Re: Debian based live chemoinformatics CD?

Egon, (and CCs to those who contributed to the thread already, as well as to Klaus and Ian re the LCC aspects below) On 17 November 2005 at 12:36, Egon Willighagen wrote: | I've been thinking about live linux CDs to demo and easily setup a developers | environment for Java based

Re: Debian based live chemoinformatics CD?

On 17 November 2005 at 16:57, Michael Banck wrote: | On Thu, Nov 17, 2005 at 09:45:23AM -0600, Dirk Eddelbuettel wrote: | Quantian already has a clear focus on science / numerics / quant stuff, | contains the 1.4.2 Java JRE and is KDE-based --- so it would fit your needs. | When you say Java

Re: Debian based live chemoinformatics CD?

On 18 November 2005 at 08:06, elijah wright wrote: | | Now, what I read from time to time on planet.debian.org concerning | progress with Java in Debian seems rather encouraging, but I am not | following it that closely. If the free stack was up for running | Eclipse, I'd be all for it.

Re: good multivariate regression packages?

On 25 November 2005 at 13:43, Maciej Kalisiak wrote: | Hello, | | Can anyone recommend any good packages for doing multivariate | regression? I'm trying to model a function over a 5D domain (i.e., f: | R^5 - R). If it has any bearing on the question, a cross-section of | the function is shown

Re: Genetics Program

On 7 December 2005 at 17:07, Christopher David Desjardins wrote: | Hi- | I am MSc student at the University of Alberta studying ecology. | Recently I've decide to dive into population genetics and I am curious | if there are any good genetics programs available for linux and debian | in

Re: Genetics Program

On 8 December 2005 at 16:55, Andreas Tille wrote: | On Thu, 8 Dec 2005, Dirk Eddelbuettel wrote: | | That ITP is officially dead. Action, if any, can be had around the pkg-bioc | project on alioth where we have some rough code to spew out hundreds of .deb | packages based on sources from both

Re: Genetics Program

On 8 December 2005 at 18:09, Steffen Moeller wrote: | What is the story with emboss? Couldn't find it for the currently ongoing | preparations of the next Quantian update. Are there binaries somewhere? | EMBOSS would be lovely to have, indeed. Go and package it, I'm sure Andreas will sponsor

Re: Packaging and Maintaining

Chris, On 8 December 2005 at 10:40, Christopher David Desjardins wrote: | Hi- | I am just starting to learn how to create and maintain debian packages. | I would like to help in package up some of these programs that we've | been discussing that might need some one to package them. I would be |

Re: [pkg-bioc] Re: Genetics Program

On 8 December 2005 at 18:03, Andreas Tille wrote: | Are you looking for biological software in and outside Debian in general? | I hope you noticed | | http://www.debian.org/devel/debian-med/microbio Nice page(s that I was in fact unaware of. I only need to know your med-* meta packages :)

Re: [pkg-bioc] Re: Genetics Program

Replying to both Steffen and Rafael here: On 9 December 2005 at 10:41, Steffen Moeller wrote: | | Could we arrange a BioC repository for Alioth? | | Well we *do* have one in pkg-bioc [ which has refocussed on pkg-CRAN and | BioC but not been renamed ]. | Hm. We store the script there, but it

Re: ubuntu-science

On 7 January 2006 at 18:16, Daniel Leidert wrote: | Am Freitag, den 06.01.2006, 23:22 -0800 schrieb Jordan Mantha: | I am | encouraging the MOTUScience team members to at least email this list | when a new science package has been added to Ubuntu so that we don't get | a lot of duplication

New Quantian release 0.7.9.2

[ Fellow debian-science folks, I hope this is not considered off-topic for the list: A new Quantian release was just announced, and it contains even more packages than before. This release should contain everything good and worthy from the math and science sections, but as I cannot

Re: alternatives to gnuplot ?

On 6 April 2006 at 01:01, Gregor Gorjanc wrote: | Bill Allombert wrote: | I am looking for a GNU GPL-compatibly licensed alternative to gnuplot, | preferably packaged in Debian. [...] | | http://www.r-project.org Seconded, though it may not be for the faint of heart. R is much, much_ more

Re: alternatives to gnuplot ?

