Re: [R-sig-Debian] Is r2u at 3.4.1? [branch about handling package collisions under Ubuntu/Debian]
On 24/08/2023 12:09, Ivan Krylov wrote: On Thu, 24 Aug 2023 11:34:45 +0200 Chris Evans wrote: I see I now have: libmagick++-dev is already the newest version (8:6.9.11.60+dfsg-1.3ubuntu0.22.04.3+esm2) That fits with what you are saying about the current version doesn't it? You're right that you already had some security updates from a different repo, https://esm.ubuntu.com/apps/ubuntu. Still, before you updated your sources.list, APT could see libmagick++-dev version 8:6.9.11.60+dfsg-1.3ubuntu0.22.04.3+esm2 from ESM but not 8:6.9.11.60+dfsg-1.3ubuntu0.22.04.3 from jammy-security, which could have been part of the problem. Aha! deb http://archive.ubuntu.com/ubuntu jammy-security main restricted deb http://archive.ubuntu.com/ubuntu jammy-security universe deb http://archive.ubuntu.com/ubuntu jammy-security multiverse That's covering all of main, universe, multiverse and restricted for security updates isn't it? I think that's right. Congratulations on fixing your sources.list! Thanks! "Small steps, small steps" I tell myself! Two final questions: 1) is there something I might|should have been doing to check that my local Ubuntu repository was up date? 2) as it seems is isn't/wasn't, is there anything I should do now to alert people to that? Huge thanks to Dirk, yourself and the list for putting up with this. I hope it may be a useful history to be in the searchable internet resources if others hit similar issues. Chris -- Chris Evans (he/him) Visiting Professor, UDLA, Quito, Ecuador & Honorary Professor, University of Roehampton, London, UK. Work web site: https://www.psyctc.org/psyctc/ CORE site: http://www.coresystemtrust.org.uk/ Personal site: https://www.psyctc.org/pelerinage2016/ ___ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
Re: [R-sig-Debian] Is r2u at 3.4.1? [branch about handling package collisions under Ubuntu/Debian]
On 24/08/2023 09:58, Ivan Krylov wrote: On Tue, 22 Aug 2023 19:38:57 +0200 Chris Evans wrote: 8:6.9.11.60+dfsg-1.3build2 500 500 http://mirror.infomaniak.ch/ubuntu jammy/universe amd64 Packages Interesting. mirror.infomaniak.ch seems to be a full mirror of Ubuntu repos, but https://packages.ubuntu.com/jammy/libmagick++-dev says that the current version of the package is 8:6.9.11.60+dfsg-1.3ubuntu0.22.04.3, not 8:6.9.11.60+dfsg-1.3build2. On the other hand, I do see the 8:6.9.11.60+dfsg-1.3build2 version in the changelog [*], it's just a bit older. Can you unpick that for me Ivan? I see I now have: libmagick++-dev is already the newest version (8:6.9.11.60+dfsg-1.3ubuntu0.22.04.3+esm2) That fits with what you are saying about the current version doesn't it? I think that your sources.list is missing the security updates repo, which seems to be separate from the main repo: deb http://security.ubuntu.com/ubuntu jammy-security main universe That's worrying. I would never knowingly have switched off security updates. Updates in the Ubuntu "Software & Updates" application has: Where there are security updates: Download and install automatically and I see this root@Clevo2:/etc/apt# grep security sources.list ## review or updates from the Ubuntu security team. ## security team. ## or updates from the Ubuntu security team. deb http://archive.ubuntu.com/ubuntu jammy-security main restricted # deb-src http://security.ubuntu.com/ubuntu jammy-security main restricted deb http://archive.ubuntu.com/ubuntu jammy-security universe # deb-src http://security.ubuntu.com/ubuntu jammy-security universe deb http://archive.ubuntu.com/ubuntu jammy-security multiverse # deb-src http://security.ubuntu.com/ubuntu jammy-security multiverse That's covering all of main, universe, multiverse and restricted for security updates isn't it? TIA, Chris -- Chris Evans (he/him) Visiting Professor, UDLA, Quito, Ecuador & Honorary Professor, University of Roehampton, London, UK. Work web site: https://www.psyctc.org/psyctc/ CORE site: http://www.coresystemtrust.org.uk/ Personal site: https://www.psyctc.org/pelerinage2016/ ___ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
Re: [R-sig-Debian] Is r2u at 3.4.1? [branch about handling package collisions under Ubuntu/Debian]
