From kammon101 at hotmail.ca Tue Nov 11 01:31:02 2014 From: kammon101 at hotmail.ca (kam kammon) Date: Mon, 10 Nov 2014 19:31:02 -0500 Subject: [Rcppoctave-user] Error in installing RcppOctave Message-ID: Hello, I am trying to install RcppOctave with install.packages('RccpOctave') with error "Error : /tmp/Rtmp6wKMIT/R.INSTALL3be86221bf01/RcppOctave/man/o_addpath.Rd:40: .onLoad failed in loadNamespace() for 'RcppOctave', details: call: lapply(X = X, FUN = FUN, ...) error: object 'dlibs' not found" My R version is 3.1.2, Octave version 3.8.2, OS Ubuntu 14.04 64 bit. I am including the full installation log for reference. Thanks, Bernard -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: RcppOctave Type: application/octet-stream Size: 6332 bytes Desc: not available URL: From edd at debian.org Tue Nov 11 01:54:21 2014 From: edd at debian.org (Dirk Eddelbuettel) Date: Mon, 10 Nov 2014 18:54:21 -0600 Subject: [Rcppoctave-user] Error in installing RcppOctave In-Reply-To: References: Message-ID: <21601.24125.468681.428666@max.nulle.part> On 10 November 2014 at 19:31, kam kammon wrote: | Hello, | | I am trying to install RcppOctave with install.packages('RccpOctave') with | error | | "Error : /tmp/Rtmp6wKMIT/R.INSTALL3be86221bf01/RcppOctave/man/o_addpath.Rd:40: | .onLoad failed in loadNamespace() for 'RcppOctave', details: | call: lapply(X = X, FUN = FUN, ...) | error: object 'dlibs' not found" | | My R version is 3.1.2, Octave version 3.8.2, OS Ubuntu 14.04 64 bit. We need more details. I just installed it again on an identical system (Ubuntu 14.04, amd64) at work today. I think the attachment didn't make it. Dirk | I am including the full installation log for reference. | | Thanks, | | Bernard | [DELETED ATTACHMENT RcppOctave, Untyped binary data] | _______________________________________________ | Rcppoctave-user mailing list | Rcppoctave-user at lists.r-forge.r-project.org | http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user -- http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org From kammon101 at hotmail.ca Tue Nov 11 02:14:21 2014 From: kammon101 at hotmail.ca (kam kammon) Date: Mon, 10 Nov 2014 20:14:21 -0500 Subject: [Rcppoctave-user] Error in installing RcppOctave In-Reply-To: <21601.24125.468681.428666@max.nulle.part> References: , <21601.24125.468681.428666@max.nulle.part> Message-ID: Hi, I am attaching the log again. Hope it makes it this time. Thanks > Date: Mon, 10 Nov 2014 18:54:21 -0600 > To: kammon101 at hotmail.ca > CC: rcppoctave-user at lists.r-forge.r-project.org > Subject: Re: [Rcppoctave-user] Error in installing RcppOctave > From: edd at debian.org > > > On 10 November 2014 at 19:31, kam kammon wrote: > | Hello, > | > | I am trying to install RcppOctave with install.packages('RccpOctave') with > | error > | > | "Error : /tmp/Rtmp6wKMIT/R.INSTALL3be86221bf01/RcppOctave/man/o_addpath.Rd:40: > | .onLoad failed in loadNamespace() for 'RcppOctave', details: > | call: lapply(X = X, FUN = FUN, ...) > | error: object 'dlibs' not found" > | > | My R version is 3.1.2, Octave version 3.8.2, OS Ubuntu 14.04 64 bit. > > We need more details. I just installed it again on an identical system > (Ubuntu 14.04, amd64) at work today. > > I think the attachment didn't make it. > > Dirk > > | I am including the full installation log for reference. > | > | Thanks, > | > | Bernard > | [DELETED ATTACHMENT RcppOctave, Untyped binary data] > | _______________________________________________ > | Rcppoctave-user mailing list > | Rcppoctave-user at lists.r-forge.r-project.org > | http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user > > -- > http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: RcppOctave Type: application/octet-stream Size: 6332 bytes Desc: not available URL: From edd at debian.org Tue Nov 11 02:51:43 2014 From: edd at debian.org (Dirk Eddelbuettel) Date: Mon, 10 Nov 2014 19:51:43 -0600 Subject: [Rcppoctave-user] Error in installing RcppOctave In-Reply-To: References: <21601.24125.468681.428666@max.nulle.part> Message-ID: <21601.27567.941695.684294@max.nulle.part> That's uninformative. As I said, works on my box ... Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org From kammon101 at hotmail.ca Tue Nov 11 03:27:16 2014 From: kammon101 at hotmail.ca (kam kammon) Date: Mon, 10 Nov 2014 21:27:16 -0500 Subject: [Rcppoctave-user] Error in installing RcppOctave In-Reply-To: <21601.27567.941695.684294@max.nulle.part> References: , <21601.24125.468681.428666@max.nulle.part>, , <21601.27567.941695.684294@max.nulle.part> Message-ID: I am not sure what info you will need then. What is the meaning of "error: object 'dlibs' not found"? That seems to be the issue. Bernard > Date: Mon, 10 Nov 2014 19:51:43 -0600 > To: kammon101 at hotmail.ca > CC: edd at debian.org; rcppoctave-user at lists.r-forge.r-project.org > Subject: RE: [Rcppoctave-user] Error in installing RcppOctave > From: edd at debian.org > > > That's uninformative. As I said, works on my box ... > > Dirk > > -- > http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From kammon101 at hotmail.ca Tue Nov 11 06:33:40 2014 From: kammon101 at hotmail.ca (kam kammon) Date: Tue, 11 Nov 2014 00:33:40 -0500 Subject: [Rcppoctave-user] Error in installing RcppOctave In-Reply-To: References: , , <21601.24125.468681.428666@max.nulle.part>, , , , <21601.27567.941695.684294@max.nulle.part>, Message-ID: Hi, there are two additional things that may be relevant. First Octave 3.8.2 was compiled from source and I have used a patch from http://octave.1599824.n4.nabble.com/Octave-3-8-1-Released-td4662831.html (post by Michael Godfrey August 18, 2014) to enable jit. Also I have compiled Octave with libhdf5-openmpi, this has caused a problem for RcppOctave in Ubuntu 13.10 (see mailing list from Feb 2014) but the problem has been fixed. Bernard From: kammon101 at hotmail.ca To: edd at debian.org Date: Mon, 10 Nov 2014 21:27:16 -0500 CC: rcppoctave-user at lists.r-forge.r-project.org Subject: Re: [Rcppoctave-user] Error in installing RcppOctave I am not sure what info you will need then. What is the meaning of "error: object 'dlibs' not found"? That seems to be the issue. Bernard > Date: Mon, 10 Nov 2014 19:51:43 -0600 > To: kammon101 at hotmail.ca > CC: edd at debian.org; rcppoctave-user at lists.r-forge.r-project.org > Subject: RE: [Rcppoctave-user] Error in installing RcppOctave > From: edd at debian.org > > > That's uninformative. As I said, works on my box ... > > Dirk > > -- > http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org _______________________________________________ Rcppoctave-user mailing list Rcppoctave-user at lists.r-forge.r-project.org http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user -------------- next part -------------- An HTML attachment was scrubbed... URL: From renaud at mancala.cbio.uct.ac.za Tue Nov 11 09:27:57 2014 From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux) Date: Tue, 11 Nov 2014 10:27:57 +0200 Subject: [Rcppoctave-user] Error in installing RcppOctave In-Reply-To: References: <21601.24125.468681.428666@max.nulle.part> <21601.27567.941695.684294@max.nulle.part> Message-ID: Hi Bernard, The error happens at loading time when rendering the man pages (which contain some calls to Octave functions). Which version of RcppOctave are you installing and how? And which