On 6 April 2006 at 15:24, [EMAIL PROTECTED] wrote: | What we are missing is a libified gnuplot. The Gnome guys once had a project call guppy (or something like it ...) but it died many years ago. GNU had plotutils, but that's not quite there either. It has becomes a lot easier to embed R with

FTBFS due to gfortran

deb-science'rs, Anybody here who could help me with a Fortran problem? I cannot compil one (old) routine in the source package fmultivar with gfortran: [EMAIL PROTECTED]:~/src/debian/CRAN/fMultivar-221.10065/src$ gfortran -c 46C-OutlierDetection.f [...] In file 46C-OutlierDetection.f:79

Re: FTBFS due to gfortran

Hi Kevin, On 2 June 2006 at 11:41, Kevin B. McCarty wrote: | Hi Dirk, | | On 5/31/06, Dirk Eddelbuettel [EMAIL PROTECTED] wrote: | | deb-science'rs, | | Anybody here who could help me with a Fortran problem? | | I cannot compil one (old) routine in the source package fmultivar

Re: GUI for R

[ resending with 8-bit clean mail header, and one fix below --edd ] On 7 October 2006 at 15:44, Janno Tuulik wrote: | Hei Cristiano, | | Take a look at RKWard (http://rkward.sourceforge.net) I would not (yet ?) recommend RKWard as it is in very stages and has fairly incomplete coverage of R.

Re: [R-sig-Debian] GUI for R

On 9 October 2006 at 14:11, Gregor Gorjanc wrote: | Tyler Smith wrote: | If you are spending any significant time working in R I would highly | recommend emacs with ESS. Both are apt-gettable for stable, testing and [...] | I also agree with Tyler. If you do not know Emacs it might be a bit of

Re: GUI for R

Hi Egon, On 7 October 2006 at 18:56, Egon Willighagen wrote: | On Saturday 07 October 2006 17:07, Dirk Eddelbuettel wrote: | The excellent JGR is a very good choice. As Janno said, it may be tricky | on stable. It just became a lot easier to install on unstable (and I still | have to post

Re: math package maintainer for Debian

On 14 October 2006 at 14:30, David Joyner wrote: | On 14 October 2006 at 13:00, David Joyner wrote: | | I am part of a development team for a | | GPL'd math software package called SAGE. We could like | | to ask a question of a contact person from the Debian team who | | deals with math

Revisiting batch/queue systems: slurm and munge

Hi all, Last August, I started a short discussion here regarding batch management / queue / scheduler / resource managment software for cluster computing. I already mentioned slumrm [1] and munge [2]. The conclusion then was unsatisfying -- we don't have anything in Debian. At the time, I was

Re: Revisiting batch/queue systems: slurm and munge

interest Same here. Thanks for your work on this -- we'll have slurm and munge in Debian before long. Dirk | | Gennaro | | [Bug] http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=351688 | | On Tue, Mar 06, 2007 at 08:40:10PM -0600, Dirk Eddelbuettel wrote: | | Hi all, | | Last August, I

Re: Batch systems: Torque, SLURM, other?

Hi Manuel, On 15 May 2007 at 13:11, Manuel Prinz wrote: | Hi everyone, | | I've to administrate a small cluster and I'm intersted in your opinion | or experience with the resource managers/batch systems you use. | | ATM, there's Torque installed, and I'm not too happy with it, especially |

Re: checkinstall lacking on stable

On 23 June 2007 at 09:31, Ross Boylan wrote: | On Fri, 2007-06-22 at 00:32 -0700, Francesco Pietra wrote: | I am now at such cases for amd64 (dual core opterons) | with OpenMPI (a parallelization support) and Amber (a | molecular dynamics package), which I wish to compile | with my installed

Re: libgsl stuck, can anybody help?

Hi Rudi, This is probably a question for debian-release or debian-devel and not debian-science ... I'll try to answer this from my vantage point, and I think that vorlon may correct any crass inaccurracies I state here. On 5 September 2007 at 06:07, Rudi Cilibrasi wrote: | Hi everybody, | | I

PyGPU

GPU programming from Python: http://www.cs.lth.se/home/Calle_Lejdfors/pygpu/ Looks promising, but I still don't really speak Python. Anybody with more skills and some free time interested in packaging this? Dirk -- Three out of two people have difficulties with fractions. -- To

Re: Science group on alioth

On 24 January 2008 at 22:02, Christophe Prud'homme wrote: | The policy is not to include the sources, just the diff. Would that be ok ? | We use svn-buildpackage but that is not mandatory Same for us at pkg-openmpi. I wasn't the one setting this up, but as the default 'sponsor and uploader' I

