClassLoader.loadClass(ClassLoader.java:306) at java.lang.ClassLoader.loadClass(ClassLoader.java:251) at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:319) at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:242) Error in .jnew("ObjectInfo") : Failed to create object of class `ObjectInfo' In addition: Warning message: createObject.FindClass ObjectInfo failed in: .jnew("ObjectInfo") Trying:> r<-.jnew("rjbridge.ObjectInfo")Gives the following: Exception in thread "main" java.lang.ClassNotFoundException at RJavaClassLoader.findClass(RJavaClassLoader.java:195) at java.lang.ClassLoader.loadClass(ClassLoader.java:306) at java.lang.ClassLoader.loadClass(ClassLoader.java:251) at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:319) at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:242) Error in .jnew("rjbridge.ObjectInfo") : Failed to create object of class `rjbridge/ObjectInfo' I've spent a lot of time trying this in a number of different ways, but to no avail. Will some kind soul help me out here? Thanks Danish - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This message is intended only for the personal and confidential use of the designated recipient(s) named above. If you are not the intended recipient of this message you are hereby notified that any review, dissemination, distribution or copying of this message is strictly prohibited. This communication is for information purposes only and should not be regarded as an offer to sell or as a solicitation of an offer to buy any financial product, an official confirmation of any transaction, or as an official statement of Lehman Brothers. Email transmission cannot be guaranteed to be secure or error-free. Therefore, we do not represent that this information is complete or accurate and it should not be relied upon as such. All information is subject to change without notice. -------- IRS Circular 230 Disclosure: Please be advised that any discussion of U.S. tax matters contained within this communication (including any attachments) is not intended or written to be used and cannot be used for the purpose of (i) avoiding U.S. tax related penalties or (ii) promoting, marketing or recommending to another party any transaction or matter addressed herein.