R version are you running? I believe I fixed this error some time ago. Can you please try the latest develop version: devtools::install_github('renozao/RcppOctave', ref = 'develop') # and also if this still fails devtools::install_github('renozao/RcppOctave', ref = 'develop', quick = TRUE) Thanks. Bests, Renaud On 11 November 2014 07:33, kam kammon wrote: > Hi, there are two additional things that may be relevant. First Octave 3.8.2 > was compiled from source and I have used a patch from > http://octave.1599824.n4.nabble.com/Octave-3-8-1-Released-td4662831.html > (post by Michael Godfrey August 18, 2014) to enable jit. > > Also I have compiled Octave with libhdf5-openmpi, this has caused a problem > for RcppOctave in Ubuntu 13.10 (see mailing list from Feb 2014) but the > problem has been fixed. > > Bernard > > ________________________________ > From: kammon101 at hotmail.ca > To: edd at debian.org > Date: Mon, 10 Nov 2014 21:27:16 -0500 > CC: rcppoctave-user at lists.r-forge.r-project.org > Subject: Re: [Rcppoctave-user] Error in installing RcppOctave > > > I am not sure what info you will need then. > > What is the meaning of "error: object 'dlibs' not found"? That seems to be > the issue. > > Bernard > >> Date: Mon, 10 Nov 2014 19:51:43 -0600 >> To: kammon101 at hotmail.ca >> CC: edd at debian.org; rcppoctave-user at lists.r-forge.r-project.org >> Subject: RE: [Rcppoctave-user] Error in installing RcppOctave >> From: edd at debian.org >> >> >> That's uninformative. As I said, works on my box ... >> >> Dirk >> >> -- >> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org > > _______________________________________________ Rcppoctave-user mailing list > Rcppoctave-user at lists.r-forge.r-project.org > http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user > > _______________________________________________ > Rcppoctave-user mailing list > Rcppoctave-user at lists.r-forge.r-project.org > http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user > > > From kammon101 at hotmail.ca Tue Nov 11 09:45:57 2014 From: kammon101 at hotmail.ca (kam kammon) Date: Tue, 11 Nov 2014 03:45:57 -0500 Subject: [Rcppoctave-user] Error in installing RcppOctave In-Reply-To: References: , <21601.24125.468681.428666@max.nulle.part>, , <21601.27567.941695.684294@max.nulle.part>, , , Message-ID: Hi, Renaud, Thanks for the quick reply. I was installing RcppOctave in R with the command install.packages('RcppOctave'), it downloaded RcppOctave_0.14.5 from cran's mirror. R version 3.1.2 and Octave 3.8.2 (Octave was compiled from source myself) The developmental version does install! > Date: Tue, 11 Nov 2014 10:27:57 +0200 > Subject: Re: [Rcppoctave-user] Error in installing RcppOctave > From: renaud at mancala.cbio.uct.ac.za > To: kammon101 at hotmail.ca > CC: edd at debian.org; rcppoctave-user at lists.r-forge.r-project.org > > Hi Bernard, > > The error happens at loading time when rendering the man pages (which > contain some calls to Octave functions). > Which version of RcppOctave are you installing and how? And which R > version are you running? > > I believe I fixed this error some time ago. > Can you please try the latest develop version: > devtools::install_github('renozao/RcppOctave', ref = 'develop') > # and also if this still fails > devtools::install_github('renozao/RcppOctave', ref = 'develop', quick = TRUE) > > Thanks. > > Bests, > Renaud > > On 11 November 2014 07:33, kam kammon wrote: > > Hi, there are two additional things that may be relevant. First Octave 3.8.2 > > was compiled from source and I have used a patch from > > http://octave.1599824.n4.nabble.com/Octave-3-8-1-Released-td4662831.html > > (post by Michael Godfrey August 18, 2014) to enable jit. > > > > Also I have compiled Octave with libhdf5-openmpi, this has caused a problem > > for RcppOctave in Ubuntu 13.10 (see mailing list from Feb 2014) but the > > problem has been fixed. > > > > Bernard > > > > ________________________________ > > From: kammon101 at hotmail.ca > > To: edd at debian.org > > Date: Mon, 10 Nov 2014 21:27:16 -0500 > > CC: rcppoctave-user at lists.r-forge.r-project.org > > Subject: Re: [Rcppoctave-user] Error in installing RcppOctave > > > > > > I am not sure what info you will need then. > > > > What is the meaning of "error: object 'dlibs' not found"? That seems to be > > the issue. > > > > Bernard > > > >> Date: Mon, 10 Nov 2014 19:51:43 -0600 > >> To: kammon101 at hotmail.ca > >> CC: edd at debian.org; rcppoctave-user at lists.r-forge.r-project.org > >> Subject: RE: [Rcppoctave-user] Error in installing RcppOctave > >> From: edd at debian.org > >> > >> > >> That's uninformative. As I said, works on my box ... > >> > >> Dirk > >> > >> -- > >> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org > > > > _______________________________________________ Rcppoctave-user mailing list > > Rcppoctave-user at lists.r-forge.r-project.org > > http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user > > > > _______________________________________________ > > Rcppoctave-user mailing list > > Rcppoctave-user at lists.r-forge.r-project.org > > http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From renaud at mancala.cbio.uct.ac.za Tue Nov 11 16:41:10 2014 From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux) Date: Tue, 11 Nov 2014 17:41:10 +0200 Subject: [Rcppoctave-user] Error in installing RcppOctave In-Reply-To: References: <21601.24125.468681.428666@max.nulle.part> <21601.27567.941695.684294@max.nulle.part> Message-ID: Great. So I guess now is a good time for me to release that version to CRAN. Dirk, which version had installed fine on your machine, CRAN or Github (master/develop)? Thanks. Bests, Renaud On 11 November 2014 10:45, kam kammon wrote: > Hi, Renaud, > > Thanks for the quick reply. > > I was installing RcppOctave in R with the command > install.packages('RcppOctave'), it downloaded RcppOctave_0.14.5 from cran's > mirror. > > R version 3.1.2 and Octave 3.8.2 (Octave was compiled from source myself) > > The developmental version does install! > > > > >> Date: Tue, 11 Nov 2014 10:27:57 +0200 >> Subject: Re: [Rcppoctave-user] Error in installing RcppOctave >> From: renaud at mancala.cbio.uct.ac.za > >> To: kammon101 at hotmail.ca >> CC: edd at debian.org; rcppoctave-user at lists.r-forge.r-project.org >> >> Hi Bernard, >> >> The error happens at loading time when rendering the man pages (which >> contain some calls to Octave functions). >> Which version of RcppOctave are you installing and how? And which R >> version are you running? >> >> I believe I fixed this error some time ago. >> Can you please try the latest develop version: >> devtools::install_github('renozao/RcppOctave', ref = 'develop') >> # and also if this still fails >> devtools::install_github('renozao/RcppOctave', ref = 'develop', quick = >> TRUE) >> >> Thanks. >> >> Bests, >> Renaud >> >> On 11 November 2014 07:33, kam kammon wrote: >> > Hi, there are two additional things that may be relevant. First Octave >> > 3.8.2 >> > was compiled from source and I have used a patch from >> > http://octave.1599824.n4.nabble.com/Octave-3-8-1-Released-td4662831.html >> > (post by Michael Godfrey August 18, 2014) to enable jit. >> > >> > Also I have compiled Octave with libhdf5-openmpi, this has caused a >> > problem >> > for RcppOctave in