Re: open source image matching software

On 6 February 2008 at 19:11, Paul E Condon wrote: | I have a large number of scanned images of photographs. They are | scanned from prints, and for some images there are several prints. I | would like to find a program that would group similar images (similar | in some sense that approximates

Re: [Pkg-corba-devel] OpenCASCADE and Salomé

On 6 March 2008 at 09:28, Adam C Powell IV wrote: | On Wed, 2008-03-05 at 23:29 +0100, Thomas Girard wrote: | Hello Adam, | | Le mercredi 05 mars 2008 à 07:34 -0500, Adam C Powell IV a écrit : | I'm not getting this error... I don't know why you would have seen that | MPI error, I'd

Re: About free-form database

This is a debian-user question. Learn to use 'apt-cache search' -- there must be at least a hundred packages in Debian for what you describe, from note taking to mind mappming to personal wikis. Don't abuse debian-science because you think of yourself as a scientist. Dirk -- Three out of two

Re: future of blas/lapack/atlas packages?

(Doku and Camm re-added to CC --Dirk) On 8 July 2008 at 16:02, Ondrej Certik wrote: | Hi, | | thanks Matthias for raising this issue. Seconded! This has always been a point of great pride for Debian, and I have provided Atlas to users of R and Octave (when I still maintained the latter)

Re: tasks overview wishlist: Canonical citing reference

On 11 October 2008 at 15:40, Chris Walker wrote: | I do like the approach of having a simple plain text file - while not | machine readable does make it clear the appropriate citation - (and in FWIW that is was R does. For the subset of CRAN package I maintain, here is the subset having such a

Re: building package with different libs

On 14 November 2008 at 23:12, Steve M. Robbins wrote: | Howdy, | | | On Thu, Oct 30, 2008 at 07:48:19PM -0400, Adam C Powell IV wrote: | [Copying -beowulf as there's likely some interest there as well.] | | On Thu, 2008-10-30 at 15:21 +0100, Manuel Prinz wrote: | | When building against

Re: [Pkg-openmpi-maintainers] building package with different libs

On 18 November 2008 at 23:03, Adam C Powell IV wrote: | All things considered, OpenMPI has my vote as the most advanced | implementation right now... Thanks for that. Given that we need to order these (presented alphabetically) LAM ? MPICH ? Open MPI I suggest the following: i) LAM

Re: Bug#522017: ITP: jblas -- jblas is a fast linear algebra library for Java

On 3 April 2009 at 07:51, Sylvestre Ledru wrote: | Le vendredi 03 avril 2009 01:24 +0200, Matthias Klose a crit : | Chris Walker schrieb: | Soeren Sonnenburg so...@debian.org writes: | | Package: wnpp | Severity: wishlist | Owner: Soeren Sonnenburg so...@debian.org | | *

Re: MPICH2 packaging

On 16 June 2009 at 10:06, Lucas Nussbaum wrote: | On 15/06/09 at 18:32 -0400, Adam C Powell IV wrote: | Hello Pavan, | | Thank you for the inquiry. I've somewhat left MPICH for now (focusing | on OpenMPI, which I don't maintain but use), and assigned its | maintenance to the Debian

Re: How about packaging a Java GUI for R?

On 1 July 2009 at 20:14, Charles Plessy wrote: | I have found today a nice R GUI written in Java, JGR (speak 'Jaguar'). | http://jgr.markushelbig.org/JGR.html Yes -- I had of course been aware of it for years and had versions on my box. JGR had won a software price in the R world when Simon (a

[ANNOUNCEMENT] cran2deb: 1700+ new Debian / R packages

Announcing cran2deb: 1700+ Debian packages from almost all of CRAN -- Last Friday's presentation at UseR! 2009 was the first really public mention of 'cran2deb'. It provides Debian packages of all of CRAN. It started as Charles'

Re: [ANNOUNCEMENT] cran2deb: 1700+ new Debian / R packages

Hi Don, That was a quick follow-up :) On 13 July 2009 at 14:02, Don Armstrong wrote: | On Mon, 13 Jul 2009, Dirk Eddelbuettel wrote: | We currently build for the testing distribution and the i386 and | amd64 architectures. This is now publically useable and we welcome | wider testing

Re: [R-sig-Debian] [ANNOUNCEMENT] cran2deb: 1700+ new Debian / R packages

Hi Michael, On 14 July 2009 at 18:44, charles blundell wrote: | 2009/7/13 Michael Rutter ma...@psu.edu | 1. Are there any negatives going from an install.packages(foo) | approach using R then switching to an apt-get install r-cran-foo | method of installing packages? If I install a deb

Re: simple batch queue system?