Just to clarify the record: this branched thread is nothing to do with r2u (but I'm definitely coming back to that later, but a new thread I think!) On 24/08/2023 02:14, Dirk Eddelbuettel wrote: Chris, This got a little long so I'll chop a few things down. On 22 August 2023 at 19:38, Chris Evans wrote: | On 16/08/2023 00:06, Dirk Eddelbuettel wrote: | > | > That can happen, and pinning can help. I would suggest to look at 'apt-cache | > polict nameofthepackagehere'. (See below for concrete example.) | | So I try this. | | root@Clevo2:/media/chris/Clevo_SSD2/Data/MyR/R/distill_blog/test2/_posts# | apt-cache policy libmagick++-dev | libmagick++-dev: | Installed: (none) | Candidate: 8:6.9.11.60+dfsg-1.3ubuntu0.22.04.3+esm2 | Version table: | 8:6.9.11.60+dfsg-1.3ubuntu0.22.04.3+esm2 500 | 500 https://esm.ubuntu.com/apps/ubuntu jammy-apps-security/main | amd64 Packages | 500 https://esm.ubuntu.com/apps/ubuntu jammy-apps-security/main | i386 Packages | 8:6.9.11.60+dfsg-1.3build2 500 | 500 http://mirror.infomaniak.ch/ubuntu jammy/universe amd64 | Packages | 500 http://mirror.infomaniak.ch/ubuntu jammy/universe i386 Packages This shows you two sources supplying libmagick++-dev: one from esm.ubuntu.com security updates. That is fine. The other is an add-on repo, just like r2u. Oddly enough, it's not really that. It's my local official repository which I selected using the "select nearest" months ago. I assume it has slipped out of synch with the main Ubuntu repositories hence my mess. Encouraged by your message to see (what was perhaps obvious) I reset my repository to the main one and a did apt-get update and apt-get upgrade which pulled a huge number of updates. Then apt-get install libmagick++-dev worked fine. But we cannot limitlessly combine those. r2u assume "everything else" comes from the standard repos and tries to (and succeeds, generally) in working with it. So here, for now, I would point at mirror.infomaniak.ch/ubuntu as a likely source of your troubles. Clearly absolutely correct. What's a bit worrying to me is that an apparently official repository can get so out of synch with no more human friendly alerts than my problem with magick! I had seen using the nearest repository as being a good citizen but now I can see it can bite you. Oddly enough the concern about "limitlessly combine" add repositories has been a concern of mine about r2u. I have felt in a bind with this whole issue of repositories and packaging as I find I now have programs I use a lot some that I can only compile myself (very rare), some that Ubuntu installs (I think) as snaps (which I don't much like), some (notably NextCloud) which seem to only promote flatpak (which I don't much like) but are available in the main Ubuntu repository and in snap and some, like r2u, which recommend adding a repository ... which I generally see as better than compiling, snap or flatpak BUT which I know risks creating package version locks. At some point I want to go through /etc/apt/sources.list.d and work out what I have and try to work out why and what should perhaps go. [snipping the rest as the key issues for me are now all solved with your help: hugely grateful. I will run things as they are for a few days/weeks (and, I hope, sort out an unconnected problem with a distill blog and git repository in R! Then I will feel that I have the system stable and will be back to the questions about r2u.] -- Chris Evans (he/him) Visiting Professor, UDLA, Quito, Ecuador & Honorary Professor, University of Roehampton, London, UK. Work web site: https://www.psyctc.org/psyctc/ CORE site: http://www.coresystemtrust.org.uk/ Personal site: https://www.psyctc.org/pelerinage2016/ Emeetings (Thursdays): https://www.psyctc.org/psyctc/booking-meetings-with-me/ (Beware: French time, generally an hour ahead of UK) <https://ombook.psyctc.org/book> ___ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
Re: [R-sig-Debian] Is r2u at 3.4.1? [branch about handling package collisions under Ubuntu/Debian]