Ubuntu 13.10 (see mailing list from Feb 2014) but the >> > problem has been fixed. >> > >> > Bernard >> > >> > ________________________________ >> > From: kammon101 at hotmail.ca >> > To: edd at debian.org >> > Date: Mon, 10 Nov 2014 21:27:16 -0500 >> > CC: rcppoctave-user at lists.r-forge.r-project.org >> > Subject: Re: [Rcppoctave-user] Error in installing RcppOctave >> > >> > >> > I am not sure what info you will need then. >> > >> > What is the meaning of "error: object 'dlibs' not found"? That seems to >> > be >> > the issue. >> > >> > Bernard >> > >> >> Date: Mon, 10 Nov 2014 19:51:43 -0600 >> >> To: kammon101 at hotmail.ca >> >> CC: edd at debian.org; rcppoctave-user at lists.r-forge.r-project.org >> >> Subject: RE: [Rcppoctave-user] Error in installing RcppOctave >> >> From: edd at debian.org >> >> >> >> >> >> That's uninformative. As I said, works on my box ... >> >> >> >> Dirk >> >> >> >> -- >> >> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org >> > >> > _______________________________________________ Rcppoctave-user mailing >> > list >> > Rcppoctave-user at lists.r-forge.r-project.org >> > >> > http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user >> > >> > _______________________________________________ >> > Rcppoctave-user mailing list >> > Rcppoctave-user at lists.r-forge.r-project.org >> > >> > http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user >> > >> > >> > From edd at debian.org Tue Nov 11 17:04:57 2014 From: edd at debian.org (Dirk Eddelbuettel) Date: Tue, 11 Nov 2014 10:04:57 -0600 Subject: [Rcppoctave-user] Error in installing RcppOctave In-Reply-To: References: <21601.24125.468681.428666@max.nulle.part> <21601.27567.941695.684294@max.nulle.part> Message-ID: <21602.13225.678357.283648@max.nulle.part> On 11 November 2014 at 17:41, Renaud Gaujoux wrote: | Great. | So I guess now is a good time for me to release that version to CRAN. | Dirk, which version had installed fine on your machine, CRAN or Github | (master/develop)? Almost surely just plain CRAN on several machines. Have not had issues in ages. But then I don't do unusual things like building with MPI, hdf5, or other local patches. Dirk | Thanks. | | Bests, | Renaud | | On 11 November 2014 10:45, kam kammon wrote: | > Hi, Renaud, | > | > Thanks for the quick reply. | > | > I was installing RcppOctave in R with the command | > install.packages('RcppOctave'), it downloaded RcppOctave_0.14.5 from cran's | > mirror. | > | > R version 3.1.2 and Octave 3.8.2 (Octave was compiled from source myself) | > | > The developmental version does install! | > | > | > | > | >> Date: Tue, 11 Nov 2014 10:27:57 +0200 | >> Subject: Re: [Rcppoctave-user] Error in installing RcppOctave | >> From: renaud at mancala.cbio.uct.ac.za | > | >> To: kammon101 at hotmail.ca | >> CC: edd at debian.org; rcppoctave-user at lists.r-forge.r-project.org | >> | >> Hi Bernard, | >> | >> The error happens at loading time when rendering the man pages (which | >> contain some calls to Octave functions). | >> Which version of RcppOctave are you installing and how? And which R | >> version are you running? | >> | >> I believe I fixed this error some time ago. | >> Can you please try the latest develop version: | >> devtools::install_github('renozao/RcppOctave', ref = 'develop') | >> # and also if this still fails | >> devtools::install_github('renozao/RcppOctave', ref = 'develop', quick = | >> TRUE) | >> | >> Thanks. | >> | >> Bests, | >> Renaud | >> | >> On 11 November 2014 07:33, kam kammon wrote: | >> > Hi, there are two additional things that may be relevant. First Octave | >> > 3.8.2 | >> > was compiled from source and I have used a patch from | >> > http://octave.1599824.n4.nabble.com/Octave-3-8-1-Released-td4662831.html | >> > (post by Michael Godfrey August 18, 2014) to enable jit. | >> > | >> > Also I have compiled Octave with libhdf5-openmpi, this has caused a | >> > problem | >> > for RcppOctave in Ubuntu 13.10 (see mailing list from Feb 2014) but the | >> > problem has been fixed. | >> > | >> > Bernard | >> > | >> > ________________________________ | >> > From: kammon101 at hotmail.ca | >> > To: edd at debian.org | >> > Date: Mon, 10 Nov 2014 21:27:16 -0500 | >> > CC: rcppoctave-user at lists.r-forge.r-project.org | >> > Subject: Re: [Rcppoctave-user] Error in installing RcppOctave | >> > | >> > | >> > I am not sure what info you will need then. | >> > | >> > What is the meaning of "error: object 'dlibs' not found"? That seems to | >> > be | >> > the issue. | >> > | >> > Bernard | >> > | >> >> Date: Mon, 10 Nov 2014 19:51:43 -0600 | >> >> To: kammon101 at hotmail.ca | >> >> CC: edd at debian.org; rcppoctave-user at lists.r-forge.r-project.org | >> >> Subject: RE: [Rcppoctave-user] Error in installing RcppOctave | >> >> From: edd at debian.org | >> >> | >> >> | >> >> That's uninformative. As I said, works on my box ... | >> >> | >> >> Dirk | >> >> | >> >> -- | >> >> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org | >> > | >> > _______________________________________________ Rcppoctave-user mailing | >> > list | >> > Rcppoctave-user at lists.r-forge.r-project.org | >> > | >> > http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user | >> > | >> > _______________________________________________ | >> > Rcppoctave-user mailing list | >> > Rcppoctave-user at lists.r-forge.r-project.org | >> > | >> > http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user | >> > | >> > | >> > | _______________________________________________ | Rcppoctave-user mailing list | Rcppoctave-user at lists.r-forge.r-project.org | http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user -- http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org From kammon101 at hotmail.ca Tue Nov 11 23:49:18 2014 From: kammon101 at hotmail.ca (kam kammon) Date: Tue, 11 Nov 2014 17:49:18 -0500 Subject: [Rcppoctave-user] Error in installing RcppOctave In-Reply-To: <21602.13225.678357.283648@max.nulle.part> References: , <21601.24125.468681.428666@max.nulle.part>, , <21601.27567.941695.684294@max.nulle.part>, , , , , , <21602.13225.678357.283648@max.nulle.part> Message-ID: Just did an experiment on a small test Ubuntu 14.04 installation on an external hd. Installed Octave 3.8.1 straight from the Ubuntu repository.If libhdf5-7 was installed, RcppOctave installed successfully, if instead libhdf5-openmpi-7 was installed (which removed libhdf5-7) then installing RcppOctave failed with error "/usr/include/H5public.h:63:20: fatal error: mpi.h: No such file or directory" Same result with both RccpOctave from cran and github. Deban/Ubuntu's Octave package is compiled with libhdf5 but without openmpi support. I think RcppOctave is sensitive to how hdf5 is compiled in octave and the cran version may have problems with hdf5 with mpi. Since Dirk built without hdf5 he didn't experience any issue. Thanks Renaud again! Bernard > Date: Tue, 11 Nov 2014 10:04:57 -0600 > To: renaud at mancala.cbio.uct.ac.za > CC: kammon101 at hotmail.ca; rcppoctave-user at lists.r-forge.r-project.org > Subject: Re: [Rcppoctave-user] Error in installing RcppOctave > From: edd at debian.org > > > On 11 November 2014 at 17:41, Renaud Gaujoux wrote: > | Great. > | So I guess now is a good time for me to release that version to CRAN. > | Dirk, which version had installed fine on your