On 22 July 2009 at 16:32, Lucas Nussbaum wrote: | On 22/07/09 at 12:30 +0200, Teemu Ikonen wrote: | Hi Debian scientists, | | I'm in the market for a simple job scheduler for a set of work nodes | in the 'cloud' (i.e. EC2). A queue for submitted non-parallel jobs, | commands to insert and

Re: [ANNOUNCEMENT] cran2deb: 1700+ new Debian / R packages

On 24 July 2009 at 12:53, Andreas Tille wrote: | On Mon, Jul 13, 2009 at 04:19:25PM -0500, Dirk Eddelbuettel wrote: | The other unspoken point: no, I do not intend to submit 1700 packages to | Debian's NEW queue. It would take a lot more effort to properly manually | maintain these at full

Rebuilding all 100+ r-cran-* packages for R 2.10.0

R 2.10.0, due out October 26, will switch to an internal html converter from the latex-alike Rd format coupled with an internal webserver. See below for the section on 'Significant user-visible changes' in the NEWS file from 2.10.0 -- taken from the Oct 13 beta currently in unstable. This means

Re: Rebuilding all 100+ r-cran-* packages for R 2.10.0

On 17 October 2009 at 01:29, Cyril Brulebois wrote: | Dirk Eddelbuettel e...@debian.org (16/10/2009): | This means we should rebuild all packages or else they will upon | load trigger a nagging message 'package foo was built under R | version x.y.z and may not function properly' as well

Re: tasks overview wishlist: Canonical citing reference

Hi Morten, On 4 November 2009 at 16:18, Morten Kjeldgaard wrote: | Charles Plessy wrote: | | In the discussion that followed, we talked about where to store this | information, and in which format, since adding more content to the | debian/control file is not an easy thing (it ‘costs’ a lot

Torque in Debian?

I seem to recall that someone once mentioned packaging of Morten's Torque packages from Ubuntu. I also seem to recall Steffen saying that he was in contact with Morten. Based on quick search of my mail folder I can't find traces of either. Could someone kindly refresh my memory? [ Google sees

Bug#560347: RFP: ncl -- Nexus Class Library

Package: wnpp Severity: wishlist * Package name: ncl (Nexus Class Library) Version : 2.1.08 (dated 2009-11-30) Upstream Author : Paul O. Lewis * URL or Web page : http://hydrodictyon.eeb.uconn.edu/ncl/ * License : GPL-2 Description : Nexus Class Library The NEXUS

Re: RFS: r-cran-scatterplot3d

On 24 January 2010 at 18:24, Philip Rinn wrote: | Dear debian-science subscribers, | | I am looking for a sponsor for my package scatterplot3d. | | * Package name: scatterplot3d | Version : 0.3-30-1 | Upstream Author : Uwe Ligges | * URL :

Re: [R-sig-hpc] License of GotoBLAS was changed to BSD

at TACC and all that. Sylvestre, any interest and equally importantly, spare cycles on your part? Cheers, Dirk -- Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com -- To UNSUBSCRIBE, email to debian-science-requ...@lists.debian.org with a subject of unsubscribe. Trouble

Re: [R-sig-hpc] License of GotoBLAS was changed to BSD

Salut Sylvestre! Thanks for the superspeedy follow-up! On 26 November 2010 at 18:00, Sylvestre Ledru wrote: | Le vendredi 26 novembre 2010 à 10:53 -0600, Dirk Eddelbuettel a écrit : | Hi science folks, | | Ei-ji, who follows this closely and who also wrote a the very nice | gotoblas2

Re: [R-sig-hpc] License of GotoBLAS was changed to BSD

On 26 November 2010 at 23:10, Thomas Weber wrote: | On Fri, Nov 26, 2010 at 10:53:09AM -0600, Dirk Eddelbuettel wrote: | Wouldn't we want GotoBLAS2 in Debian now that it is BSD-licensed? | | Uh, are you guys aware of | http://www.tacc.utexas.edu/tacc-projects/gotoblas2/faq/ ? | | GotoBLAS

Re: How to properly integrate cran2deb into Debian?