This is definitely tangential to the list: I'm on Ubuntu (22.04.2 LTS) not Debian and I'm sure this is about issues in the Ubuntu package management on my machine, R is only revealing them. The original subject line came from me wondering if my going over to the r2u repository would solve the problem. However, as I think Dirk said, that's only really likely to be answered by trying it and I would rather see if I can understand what has gone wrong before I do anything radical. I am also hoping that having this, partially OTT thread on the list may help as I doubt if I'll be the last to hit this sort of package management nightmare. Some of the issues clearly are pure OS issues but the impact for me is definitely on R. On 16/08/2023 00:06, Dirk Eddelbuettel wrote: Hi Chris, Thanks for posting here, and sorry I missed it for two days due to sorting mailing list traffic into folders and clearly not glancing at all of them. Don't think I said before how much I appreciate you responding at all. On 13 August 2023 at 09:12, Chris Evans wrote: | I am putting this here as it may be of general and not just my own | interest. I am currently running 4.3.1 on Ubuntu 22.04.2 LTS but am | hitting an issue that the magick package won't update because | libmagick++-dev won't update because, presumably, of two repositories in | my sources.list disagreeing about versions required. That's not so That can happen, and pinning can help. I would suggest to look at 'apt-cache polict nameofthepackagehere'. (See below for concrete example.) So I try this. root@Clevo2:/media/chris/Clevo_SSD2/Data/MyR/R/distill_blog/test2/_posts# apt-cache policy libmagick++-dev libmagick++-dev: Installed: (none) Candidate: 8:6.9.11.60+dfsg-1.3ubuntu0.22.04.3+esm2 Version table: 8:6.9.11.60+dfsg-1.3ubuntu0.22.04.3+esm2 500 500 https://esm.ubuntu.com/apps/ubuntu jammy-apps-security/main amd64 Packages 500 https://esm.ubuntu.com/apps/ubuntu jammy-apps-security/main i386 Packages 8:6.9.11.60+dfsg-1.3build2 500 500 http://mirror.infomaniak.ch/ubuntu jammy/universe amd64 Packages 500 http://mirror.infomaniak.ch/ubuntu jammy/universe i386 Packages And the key problems remains this (actually, it's got a bit worse): root@Clevo2:/media/chris/Clevo_SSD2/Data/MyR/R/distill_blog/test2/_posts# apt-get install libmagick++-dev Reading package lists... Done Building dependency tree... Done Reading state information... Done Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies. libcairo2-dev : Depends: libfontconfig1-dev (>= 2.2.95) Depends: libfreetype6-dev (>= 2.1.10) libglib2.0-dev : Depends: libglib2.0-0 (= 2.72.4-0ubuntu1) but 2.72.4-0ubuntu2.2 is to be installed Depends: libglib2.0-bin (= 2.72.4-0ubuntu1) Depends: libglib2.0-dev-bin (= 2.72.4-0ubuntu1) libmagickcore-6.q16-dev : Depends: libfreetype6-dev libwmf-dev : Depends: libfreetype-dev but it is not installable E: Unable to correct problems, you have held broken packages. Which brings me to Dirk's on the nail question: (Also: how come there are two libmagick++-dev, ie why do you have a 2nd one, ie do you know which additional repo you turned on?) Exactly!!! The weird thing is is that it was weeks back that I added a repo., or I think I did, probably more than one about handling gpx files in Ubuntu/Debian. But that was weeks before this started and as you see from that apt-cache policy (if I understand it correctly), the repos involved seem to be the mainstream ones. That's true when I do apt-cache policy on any of the packages that are being complained about. aptitude doesn't help and dpkg --get-selections | grep hold returns nothing (literally) and none of the other things I could find on the web about these sorts of collisions helped ... and I can't see that others have this problem (apart from some very old reports for Ubuntu 14 and 16!) Are there any more suggestions? Are there good Debian/Ubuntu places where I should be putting this? If so, any advice about how to word it?! Are there frightening radical steps I should take next?! ... and back to the human Cheers, Dirk Cheers indeed. | Visiting Professor, UDLA, Quito, Ecuador & Honorary Professor, | University of Roehampton, London, UK. Nice. I got to workshop-keynote once in Guayaquil and regret not making over to Quito. Ah, I'm the reverse. Ecuador seems to be sliding into a frightening narcogang dominated state that previously it had always avoided. I guess that puts my problems in perspective. -- Chris Evans (he/him) Visiting Professor, UDLA, Quito, Ecuador & Honorary Professo
Re: [R-sig-Debian] Is r2u at 4.3.1 [edited]?