machine, CRAN or Github > | (master/develop)? > > Almost surely just plain CRAN on several machines. Have not had issues in ages. > > But then I don't do unusual things like building with MPI, hdf5, or other > local patches. > > Dirk > > > | Thanks. > | > | Bests, > | Renaud > | > | On 11 November 2014 10:45, kam kammon wrote: > | > Hi, Renaud, > | > > | > Thanks for the quick reply. > | > > | > I was installing RcppOctave in R with the command > | > install.packages('RcppOctave'), it downloaded RcppOctave_0.14.5 from cran's > | > mirror. > | > > | > R version 3.1.2 and Octave 3.8.2 (Octave was compiled from source myself) > | > > | > The developmental version does install! > | > > | > > | > > | > > | >> Date: Tue, 11 Nov 2014 10:27:57 +0200 > | >> Subject: Re: [Rcppoctave-user] Error in installing RcppOctave > | >> From: renaud at mancala.cbio.uct.ac.za > | > > | >> To: kammon101 at hotmail.ca > | >> CC: edd at debian.org; rcppoctave-user at lists.r-forge.r-project.org > | >> > | >> Hi Bernard, > | >> > | >> The error happens at loading time when rendering the man pages (which > | >> contain some calls to Octave functions). > | >> Which version of RcppOctave are you installing and how? And which R > | >> version are you running? > | >> > | >> I believe I fixed this error some time ago. > | >> Can you please try the latest develop version: > | >> devtools::install_github('renozao/RcppOctave', ref = 'develop') > | >> # and also if this still fails > | >> devtools::install_github('renozao/RcppOctave', ref = 'develop', quick = > | >> TRUE) > | >> > | >> Thanks. > | >> > | >> Bests, > | >> Renaud > | >> > | >> On 11 November 2014 07:33, kam kammon wrote: > | >> > Hi, there are two additional things that may be relevant. First Octave > | >> > 3.8.2 > | >> > was compiled from source and I have used a patch from > | >> > http://octave.1599824.n4.nabble.com/Octave-3-8-1-Released-td4662831.html > | >> > (post by Michael Godfrey August 18, 2014) to enable jit. > | >> > > | >> > Also I have compiled Octave with libhdf5-openmpi, this has caused a > | >> > problem > | >> > for RcppOctave in Ubuntu 13.10 (see mailing list from Feb 2014) but the > | >> > problem has been fixed. > | >> > > | >> > Bernard > | >> > > | >> > ________________________________ > | >> > From: kammon101 at hotmail.ca > | >> > To: edd at debian.org > | >> > Date: Mon, 10 Nov 2014 21:27:16 -0500 > | >> > CC: rcppoctave-user at lists.r-forge.r-project.org > | >> > Subject: Re: [Rcppoctave-user] Error in installing RcppOctave > | >> > > | >> > > | >> > I am not sure what info you will need then. > | >> > > | >> > What is the meaning of "error: object 'dlibs' not found"? That seems to > | >> > be > | >> > the issue. > | >> > > | >> > Bernard > | >> > > | >> >> Date: Mon, 10 Nov 2014 19:51:43 -0600 > | >> >> To: kammon101 at hotmail.ca > | >> >> CC: edd at debian.org; rcppoctave-user at lists.r-forge.r-project.org > | >> >> Subject: RE: [Rcppoctave-user] Error in installing RcppOctave > | >> >> From: edd at debian.org > | >> >> > | >> >> > | >> >> That's uninformative. As I said, works on my box ... > | >> >> > | >> >> Dirk > | >> >> > | >> >> -- > | >> >> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org > | >> > > | >> > _______________________________________________ Rcppoctave-user mailing > | >> > list > | >> > Rcppoctave-user at lists.r-forge.r-project.org > | >> > > | >> > http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user > | >> > > | >> > _______________________________________________ > | >> > Rcppoctave-user mailing list > | >> > Rcppoctave-user at lists.r-forge.r-project.org > | >> > > | >> > http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user > | >> > > | >> > > | >> > > | _______________________________________________ > | Rcppoctave-user mailing list > | Rcppoctave-user at lists.r-forge.r-project.org > | http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user > > -- > http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From renaud at mancala.cbio.uct.ac.za Wed Nov 12 08:25:30 2014 From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux) Date: Wed, 12 Nov 2014 09:25:30 +0200 Subject: [Rcppoctave-user] Error in installing RcppOctave In-Reply-To: References: <21601.24125.468681.428666@max.nulle.part> <21601.27567.941695.684294@max.nulle.part> <21602.13225.678357.283648@max.nulle.part> Message-ID: Can you please provide us with the install log of the failed installation, the one with mpi.h not found? Can you confirm: * Octave 3.8.1 from Ubuntu repo works. * Octave 3.8.2 locally compiled against libhdf5-openmpi-7 fails. * Octave 3.8.2 locally compiled against libhdf5-7 works (?) RcppOctave uses compilation flags given by mkoctfile, which in theory should fit each type of installation. I thought I had fixed this problem back then (http://lists.r-forge.r-project.org/pipermail/rcppoctave-user/2014-March/000097.html). Maybe I am not retrieving them correctly, or maybe there is a conflict between installations. Do you have both versions of Octave (mpi and non-mpi) installed when testing? It would help to see if you can effectively identify differences in octave compilation flags between the two versions (have a look at the variables in mkoctfile -h). Thanks. Renaud On 12 November 2014 00:49, kam kammon wrote: > Just did an experiment on a small test Ubuntu 14.04 installation on an > external hd. Installed Octave 3.8.1 straight from the Ubuntu repository.If > libhdf5-7 was installed, RcppOctave installed successfully, if instead > libhdf5-openmpi-7 was installed (which removed libhdf5-7) then installing > RcppOctave failed with error "/usr/include/H5public.h:63:20: fatal error: > mpi.h: No such file or directory" Same result with both RccpOctave from cran > and github. > > Deban/Ubuntu's Octave package is compiled with libhdf5 but without openmpi > support. > > I think RcppOctave is sensitive to how hdf5 is compiled in octave and the > cran version may have problems with hdf5 with mpi. Since Dirk built without > hdf5 he didn't experience any issue. > > Thanks Renaud again! > > Bernard > > > >> Date: Tue, 11 Nov 2014 10:04:57 -0600 >> To: renaud at mancala.cbio.uct.ac.za >> CC: kammon101 at hotmail.ca; rcppoctave-user at lists.r-forge.r-project.org >> Subject: Re: [Rcppoctave-user] Error in installing RcppOctave >> From: edd at debian.org > >> >> >> On 11 November 2014 at 17:41, Renaud Gaujoux wrote: >> | Great. >> | So I guess now is a good time for me to release that version to CRAN. >> | Dirk, which version had installed fine on your machine, CRAN or Github >> | (master/develop)? >> >> Almost surely just plain CRAN on several machines. Have not had issues in >> ages. >> >> But then I don't do unusual things like building with MPI, hdf5, or other >> local patches. >> >> Dirk >> >> >> | Thanks. >> | >> | Bests, >> | Renaud >> | >> | On 11 November 2014 10:45, kam kammon wrote: >> | > Hi, Renaud, >> | > >> | > Thanks for the quick reply. >> | > >> | > I was installing RcppOctave in R with the command >> | > install.packages('RcppOctave'), it downloaded RcppOctave_0.14.5 from >> cran's >> | > mirror. >> | > >> | > R version 3.1.2 and Octave 3.8.2 (Octave was compiled from source >> myself) >> | > >> | > The developmental version does install! >> | > >> | > >> | > >> | > >> | >> Date: Tue, 11 Nov 2014 