On 18 February 2011 at 13:10, Manuel Prinz wrote: | On Fri, Feb 18, 2011 at 11:08:20AM +0100, Andreas Tille wrote: | probably not the right list, debian-science list comes rather to mind | because Dirk Eddelbuettel (in CC) is also reading there. So please move | to this list in case you want

Re: Bug#589685: KDE 3's libs removal ping

' are not feature-by-feature substitutes. Not sure if it worth dealing with /etc/alternatives/ though. Dirk -- Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com -- To UNSUBSCRIBE, email to debian-science-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact

Re: OpenMPI-bin missing on some arches (Was: mrbayes-mpi: uninstallable on mipsen and s390)

On 29 June 2011 at 15:01, Andreas Tille wrote: | Hi, | | Your package is uninstallable on some archs: | | mrbayes-mpi/mips unsatisfiable Depends: openmpi-bin | mrbayes-mpi/mipsel unsatisfiable Depends: openmpi-bin | mrbayes-mpi/s390 unsatisfiable Depends: openmpi-bin | | I admit

Re: OpenMPI-bin missing on some arches (Was: mrbayes-mpi: uninstallable on mipsen and s390)

On 29 June 2011 at 08:30, Dirk Eddelbuettel wrote: | | On 29 June 2011 at 15:01, Andreas Tille wrote: | | Hi, | | | | Your package is uninstallable on some archs: | | | | mrbayes-mpi/mips unsatisfiable Depends: openmpi-bin | | mrbayes-mpi/mipsel unsatisfiable Depends: openmpi-bin

Julia language in Debian ?

Doug Bates pointed me to this the other day: http://julialang.org/ which will redirect to github at https://github.com/JuliaLang/julia Looks promising, is open source (mostly MIT license) and pretty fast. Anybody have spare time / bandwidth to think about packaging it? Dirk -- Outside

Re: Bug#690544: ITP: xts -- GNU R package for time series analysis

[Press RETURN to save to a file] -- Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com -- To UNSUBSCRIBE, email to debian-science-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org

Re: Stupid fumble with bug numbers

...@lists.debian.org | Archive: http://lists.debian.org/514576fe.50...@laposte.net | -- Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com -- To UNSUBSCRIBE, email to debian-science-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org

Re: packaging stan

to store/cache compiled modules for their use. That said, I know next to nothing about (R)Stan internals and builds. I am not an (R)Stan user myself. Dirk -- Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com -- To UNSUBSCRIBE, email to debian-science-requ...@lists.debian.org

Re: Bug#737533: ITP: r-cran-rnetcdf -- GNU R package that provides an R Interface to NetCDF Datasets

| with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org | Archive: http://lists.debian.org/20140205132020.ge26...@an3as.eu | -- Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com -- To UNSUBSCRIBE, email to debian-science-requ...@lists.debian.org

Re: Bug#737533: ITP: r-cran-rnetcdf -- GNU R package that provides an R Interface to NetCDF Datasets

On 5 February 2014 at 19:19, Sebastian Gibb wrote: | On Wednesday 05 February 2014 14:37:00 Dirk Eddelbuettel wrote: | Also, there are three packages on CRAN interfacing the NetCDF library: | |RNetCDF |ncdf4 |ncdf | | I never know which one is maintained and good

Re: Bug#761364: ITP: abc -- A System for Sequential Synthesis and Verification

On 15 September 2014 at 17:33, Andreas Tille wrote: | On Sat, Sep 13, 2014 at 11:38:48AM +0200, ruben.undh...@gmail.com wrote: | Please provide feedback on the naming of the package! | Perhaps the name abc is a bad name to use in debian although | it's the correct upstream name. | | I admit I

Re: copyright issues on debian

On 12 October 2015 at 17:29, Drew Parsons wrote: [...] | argument, the question is whether GPL licenced software is allowed to | link against GPL-licenced software. Well put. | When you read it that way, it might make it easier to understand why | people aren't so worried about the violation.