Huge thanks for both replies Dirk, I'm replying to this one first, the other probably tomorrow when I've thought more. This got long but I think most on the list can just [skip|delete] as it's not for them! However, I hope this may help a few others in my rather marginal position on this and other R lists and maybe help others like yourself who do so much to make R as accessible as possible to as many as possible. On 16/08/2023 15:10, Dirk Eddelbuettel wrote: Chris, I edited the README.md for r2u (also the main page at https://eddelbuettel.github.io/r2u) in a few places, that should hopefully address a few of the snafus you found. That has clearly tweaked the issue of the versions and I can also see that you have made some other changes that do look clearer to me. That takes me into something that is perhaps very tangential ... but perhaps not. I suspect that I'm in a very small minority of R users: * I'm not a programmer and have had no programming education (except one week introduction to Fortan as a freebie for undergraduates when I hit university in 1975!) * so all my programming is self-taught, bad, and now pretty much only in R! * I do try to do everything I can using open source s'ware hence I run Ubuntu (for some years now, previously Debian for ages) * I'm not a statistician either and have even less formal statistical training than computing training! * I do love (>95% of the time!) R and get things done in it as my substantive niche (psychotherapy/MH research) hasn't given me access to statisticians since about 1990 * I try to do things in R both to solve what I need to do to crunch data but also to make it easier for practitioner researchers to use R and get rid of SPSS and Excel So I think I'm an oddity but perhaps not unique. Sometimes, as you suggested I think in your other post, I can be useful to provide things that might help others who lack the skills and experience that I think so many on this list and other R lists have use things and I'm very happy to try to do that for r2u as I'm sure I should be transferring to using it (more in response to your other kind reply). I have an "Rblog" (https://github.com/cpsyctc/CECPfuns not a very good name for it but too late to change it now) and I think I need to create a "How to use r2u if you use R on Ubuntu but are at my level of IT knowledge" post. That's because I think what you have above is correct for your likely audience but goes a bit beyond me and any others in my little niche in places. Responses to your next bit may help explain why I say that. As for your question 'is r2u running R version x.y.z' there are few way to find out - if you have docker: docker run --rm -ti rocker/r2u with the default 'latest' tag for 22.04, tags 22.04 and 20.04 also work I have stayed away from docker having only a fairly tenuous understanding of it and on the basis that my ageing brain needs to be sure the gains from learning new things will outweigh the time it will take me to get up to speed with the ideas. I saw docker as likely to be brilliant on that balance for people writing and sharing apps but all I write and share is very clunky, R code only, github R package: CECPfuns (https://github.com/cpsyctc/CECPfuns). Not convinced that's the wrong choice but for now, no docking for me I think. - in the webbrowser (!!) as long demonstrated on that page via gitpad.io Is that the section headed "Via gitpod.io"? If so, similar issue to docker: I haven't gone into gitpond or ... - in the webbrowser (!!) or via the 'code' editor as added last weekend in a new vignette https://eddelbuettel.github.io/r2u/vignettes/Codespaces/ (also on my blog, and tweeted & tooted about). Codespaces (nor, I confess, your blog!) That last part is compelling as GitHub gives a number of free compute hours for codespace on either a 2-core, 4gb instance or a 4-core, 16gb instance which is really not too shabby. (Instead of clicking on '+' select '...' and 'new with options', pick bigger instance and/or other options). So I see now, but feels like another layer of complexity to understand ... of course, as with docker and gitpod.io, maybe it would repay learning but I suspect I'm not alone in being reluctant to learn these things when running R, Rstudio and Ubuntu (and now an shiny server) has been enough for me! Sorry if I'm sounding ungrateful and cowardly ... maybe I am the sole inhabitant of my timid but actually profoundly grateful niche in the R/Linux ecospheres! Tomorrow now for my next steps to understand the issue with libmagick++-dev which are really OT, and to come back to r2u responding to your other, wonderful, Email. Many thanks again! Cheers, Dirk -- Chris Evans (he/him) Visiting Professor, UDLA, Quito, Ecuador & Honorary Professor, University of Roehampton, London, UK. Work web site: https
[R-sig-Debian] Is r2u at 3.4.1?