10:27:57 +0200 >> | >> Subject: Re: [Rcppoctave-user] Error in installing RcppOctave >> | >> From: renaud at mancala.cbio.uct.ac.za >> | > >> | >> To: kammon101 at hotmail.ca >> | >> CC: edd at debian.org; rcppoctave-user at lists.r-forge.r-project.org >> | >> >> | >> Hi Bernard, >> | >> >> | >> The error happens at loading time when rendering the man pages (which >> | >> contain some calls to Octave functions). >> | >> Which version of RcppOctave are you installing and how? And which R >> | >> version are you running? >> | >> >> | >> I believe I fixed this error some time ago. >> | >> Can you please try the latest develop version: >> | >> devtools::install_github('renozao/RcppOctave', ref = 'develop') >> | >> # and also if this still fails >> | >> devtools::install_github('renozao/RcppOctave', ref = 'develop', quick >> = >> | >> TRUE) >> | >> >> | >> Thanks. >> | >> >> | >> Bests, >> | >> Renaud >> | >> >> | >> On 11 November 2014 07:33, kam kammon wrote: >> | >> > Hi, there are two additional things that may be relevant. First >> Octave >> | >> > 3.8.2 >> | >> > was compiled from source and I have used a patch from >> | >> > >> http://octave.1599824.n4.nabble.com/Octave-3-8-1-Released-td4662831.html >> | >> > (post by Michael Godfrey August 18, 2014) to enable jit. >> | >> > >> | >> > Also I have compiled Octave with libhdf5-openmpi, this has caused a >> | >> > problem >> | >> > for RcppOctave in Ubuntu 13.10 (see mailing list from Feb 2014) but >> the >> | >> > problem has been fixed. >> | >> > >> | >> > Bernard >> | >> > >> | >> > ________________________________ >> | >> > From: kammon101 at hotmail.ca >> | >> > To: edd at debian.org >> | >> > Date: Mon, 10 Nov 2014 21:27:16 -0500 >> | >> > CC: rcppoctave-user at lists.r-forge.r-project.org >> | >> > Subject: Re: [Rcppoctave-user] Error in installing RcppOctave >> | >> > >> | >> > >> | >> > I am not sure what info you will need then. >> | >> > >> | >> > What is the meaning of "error: object 'dlibs' not found"? That >> seems to >> | >> > be >> | >> > the issue. >> | >> > >> | >> > Bernard >> | >> > >> | >> >> Date: Mon, 10 Nov 2014 19:51:43 -0600 >> | >> >> To: kammon101 at hotmail.ca >> | >> >> CC: edd at debian.org; rcppoctave-user at lists.r-forge.r-project.org >> | >> >> Subject: RE: [Rcppoctave-user] Error in installing RcppOctave >> | >> >> From: edd at debian.org >> | >> >> >> | >> >> >> | >> >> That's uninformative. As I said, works on my box ... >> | >> >> >> | >> >> Dirk >> | >> >> >> | >> >> -- >> | >> >> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org >> | >> > >> | >> > _______________________________________________ Rcppoctave-user >> mailing >> | >> > list >> | >> > Rcppoctave-user at lists.r-forge.r-project.org >> | >> > >> | >> > >> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user >> | >> > >> | >> > _______________________________________________ >> | >> > Rcppoctave-user mailing list >> | >> > Rcppoctave-user at lists.r-forge.r-project.org >> | >> > >> | >> > >> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user >> | >> > >> | >> > >> | >> > >> | _______________________________________________ >> | Rcppoctave-user mailing list >> | Rcppoctave-user at lists.r-forge.r-project.org >> | >> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user >> >> -- >> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org From kammon101 at hotmail.ca Wed Nov 12 09:28:39 2014 From: kammon101 at hotmail.ca (kam kammon) Date: Wed, 12 Nov 2014 03:28:39 -0500 Subject: [Rcppoctave-user] Error in installing RcppOctave In-Reply-To: References: , <21601.24125.468681.428666@max.nulle.part>, , <21601.27567.941695.684294@max.nulle.part>, , , , , , <21602.13225.678357.283648@max.nulle.part>, , Message-ID: Hi, Renaud, The failed install where mpi not found was for octave 3.8.1 from Ubuntu's repo. I think that is just because Debian doesn't compile octave with mpi. It works after I removed libhdf5-openmpi-7 and replaced it with libhdf5-7.The log is attached here. Cran's version of RcppOctave fails on Octave 3.8.2 compiled with hdf5-openmpi-7, the log was attached in my first message of this thread. However the develop version works. I have not compiled Octave 3.8.2 with hdf5-7 so I can't confirm either way. Bernard > Date: Wed, 12 Nov 2014 09:25:30 +0200 > Subject: Re: [Rcppoctave-user] Error in installing RcppOctave > From: renaud at mancala.cbio.uct.ac.za > To: kammon101 at hotmail.ca > CC: edd at debian.org; renaud at mancala.cbio.uct.ac.za; rcppoctave-user at lists.r-forge.r-project.org > > Can you please provide us with the install log of the failed > installation, the one with mpi.h not found? > Can you confirm: > * Octave 3.8.1 from Ubuntu repo works. > * Octave 3.8.2 locally compiled against libhdf5-openmpi-7 fails. > * Octave 3.8.2 locally compiled against libhdf5-7 works (?) > > RcppOctave uses compilation flags given by mkoctfile, which in theory > should fit each type of installation. I thought I had fixed this > problem back then > (http://lists.r-forge.r-project.org/pipermail/rcppoctave-user/2014-March/000097.html). > Maybe I am not retrieving them correctly, or maybe there is a conflict > between installations. Do you have both versions of Octave (mpi and > non-mpi) installed when testing? > It would help to see if you can effectively identify differences in > octave compilation flags between the two versions (have a look at the > variables in mkoctfile -h). > Thanks. > > > Renaud > > On 12 November 2014 00:49, kam kammon wrote: > > Just did an experiment on a small test Ubuntu 14.04 installation on an > > external hd. Installed Octave 3.8.1 straight from the Ubuntu repository.If > > libhdf5-7 was installed, RcppOctave installed successfully, if instead > > libhdf5-openmpi-7 was installed (which removed libhdf5-7) then installing > > RcppOctave failed with error "/usr/include/H5public.h:63:20: fatal error: > > mpi.h: No such file or directory" Same result with both RccpOctave from cran > > and github. > > > > Deban/Ubuntu's Octave package is compiled with libhdf5 but without openmpi > > support. > > > > I think RcppOctave is sensitive to how hdf5 is compiled in octave and the > > cran version may have problems with hdf5 with mpi. Since Dirk built without > > hdf5 he didn't experience any issue. > > > > Thanks Renaud again! > > > > Bernard > > > > > > > >> Date: Tue, 11 Nov 2014 10:04:57 -0600 > >> To: renaud at mancala.cbio.uct.ac.za > >> CC: kammon101 at hotmail.ca; rcppoctave-user at lists.r-forge.r-project.org > >> Subject: Re: [Rcppoctave-user] Error in installing RcppOctave > >> From: edd at debian.org > > > >> > >> > >> On 11 November 2014 at 17:41, Renaud Gaujoux wrote: > >> | Great. > >> | So I guess now is a good time for me to release that version to CRAN. > >> | Dirk, which version had installed fine on your machine, CRAN or Github > >> | (master/develop)? > >> > >> Almost surely just plain CRAN on several machines. Have not had issues in > >> ages. > >> > >> But then I don't do unusual things like building with MPI, hdf5, or other > >> local patches. > >> > >> Dirk > >> > >> > >> | Thanks. > >> | > >> | Bests, > >> | Renaud > >> | > >> | On 11 November 2014 10:45, kam kammon wrote: > >> | > Hi, Renaud, > >> | > > >> | > Thanks for the quick reply. > >> | > > >> | > I was installing RcppOctave in R with