Re: r-cran-rinside good to go

On 2 September 2015 at 17:26, Andreas Tille wrote: | Hi Jonathon, | | On Wed, Sep 02, 2015 at 03:09:59PM +0200, Jonathon Love wrote: | > > | > > I would have loved if the patch would have been discussed - IMHO it is | > > sensible. | > | > oh ok. still figuring out how much autonomy i'm

Re: r-cran-rinside good to go

On 2 September 2015 at 15:09, Jonathon Love wrote: | fixed now. a lot of these R packages don't do you any favours coming up | with a < 80 char description. Simply a different (if related in spirit and scope) spec -- R itself has rather stringent checks in 'R CMD check ...' which, not unlike

Re: packaging an alternative R

On 28 September 2015 at 13:15, Jonathon Love wrote: | essentially, JASP depends on package A. package A gets updated in a way | that breaks compatibility with us (this has happened to us with three | different R packages making breaking changes between releases in the | last couple of years,

Re: packaging an alternative R

Also: http://debian-r.debian.net tends to have current packages. You could (programmatically !!) compare the state of required CRAN packages within Debian (my very small RcppAPT package on CRAN interfaces apt), compare to what available.packages() in R says and maybe warn on discrepancy. Dirk

Re: Bug#617296: RFP: rstudio -- IDE for GNU R

FWIW I am very good and close friends with the RStudio founders and several of their engineers. But most (power R) users I know (myself included) happily use their dailies from http://www.rstudio.org/download/daily/ It would be a lot of work to get (and keep) this packaged as RStudio found over

Re: packaging an alternate R engine

[ Suggestion: s/parallel/alternate/ as "parallel" has some other connotation in the context of computing / programming with data. ] On 25 September 2015 at 14:35, Jonathon Love wrote: | hi, | | i'm wanting to create a deb package for a parallel R installation. | | the software i'm working

Re: Bug#819343: ITP: r-cran-dplyr -- A Grammar of Data Manipulation for GNU R

On 29 March 2016 at 08:28, Andreas Tille wrote: | Hi Chris, | | On Mon, Mar 28, 2016 at 08:45:41PM -0400, Chris Lawrence wrote: | > On Mon, Mar 28, 2016 at 9:21 AM, Andreas Tille wrote: | > > Thanks for this ITP since it is also on my list of needed packages for | > >

Re: Bug#819343: ITP: r-cran-dplyr -- A Grammar of Data Manipulation for GNU R

On 30 March 2016 at 13:34, Andreas Tille wrote: | On Wed, Mar 30, 2016 at 06:21:55AM -0500, Dirk Eddelbuettel wrote: | > | > | I talked about this with Dirk[1] and may be I should have done this for | > | the moment as well. Meanwhile Dirk has ITPed r-cran-bh (#819389) and | > |

Re: R package CI test failures

On 3 May 2016 at 22:53, Andreas Tille wrote: | If we do not receive any hint from upstream removing this test seems to [...] | Hoping for upstream to respond to my first mail. I might ping at [...] | I might ping upstream. [...] They won't know what you are talking about, and for a reason. The

Re: Need help with upgrading R package which verifies that the dir it builds in matches its name (r-bioc-tracklayer)

On 9 May 2016 at 20:37, Andreas Tille wrote: | Hi again, | | I solved this by simply removing the whole configure script in a quilt patch. That sounds crazy so I took a look. BioConductor just had a 3.3 release (matching the R release cycle) and they seemingly simplified it a lot. Compare

Re: Need help with upgrading R package which verifies that the dir it builds in matches its name (r-bioc-tracklayer)

On 9 May 2016 at 21:10, Andreas Tille wrote: | > Or rather, I take the 'self-directory' | > test out in 3.2. | | You probably mean 3.3, right? Version 3.2 has no such test as far as I | can see. Sorry, meant whichever version (of rtracklayer) gave you that issue. I would rather not remove

Re: Debhelper for R packages

On 9 September 2016 at 15:14, Gordon Ball wrote: | On 09/09/16 14:17, Dirk Eddelbuettel wrote: | > | The plan was to avoid seeing eg, lintian hardening-no-bindnow warnings | > | on packages with compiled extensions. I tried injecting dpkg-buildflags | > | LDFLAGS output into the

Re: Debhelper for R packages

(chopping down a little to shorten) On 9 September 2016 at 10:50, Gordon Ball wrote: | On 08/09/16 23:25, Dirk Eddelbuettel wrote: | > Our Depends also need to cover R's "Imports:" which we will not see via ldd. I | > presume you have that covered, I just thought I'd ment

Re: Debhelper for R packages

Gordon, Andreas, On 8 September 2016 at 22:37, Andreas Tille wrote: | R is not team maintained and Dirk is not reading all threads on Debian | Science - make sure you CC him (as I did) if you want to be sure he | notices your mail. Well ... procmail still sticks it into the same folder and I