I am putting this here as it may be of general and not just my own interest. I am currently running 4.3.1 on Ubuntu 22.04.2 LTS but am hitting an issue that the magick package won't update because libmagick++-dev won't update because, presumably, of two repositories in my sources.list disagreeing about versions required. That's not so urgent an issue for me that I wont just wait to see if it sorts itself out. In my experience such collisions sometimes do. However, it prompted me to some questions: 1) Is this telling me it's time I went to r2u which does seem a "very good thing"? Any reason NOT to change? 2) I read https://eddelbuettel.github.io/r2u/, not for the first time, and it looks simple, even I should be able to do that. Any gotchas? See #3: 3) but it says things I don't really understand about the R version: "Current versions are based on R 4.3.0, and BioConductor release 3.17 packages are provided when required by CRAN packages. Binaries are still R 4.2.* based (unless a forced rebuild was required) but the containers provide R 4.3.0. We expect to switch to R 4.3.0-based builds very soon." 3a) I don't understand why "binaries", presumably binary packages, would be at a different release from ... what? What is not binary? Pure R source packages? 3b) _IS_ it still at 4.3.0 as I'm at 3.4.1 and would be a bit reluctant to go backwards down the release sequence? TIA and enormous respect to Dirk for this and all the other work he does for R, Chris -- Chris Evans (he/him) Visiting Professor, UDLA, Quito, Ecuador & Honorary Professor, University of Roehampton, London, UK. Work web site: https://www.psyctc.org/psyctc/ CORE site: http://www.coresystemtrust.org.uk/ Personal site: https://www.psyctc.org/pelerinage2016/ ___ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
Re: [R-sig-Debian] Failing to install R 4.0.? on Raspian
- Original Message -
> From: "Dirk Eddelbuettel"
> To: "Chris Evans"
> Cc: "r-sig-debian"
> Sent: Wednesday, 24 March, 2021 15:00:42
> Subject: Re: [R-sig-Debian] Failing to install R 4.0.? on Raspian
> On 24 March 2021 at 14:47, Chris Evans wrote:
>| I have just invested very few pennies in a Raspian machine hosted by my ISP.
>|
>| The machine tells me:
>|
>| root@www:~# cat /etc/os-release
>| PRETTY_NAME="Raspbian GNU/Linux 10 (buster)"
>| NAME="Raspbian GNU/Linux"
>| VERSION_ID="10"
>| VERSION="10 (buster)"
>| VERSION_CODENAME=buster
>| ID=raspbian
>|
>| So I have added a line to /etc/apt/sources.list
>|
>| root@www:~# cat /etc/apt/sources.list
>| deb http://raspbian.raspberrypi.org/raspbian/ buster main contrib non-free
>rpi
>| deb http://archive.raspberrypi.org/debian/ buster main
>| deb http://cloud.r-project.org/bin/linux/debian buster-cran40/
>
> Hm, doesn't that third line make the heroic assumptions that there were a
> non x86_64 repository? So I think the error below may be a side effect.
>
> Just because you are getting armhf packages from some repositories does not
> imply you get them from all, methinks. apt may happily look at the
> binary:all packages which it could install, but then get sidelined by their
> dependencies which it may not.
Arrgghhh. SO embarrassing. I had completely forgotten that it was an ARM
CPU!!!
Anyone got any advice on getting R 4.0.? (and then shiny I was hoping) onto
ARM? Would
I have to roll my sleeves up and compile? I suspect that's not a good route for
me but I will certainly give it a stab if there aren't easier options. (I have
searched and they're not leaping out at me!)
Thanks Dirk,
Chris
>
> Dirk
>
>| root@www:~#
>|
>| and added the key using
>|
>| apt-key adv --keyserver keys.gnupg.net --recv-key
>| 'E19F5F87128899B192B1A2C2AD5F960A256A04AF'
>|
>| following https://cran.r-project.org/bin/linux/debian/#debian-buster-stable
>|
>| apt-get update
>|
>| runs fine but apt install -t buster-cran40 r-base gets me this:
>|
>| root@www:~# apt install -t buster-cran40 r-base
>| Reading package lists... Done
>| Building dependency tree
>| Reading state information... Done
>| Some packages could not be installed. This may mean that you have
>| requested an impossible situation or if you are using the unstable
>| distribution that some required packages have not yet been created
>| or been moved out of Incoming.
>| The following information may help to resolve the situation:
>|
>| The following packages have unmet dependencies:
>| r-base : Depends: r-base-core (>= 4.0.4-1~bustercran.0) but it is not going
>to
>| be installed
>| Depends: r-recommended (= 4.0.4-1~bustercran.0) but it is not
>going to be
>| installed
>| Recommends: r-base-html but it is not going to be installed
>| Recommends: r-doc-html but it is not going to be installed
>| E: Unable to correct problems, you have held broken packages.