the command > >> | > install.packages('RcppOctave'), it downloaded RcppOctave_0.14.5 from > >> cran's > >> | > mirror. > >> | > > >> | > R version 3.1.2 and Octave 3.8.2 (Octave was compiled from source > >> myself) > >> | > > >> | > The developmental version does install! > >> | > > >> | > > >> | > > >> | > > >> | >> Date: Tue, 11 Nov 2014 10:27:57 +0200 > >> | >> Subject: Re: [Rcppoctave-user] Error in installing RcppOctave > >> | >> From: renaud at mancala.cbio.uct.ac.za > >> | > > >> | >> To: kammon101 at hotmail.ca > >> | >> CC: edd at debian.org; rcppoctave-user at lists.r-forge.r-project.org > >> | >> > >> | >> Hi Bernard, > >> | >> > >> | >> The error happens at loading time when rendering the man pages (which > >> | >> contain some calls to Octave functions). > >> | >> Which version of RcppOctave are you installing and how? And which R > >> | >> version are you running? > >> | >> > >> | >> I believe I fixed this error some time ago. > >> | >> Can you please try the latest develop version: > >> | >> devtools::install_github('renozao/RcppOctave', ref = 'develop') > >> | >> # and also if this still fails > >> | >> devtools::install_github('renozao/RcppOctave', ref = 'develop', quick > >> = > >> | >> TRUE) > >> | >> > >> | >> Thanks. > >> | >> > >> | >> Bests, > >> | >> Renaud > >> | >> > >> | >> On 11 November 2014 07:33, kam kammon wrote: > >> | >> > Hi, there are two additional things that may be relevant. First > >> Octave > >> | >> > 3.8.2 > >> | >> > was compiled from source and I have used a patch from > >> | >> > > >> http://octave.1599824.n4.nabble.com/Octave-3-8-1-Released-td4662831.html > >> | >> > (post by Michael Godfrey August 18, 2014) to enable jit. > >> | >> > > >> | >> > Also I have compiled Octave with libhdf5-openmpi, this has caused a > >> | >> > problem > >> | >> > for RcppOctave in Ubuntu 13.10 (see mailing list from Feb 2014) but > >> the > >> | >> > problem has been fixed. > >> | >> > > >> | >> > Bernard > >> | >> > > >> | >> > ________________________________ > >> | >> > From: kammon101 at hotmail.ca > >> | >> > To: edd at debian.org > >> | >> > Date: Mon, 10 Nov 2014 21:27:16 -0500 > >> | >> > CC: rcppoctave-user at lists.r-forge.r-project.org > >> | >> > Subject: Re: [Rcppoctave-user] Error in installing RcppOctave > >> | >> > > >> | >> > > >> | >> > I am not sure what info you will need then. > >> | >> > > >> | >> > What is the meaning of "error: object 'dlibs' not found"? That > >> seems to > >> | >> > be > >> | >> > the issue. > >> | >> > > >> | >> > Bernard > >> | >> > > >> | >> >> Date: Mon, 10 Nov 2014 19:51:43 -0600 > >> | >> >> To: kammon101 at hotmail.ca > >> | >> >> CC: edd at debian.org; rcppoctave-user at lists.r-forge.r-project.org > >> | >> >> Subject: RE: [Rcppoctave-user] Error in installing RcppOctave > >> | >> >> From: edd at debian.org > >> | >> >> > >> | >> >> > >> | >> >> That's uninformative. As I said, works on my box ... > >> | >> >> > >> | >> >> Dirk > >> | >> >> > >> | >> >> -- > >> | >> >> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org > >> | >> > > >> | >> > _______________________________________________ Rcppoctave-user > >> mailing > >> | >> > list > >> | >> > Rcppoctave-user at lists.r-forge.r-project.org > >> | >> > > >> | >> > > >> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user > >> | >> > > >> | >> > _______________________________________________ > >> | >> > Rcppoctave-user mailing list > >> | >> > Rcppoctave-user at lists.r-forge.r-project.org > >> | >> > > >> | >> > > >> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user > >> | >> > > >> | >> > > >> | >> > > >> | _______________________________________________ > >> | Rcppoctave-user mailing list > >> | Rcppoctave-user at lists.r-forge.r-project.org > >> | > >> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user > >> > >> -- > >> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: rcppoctave Type: application/octet-stream Size: 4423 bytes Desc: not available URL: From kammon101 at hotmail.ca Thu Nov 13 02:22:41 2014 From: kammon101 at hotmail.ca (kam kammon) Date: Wed, 12 Nov 2014 20:22:41 -0500 Subject: [Rcppoctave-user] Error in installing RcppOctave In-Reply-To: References: , , <21601.24125.468681.428666@max.nulle.part>, , , , <21601.27567.941695.684294@max.nulle.part>, , , , , , , , , , , , <21602.13225.678357.283648@max.nulle.part>, , , , , Message-ID: Hi, Renaud, I have compiled Octave 3.8.2 with hdf5-7 (no openmpi) to test RcppOctave. Again version from cran did not install (see attached log) but the development version did. Took a while to get back because the test partition went out of space. This is kind of strange since Dirk's installation worked. From: kammon101 at hotmail.ca To: renaud at mancala.cbio.uct.ac.za Date: Wed, 12 Nov 2014 03:28:39 -0500 CC: rcppoctave-user at lists.r-forge.r-project.org Subject: Re: [Rcppoctave-user] Error in installing RcppOctave Hi, Renaud, The failed install where mpi not found was for octave 3.8.1 from Ubuntu's repo. I think that is just because Debian doesn't compile octave with mpi. It works after I removed libhdf5-openmpi-7 and replaced it with libhdf5-7.The log is attached here. Cran's version of RcppOctave fails on Octave 3.8.2 compiled with hdf5-openmpi-7, the log was attached in my first message of this thread. However the develop version works. I have not compiled Octave 3.8.2 with hdf5-7 so I can't confirm either way. Bernard > Date: Wed, 12 Nov 2014 09:25:30 +0200 > Subject: Re: [Rcppoctave-user] Error in installing RcppOctave > From: renaud at mancala.cbio.uct.ac.za > To: kammon101 at hotmail.ca > CC: edd at debian.org; renaud at mancala.cbio.uct.ac.za; rcppoctave-user at lists.r-forge.r-project.org > > Can you please provide us with the install log of the failed > installation, the one with mpi.h not found? > Can you confirm: > * Octave 3.8.1 from Ubuntu repo works. > * Octave 3.8.2 locally compiled against libhdf5-openmpi-7 fails. > * Octave 3.8.2 locally compiled against libhdf5-7 works (?) > > RcppOctave uses compilation flags given by mkoctfile, which in theory > should fit each type of installation. I thought I had fixed this > problem back then > (http://lists.r-forge.r-project.org/pipermail/rcppoctave-user/2014-March/000097.html). > Maybe I am not retrieving them correctly, or maybe there is a conflict > between installations. Do you have both versions of Octave (mpi and > non-mpi) installed when testing? > It would help to see if you can effectively identify differences in > octave compilation flags between the two versions (have a look at the > variables in mkoctfile -h). > Thanks. > > > Renaud > > On 12 November 2014 00:49, kam kammon wrote: > > Just did an experiment on a small test Ubuntu 14.04 installation on an > > external hd. Installed Octave 3.8.1 straight from the Ubuntu repository.If > > libhdf5-7 was installed, RcppOctave installed successfully, if instead > > libhdf5-openmpi-7 was installed (which removed libhdf5-7) then installing > > RcppOctave failed with error "/usr/include/H5public.h:63:20: fatal error: > > mpi.h: No such file or directory" Same result with both RccpOctave from cran > > and github. > > > > Deban/Ubuntu's Octave package is compiled with libhdf5 but without openmpi > > support. > > > > I think RcppOctave is sensitive to how hdf5 is compiled in