Re: Debhelper for R packages

On 8 September 2016 at 16:49, Don Armstrong wrote: | On Thu, 08 Sep 2016, Dirk Eddelbuettel wrote: | > On 8 September 2016 at 22:37, Andreas Tille wrote: | > To me github is as good / preferable. Other DDs have no issue developing via | > GH. I'd maybe make alioth another remote

Re: Debhelper for R packages

On 7 October 2016 at 15:09, Andreas Tille wrote: | I'm fine with these changes. If you want to let this propagate to all | R+BioConductor packages probably a lintian warning makes sense. May be Really? We don't have an officially sanctioned policy that _mandates_ this. We are about giving

Re: Debhelper for R packages

On 8 October 2016 at 17:45, Joost van Baal-Ilić wrote: | Otoh: currently R stuff is mainly maintained within debian-science and debian-med. Well: the R package itself, addons like ess, rpy2, rkward, ... , and several dozen r-cran-packages maintained are not. Dirk --

Re: Debhelper for R packages

On 7 October 2016 at 22:24, Dylan wrote: | 2016-10-07 16:25 GMT+02:00 Gordon Ball <gor...@chronitis.net>: | > On 07/10/16 15:33, Dirk Eddelbuettel wrote: | >> | >> On 7 October 2016 at 15:09, Andreas Tille wrote: | >> | I'm fine with these changes. If you want t

Re: Debhelper for R packages

On 8 October 2016 at 20:01, Joost van Baal-Ilić wrote: | I couldn't agree more. I'm a cdbs fan, and some of my packages I maintain with | neither cdbs nor dh. So I was _very_ happy to find out cdbs was the tool used | by many r-cran packages, when I started packaging r-cran stuff. Don't get

statistics: who maintains R packages in Debian (was: Re: Debhelper for R packages)

On 8 October 2016 at 20:32, Joost van Baal-Ilić wrote: | On Sat, Oct 08, 2016 at 12:08:50PM -0500, Dirk Eddelbuettel wrote: | > On 8 October 2016 at 17:45, Joost van Baal-Ilić wrote: | > | Otoh: currently R stuff is mainly maintained within debian-science and | > | debian-med. | &g

Re: What's the difference between CRAN Cairo and cairoDevice

Hi Andreas, [ Lucky I found this -- procmail sticks this into the debian-science folder which I do not visit as often as my normal inbox ... ] On 18 August 2016 at 08:52, Andreas Tille wrote: | Hi Dirk, | | I've got a request to install Cairo[1] which from the description sounds | pretty

Re: statistics: who maintains R packages in Debian (was: Re: Debhelper for R packages)

On 18 October 2016 at 18:28, Andreas Tille wrote: | On Tue, Oct 18, 2016 at 06:27:13PM +0300, Michael Crusoe wrote: | > > > r-other-hms-dbmi-spp | > > > | > > > It is _a lot_ easier for all of us if we only have top-level | > > > | > > > r-cran-* | > > > r-bioc-* | > > > r-other-*

Re: statistics: who maintains R packages in Debian (was: Re: Debhelper for R packages)

Shouldn't the new package r-hms-dbmi-spp been renamed r-other-$author-$package ie r-other-hms-dbmi-spp It is _a lot_ easier for all of us if we only have top-level r-cran-* r-bioc-* r-other-* Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

Re: statistics: who maintains R packages in Debian (was: Re: Debhelper for R packages)

. That is almost as bad your top-reply ;-) Dirk | On Tue, Oct 18, 2016 at 06:58:15AM -0500, Dirk Eddelbuettel wrote: | > | > Shouldn't the new package | > | > r-hms-dbmi-spp | > | > been renamed | > | > r-other-$author-$package | > | > ie | &

Re: ITP: r-cran-bh -- GNU R package with Boost headers

On 3 December 2016 at 08:51, Andreas Tille wrote: | Hi Dirk, | | I just realised that this ITP seems not to be closes. I somehow forgot | this since the former requirement I had for this package seems to have | vanished. However, my attempt to upgrade r-cran-rsqlite to its latest | upstream

Re: Status of dh-r and problems building r-cran-yaml

On 5 December 2016 at 17:57, Gordon Ball wrote: | On 01/12/16 09:46, Andreas Tille wrote: | > However, yesterday I stumbled upon r-cran-yaml[1] which causes a problem | > I was not able to solve quickly. Upstream has injected an additional | > declaration to the code copy of libyaml which I

Re: Bug#862039: r-bioc-gviz: accesses the internet during build

On 9 May 2017 at 14:57, Andreas Tille wrote: | Hi Chris, | | On Sun, May 07, 2017 at 06:06:10PM +0100, Chris Lamb wrote: | > | > Whilst r-bioc-gviz builds successfully on unstable/amd64, according to | > Debian Policy 4.9 packages may not attempt network access during | > a build. | > | >

Re: Upcoming new round of R package rebuilds [FWD: [Rd] R-devel object header changes that require reinstalling packages]

On 18 September 2017 at 22:41, Charles Plessy wrote: | Hello everybody, | | I just wanted to relay the information that some R packages will need a | rebuild after the next upgrade of R. (see the email forwarded below.) Common knowledge. I referenced it half-a-dozen times in the damned thread

Re: Upcoming new round of R package rebuilds [FWD: [Rd] R-devel object header changes that require reinstalling packages]

On 19 September 2017 at 14:15, Johannes Ranke wrote: | > But you escalated it | | Mhm. I reported a bug with severity "normal". Maybe the language I used was | too dramatic? The whole bug report was, pardon my French, complete and utter nonsense. The folks who needed to know already knew. But

Re: Upcoming new round of R package rebuilds [FWD: [Rd] R-devel object header changes that require reinstalling packages]

On 19 September 2017 at 11:07, Johannes Ranke wrote: | Am Montag, 18. September 2017, 10:39:02 CEST schrieb Dirk Eddelbuettel: | > Common knowledge. I referenced it half-a-dozen times in the damned thread | > about the binNMUs. | | This (https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=

Re: Would you please not upload new r-* packages until transition is finalised (Re: r-api-3.4)

On 12 October 2017 at 14:26, Andreas Tille wrote: | On Thu, Oct 12, 2017 at 07:06:33AM -0500, Dirk Eddelbuettel wrote: | > | > On 12 October 2017 at 11:36, Andreas Tille wrote: | > | yesterday you uploaded | > | | > | r-cran-rcpparmadillo 0.8.100.1.0-1 | > | | &

Would you please not upload new r-* packages until transition is finalised (Re: r-api-3.4)

transition at all. Dirk | it would be helpful if you would not upload r-* packages as long as the | testing migration has not happened. | | Thank you | | Andreas. | | On Sat, Sep 23, 2017 at 11:58:20AM -0500, Dirk Eddelbuettel wrote: | > | > See below for upcoming R 3.4.2 "pre-rele

Re: Why does r-cran-rcppgsl not migrate to testing?

On 8 September 2017 at 22:47, Andreas Tille wrote: | Hi Dirk, | | On Thu, Sep 07, 2017 at 02:46:04PM -0500, Dirk Eddelbuettel wrote: | > | > On 7 September 2017 at 21:20, Andreas Tille wrote: | > | Hi Dirk, | > | | > | On Wed, Sep 06, 2017 at 04:22:33PM -0500, Dirk Edd

Re: Why does r-cran-rcppgsl not migrate to testing?

Andreas, Mail CC'ed to debian-science goes into the debian-science folder which I don't regularly open, so sorry for the delay. If in doubt or if I don't reply please email (or DM) me directly, On 2 September 2017 at 16:17, Andreas Tille wrote: | according to | |

Re: Why does r-cran-rcppgsl not migrate to testing?

On 6 September 2017 at 15:12, Mattia Rizzolo wrote: | On Wed, Sep 06, 2017 at 07:37:07AM -0500, Dirk Eddelbuettel wrote: | > It is a trivial "monstly non-bug" bug report. But the release team won't act, | > so I am now resigned to waiting. I explained the case in

Re: Why does r-cran-rcppgsl not migrate to testing?

On 6 September 2017 at 16:49, Andreas Tille wrote: | On Wed, Sep 06, 2017 at 07:37:07AM -0500, Dirk Eddelbuettel wrote: | > I can actually no longer replicate the original issue | > | > https://bugs.debian.org/861333 | > | > with any of the few (40-some now) packages

Re: Why does r-cran-rcppgsl not migrate to testing?

Hi Andreas, On 7 September 2017 at 21:20, Andreas Tille wrote: | Hi Dirk, | | On Wed, Sep 06, 2017 at 04:22:33PM -0500, Dirk Eddelbuettel wrote: | > On 6 September 2017 at 22:48, Andreas Tille wrote: | > | [Chris, I took the freedom to move r-cran-mcmc to Debian Science | > | team si

  1   2   >