octave and the > > cran version may have problems with hdf5 with mpi. Since Dirk built without > > hdf5 he didn't experience any issue. > > > > Thanks Renaud again! > > > > Bernard > > > > > > > >> Date: Tue, 11 Nov 2014 10:04:57 -0600 > >> To: renaud at mancala.cbio.uct.ac.za > >> CC: kammon101 at hotmail.ca; rcppoctave-user at lists.r-forge.r-project.org > >> Subject: Re: [Rcppoctave-user] Error in installing RcppOctave > >> From: edd at debian.org > > > >> > >> > >> On 11 November 2014 at 17:41, Renaud Gaujoux wrote: > >> | Great. > >> | So I guess now is a good time for me to release that version to CRAN. > >> | Dirk, which version had installed fine on your machine, CRAN or Github > >> | (master/develop)? > >> > >> Almost surely just plain CRAN on several machines. Have not had issues in > >> ages. > >> > >> But then I don't do unusual things like building with MPI, hdf5, or other > >> local patches. > >> > >> Dirk > >> > >> > >> | Thanks. > >> | > >> | Bests, > >> | Renaud > >> | > >> | On 11 November 2014 10:45, kam kammon wrote: > >> | > Hi, Renaud, > >> | > > >> | > Thanks for the quick reply. > >> | > > >> | > I was installing RcppOctave in R with the command > >> | > install.packages('RcppOctave'), it downloaded RcppOctave_0.14.5 from > >> cran's > >> | > mirror. > >> | > > >> | > R version 3.1.2 and Octave 3.8.2 (Octave was compiled from source > >> myself) > >> | > > >> | > The developmental version does install! > >> | > > >> | > > >> | > > >> | > > >> | >> Date: Tue, 11 Nov 2014 10:27:57 +0200 > >> | >> Subject: Re: [Rcppoctave-user] Error in installing RcppOctave > >> | >> From: renaud at mancala.cbio.uct.ac.za > >> | > > >> | >> To: kammon101 at hotmail.ca > >> | >> CC: edd at debian.org; rcppoctave-user at lists.r-forge.r-project.org > >> | >> > >> | >> Hi Bernard, > >> | >> > >> | >> The error happens at loading time when rendering the man pages (which > >> | >> contain some calls to Octave functions). > >> | >> Which version of RcppOctave are you installing and how? And which R > >> | >> version are you running? > >> | >> > >> | >> I believe I fixed this error some time ago. > >> | >> Can you please try the latest develop version: > >> | >> devtools::install_github('renozao/RcppOctave', ref = 'develop') > >> | >> # and also if this still fails > >> | >> devtools::install_github('renozao/RcppOctave', ref = 'develop', quick > >> = > >> | >> TRUE) > >> | >> > >> | >> Thanks. > >> | >> > >> | >> Bests, > >> | >> Renaud > >> | >> > >> | >> On 11 November 2014 07:33, kam kammon wrote: > >> | >> > Hi, there are two additional things that may be relevant. First > >> Octave > >> | >> > 3.8.2 > >> | >> > was compiled from source and I have used a patch from > >> | >> > > >> http://octave.1599824.n4.nabble.com/Octave-3-8-1-Released-td4662831.html > >> | >> > (post by Michael Godfrey August 18, 2014) to enable jit. > >> | >> > > >> | >> > Also I have compiled Octave with libhdf5-openmpi, this has caused a > >> | >> > problem > >> | >> > for RcppOctave in Ubuntu 13.10 (see mailing list from Feb 2014) but > >> the > >> | >> > problem has been fixed. > >> | >> > > >> | >> > Bernard > >> | >> > > >> | >> > ________________________________ > >> | >> > From: kammon101 at hotmail.ca > >> | >> > To: edd at debian.org > >> | >> > Date: Mon, 10 Nov 2014 21:27:16 -0500 > >> | >> > CC: rcppoctave-user at lists.r-forge.r-project.org > >> | >> > Subject: Re: [Rcppoctave-user] Error in installing RcppOctave > >> | >> > > >> | >> > > >> | >> > I am not sure what info you will need then. > >> | >> > > >> | >> > What is the meaning of "error: object 'dlibs' not found"? That > >> seems to > >> | >> > be > >> | >> > the issue. > >> | >> > > >> | >> > Bernard > >> | >> > > >> | >> >> Date: Mon, 10 Nov 2014 19:51:43 -0600 > >> | >> >> To: kammon101 at hotmail.ca > >> | >> >> CC: edd at debian.org; rcppoctave-user at lists.r-forge.r-project.org > >> | >> >> Subject: RE: [Rcppoctave-user] Error in installing RcppOctave > >> | >> >> From: edd at debian.org > >> | >> >> > >> | >> >> > >> | >> >> That's uninformative. As I said, works on my box ... > >> | >> >> > >> | >> >> Dirk > >> | >> >> > >> | >> >> -- > >> | >> >> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org > >> | >> > > >> | >> > _______________________________________________ Rcppoctave-user > >> mailing > >> | >> > list > >> | >> > Rcppoctave-user at lists.r-forge.r-project.org > >> | >> > > >> | >> > > >> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user > >> | >> > > >> | >> > _______________________________________________ > >> | >> > Rcppoctave-user mailing list > >> | >> > Rcppoctave-user at lists.r-forge.r-project.org > >> | >> > > >> | >> > > >> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user > >> | >> > > >> | >> > > >> | >> > > >> | _______________________________________________ > >> | Rcppoctave-user mailing list > >> | Rcppoctave-user at lists.r-forge.r-project.org > >> | > >> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user > >> > >> -- > >> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org _______________________________________________ Rcppoctave-user mailing list Rcppoctave-user at lists.r-forge.r-project.org http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: rcppoctave_nompi Type: application/octet-stream Size: 810 bytes Desc: not available URL: From renaud at mancala.cbio.uct.ac.za Thu Nov 13 08:57:04 2014 From: renaud at mancala.cbio.uct.ac.za (Renaud Gaujoux) Date: Thu, 13 Nov 2014 09:57:04 +0200 Subject: [Rcppoctave-user] Error in installing RcppOctave In-Reply-To: References: <21601.24125.468681.428666@max.nulle.part> <21601.27567.941695.684294@max.nulle.part> <21602.13225.678357.283648@max.nulle.part> Message-ID: I will check if/how you can pass extra flags to the compilation. I may need to change the configure script for this to work. Otherwise, if you know of a way to detect if libhdf5 is the mpi version, I can add relevant flags for this case. On 13 November 2014 03:22, kam kammon wrote: > Hi, Renaud, > > I have compiled Octave 3.8.2 with hdf5-7 (no openmpi) to test RcppOctave. > Again version from cran did not install (see attached log) but the > development version did. Took a while to get back because the test partition > went out of space. > > This is kind of strange since Dirk's installation worked. > > ________________________________ > From: kammon101 at hotmail.ca > To: renaud at mancala.cbio.uct.ac.za > Date: Wed, 12 Nov 2014 03:28:39 -0500 > > CC: rcppoctave-user at lists.r-forge.r-project.org > Subject: Re: [Rcppoctave-user] Error in installing RcppOctave > > Hi, Renaud, > > The failed install where mpi not found was for octave 3.8.1 from Ubuntu's > repo. I think that is just because Debian doesn't compile octave with mpi. > It works after I removed libhdf5-openmpi-7 and replaced it with > libhdf5-7.The log is attached here. > > Cran's version of RcppOctave fails on Octave 3.8.2 compiled with > hdf5-openmpi-7, the log was attached in my first message of this thread. > However the develop version works. > > I have not compiled Octave 3.8.2 with hdf5-7 so I can't confirm either way. > > Bernard > > > > >> Date: Wed, 12 Nov 2014 09:25:30 +0200 >> Subject: Re: [Rcppoctave-user] Error in installing RcppOctave >> From: renaud at mancala.cbio.uct.ac.za >> To: kammon101 at hotmail.ca >> CC: edd at debian.org; renaud at mancala.cbio.uct.ac.za; >> rcppoctave-user at lists.r-forge.r-project.org >> >> Can you please provide us with the install log of the failed >> installation, the one with mpi.h not found? >> Can you confirm: >> * Octave 3.8.1 from Ubuntu repo works. >> * Octave 3.8.2 locally compiled against libhdf5-openmpi-7 fails. >> * Octave 3.8.2 locally compiled against libhdf5-7 works (?) >> >> RcppOctave uses compilation flags given by mkoctfile, which in theory >> should fit each type of installation. I thought I had fixed this >> problem back then >> >> (http://lists.r-forge.r-project.org/pipermail/rcppoctave-user/2014-March/000097.html). >> Maybe I am not retrieving them correctly, or maybe there is a conflict >> between installations. Do you have both versions of Octave (mpi and >> non-mpi) installed when testing? >> It would help to see if you can effectively identify differences in >> octave compilation flags between the two versions (have a look at the >> variables in mkoctfile -h). >> Thanks. >> >> >> Renaud >> >> On 12 November 2014 00:49, kam kammon wrote: >> > Just did an experiment on a small test Ubuntu 14.04 installation on an >> > external hd. Installed Octave 3.8.1 straight from the Ubuntu >> > repository.If >> > libhdf5-7 was installed, RcppOctave installed successfully, if instead >> > libhdf5-openmpi-7 was installed (which removed libhdf5-7) then >> > installing >> > RcppOctave failed with error "/usr/include/H5public.h:63:20: fatal >> > error: >> > mpi.h: No such file or directory" Same result with both RccpOctave from >> > cran >> > and github. >> > >> > Deban/Ubuntu's Octave package is compiled with libhdf5 but without >> > openmpi >> > support. >> > >> > I think RcppOctave is sensitive to how hdf5 is compiled in octave and >> > the >> > cran version may have problems with hdf5 with mpi. Since Dirk built >> > without >> > hdf5 he didn't experience any issue. >> > >> > Thanks Renaud again! >> > >> > Bernard >> > >> > >> > >> >> Date: Tue, 11 Nov 2014 10:04:57 -0600 >> >> To: renaud at mancala.cbio.uct.ac.za >> >> CC: kammon101 at hotmail.ca; rcppoctave-user at lists.r-forge.r-project.org >> >> Subject: Re: [Rcppoctave-user] Error in installing RcppOctave >> >> From: edd at debian.org >> > >> >> >> >> >> >> On 11 November 2014 at 17:41, Renaud Gaujoux wrote: >> >> | Great. >> >> | So I guess now is a good time for me to release that version to CRAN. >> >> | Dirk, which version had installed fine on your machine, CRAN or >> >> Github >> >> | (master/develop)? >> >> >> >> Almost surely just plain CRAN on several machines. Have not had issues >> >> in >> >> ages. >> >> >> >> But then I don't do unusual things like building with MPI, hdf5, or >> >> other >> >> local patches. >> >> >> >> Dirk >> >> >> >> >> >> | Thanks. >> >> | >> >> | Bests, >> >> | Renaud >> >> | >> >> | On 11 November 2014 10:45, kam kammon wrote: >> >> | > Hi, Renaud, >> >> | > >> >> | > Thanks for the quick reply. >> >> | > >> >> | > I was installing RcppOctave in R with the command >> >> | > install.packages('RcppOctave'), it downloaded RcppOctave_0.14.5 >> >> from >> >> cran's >> >> | > mirror. >> >> | > >> >> | > R version 3.1.2 and Octave 3.8.2 (Octave was compiled from source >> >> myself) >> >> | > >> >> | > The developmental version does install! >> >> | > >> >> | > >> >> | > >> >> | > >> >> | >> Date: Tue, 11 Nov 2014 10:27:57 +0200 >> >> | >> Subject: Re: [Rcppoctave-user] Error in installing RcppOctave >> >> | >> From: renaud at mancala.cbio.uct.ac.za >> >> | > >> >> | >> To: kammon101 at hotmail.ca >> >> | >> CC: edd at debian.org; rcppoctave-user at lists.r-forge.r-project.org >> >> | >> >> >> | >> Hi Bernard, >> >> | >> >> >> | >> The error happens at loading time when rendering the man pages >> >> (which >> >> | >> contain some calls to Octave functions). >> >> | >> Which version of RcppOctave are you installing and how? And which >> >> R >> >> | >> version are you running? >> >> | >> >> >> | >> I believe I fixed this error some time ago. >> >> | >> Can you please try the latest develop version: >> >> | >> devtools::install_github('renozao/RcppOctave', ref = 'develop') >> >> | >> # and also if this still fails >> >> | >> devtools::install_github('renozao/RcppOctave', ref = 'develop', >> >> quick >> >> = >> >> | >> TRUE) >> >> | >> >> >> | >> Thanks. >> >> | >> >> >> | >> Bests, >> >> | >> Renaud >> >> | >> >> >> | >> On 11 November 2014 07:33, kam kammon >> >> wrote: >> >> | >> > Hi, there are two additional things that may be relevant. First >> >> Octave >> >> | >> > 3.8.2 >> >> | >> > was compiled from source and I have used a patch from >> >> | >> > >> >> >> >> http://octave.1599824.n4.nabble.com/Octave-3-8-1-Released-td4662831.html >> >> | >> > (post by Michael Godfrey August 18, 2014) to enable jit. >> >> | >> > >> >> | >> > Also I have compiled Octave with libhdf5-openmpi, this has >> >> caused a >> >> | >> > problem >> >> | >> > for RcppOctave in Ubuntu 13.10 (see mailing list from Feb 2014) >> >> but >> >> the >> >> | >> > problem has been fixed. >> >> | >> > >> >> | >> > Bernard >> >> | >> > >> >> | >> > ________________________________ >> >> | >> > From: kammon101 at hotmail.ca >> >> | >> > To: edd at debian.org >> >> | >> > Date: Mon, 10 Nov 2014 21:27:16 -0500 >> >> | >> > CC: rcppoctave-user at lists.r-forge.r-project.org >> >> | >> > Subject: Re: [Rcppoctave-user] Error in installing RcppOctave >> >> | >> > >> >> | >> > >> >> | >> > I am not sure what info you will need then. >> >> | >> > >> >> | >> > What is the meaning of "error: object 'dlibs' not found"? That >> >> seems to >> >> | >> > be >> >> | >> > the issue. >> >> | >> > >> >> | >> > Bernard >> >> | >> > >> >> | >> >> Date: Mon, 10 Nov 2014 19:51:43 -0600 >> >> | >> >> To: kammon101 at hotmail.ca >> >> | >> >> CC: edd at debian.org; rcppoctave-user at lists.r-forge.r-project.org >> >> | >> >> Subject: RE: [Rcppoctave-user] Error in installing RcppOctave >> >> | >> >> From: edd at debian.org >> >> | >> >> >> >> | >> >> >> >> | >> >> That's uninformative. As I said, works on my box ... >> >> | >> >> >> >> | >> >> Dirk >> >> | >> >> >> >> | >> >> -- >> >> | >> >> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org >> >> | >> > >> >> | >> > _______________________________________________ Rcppoctave-user >> >> mailing >> >> | >> > list >> >> | >> > Rcppoctave-user at lists.r-forge.r-project.org >> >> | >> > >> >> | >> > >> >> >> >> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user >> >> | >> > >> >> | >> > _______________________________________________ >> >> | >> > Rcppoctave-user mailing list >> >> | >> > Rcppoctave-user at lists.r-forge.r-project.org >> >> | >> > >> >> | >> > >> >> >> >> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user >> >> | >> > >> >> | >> > >> >> | >> > >> >> | _______________________________________________ >> >> | Rcppoctave-user mailing list >> >> | Rcppoctave-user at lists.r-forge.r-project.org >> >> | >> >> >> >> http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user >> >> >> >> -- >> >> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org > > _______________________________________________ Rcppoctave-user mailing list > Rcppoctave-user at lists.r-forge.r-project.org > http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcppoctave-user