>|
>|
>| aptitude why-not r-base says:
>|
>| root@www:~# aptitude why-not r-base
>| Not currently installed
>| The candidate version 4.0.4-1~bustercran.0 has priority optional
>| No dependencies require to remove r-base
>|
>| and aptitude install r-base says
>|
>| root@www:~# aptitude install r-base
>| The following NEW packages will be installed:
>| gfortran{a} gfortran-8{a} icu-devtools{a} libblas-dev{a} libblas3{a}
>| libbz2-dev{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-nouveau2{a}
>| libdrm-radeon1{a} libdrm2{a} libfile-basedir-perl{a}
>| libfile-desktopentry-perl{a} libfile-mimeinfo-perl{a} libfontenc1{a}
>| libgfortran-8-dev{a} libgfortran4{a} libgfortran5{a} libgl1{a}
>| libgl1-mesa-dri{a} libglapi-mesa{a} libglvnd0{a} libglx-mesa0{a} libglx0{a}
>| libicu-dev{a} libio-stringy-perl{a} libipc-system-simple-perl{a}
>libjpeg-dev{a}
>| libjpeg62-turbo-dev{a} liblapack-dev{a} liblapack3{a}
>| libllvm9{a} liblzma-dev{a} libncurses-dev{a} libncurses5-dev{a}
>| libnet-dbus-perl{a} libpcre16-3{a} libpcre2-16-0{a} libpcre2-32-0{a}
>| libpcre2-dev{a} libpcre2-posix0{a} libpcre3-dev{a} libpcre32-3{a}
>| libpcrecpp0v5{a} libpng-dev{a} libpng-tools{a} libreadline-dev{a}
>| libsensors-config{a} libsensors5{a} libtcl8.6{a} libtie-ixhash-perl{a}
>| libtk8.6{a} libx11-protocol-perl{a} libxaw7{a} libxcb-dri2-0{a}
>| libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-shape0{a}
>| libxcb-sync1{a} libxml-parser-perl{a} libxml-twig-perl{a}
>| libxml-xpathengine-perl{a} libxmu6{a} libxshmfence1{a} libxss1{a} libxv1{a}
>| libxxf86dga1{a} libxxf86vm1{a} pkg-config{a} r-base{b} r-base
[R-sig-Debian] Failing to install R 4.0.? on Raspian
ed] 5) r-recommended [Not Installed] Leave the following dependencies unresolved: 6) r-base-core recommends r-recommended 7) r-base-core recommends r-base-dev I assume that I have some part of R 3.5.? stuck in the apt system from previously installing R from the default raspian repositories (stupid of me). There is nothing in /usr/lib/R (no directory) nor does /usr/bin/R exist and I have (in desperation: not something I remember doing often with Debian machines) even rebooted the machine but no change. I could wipe the machine and start over and not install R until after adding the buster line deb http://cloud.r-project.org/bin/linux/debian buster-cran40/ to /etc/apt/sources.list and doing apt-get update However, I thought I'd check things out here first. Thanks in advance for any suggestions. Chris -- Small contribution in our coronavirus rigours: https://www.coresystemtrust.org.uk/home/free-options-to-replace-paper-core-forms-during-the-coronavirus-pandemic/ Chris Evans Visiting Professor, University of Sheffield I do some consultation work for the University of Roehampton and other places but remains my main Email address. I have a work web site at: https://www.psyctc.org/psyctc/ and a site I manage for CORE and CORE system trust at: http://www.coresystemtrust.org.uk/ I have "semigrated" to France, see: https://www.psyctc.org/pelerinage2016/semigrating-to-france/ https://www.psyctc.org/pelerinage2016/register-to-get-updates-from-pelerinage2016/ If you want an Emeeting, I am trying to keep them to Thursdays and my diary is at: https://www.psyctc.org/pelerinage2016/ceworkdiary/ Beware: French time, generally an hour ahead of UK. ___ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
Re: [R-sig-Debian] Problem installing tkrplot package on Ubuntu 20.04
Perfect. I can confirm that's fixed it. Clearly I missed on those repository
changes somehow.
As, ever, in awe at all the help here and the incredible work that you and
others do for us Michael.
Chris
- Original Message -
> From: "Michael Rutter"
> To: "r-sig-debian"
> Sent: Sunday, 7 February, 2021 15:05:56
> Subject: Re: [R-sig-Debian] Problem installing tkrplot package on Ubuntu
> 20.04
> Chris,
>
> The following should solve your issues. Run from the command line in
> Ubuntu, not in R.
>
> sudo add-apt-repository ppa:marutter/rrutter4.0
> sudo add-apt-repository ppa:c2d4u.team/c2d4u4.0+
> sudo apt update
> sudo apt install r-cran-tkrplot
>
> There is a good chance the package you are interested in is on my PPA
> c2d4u4.0+.
>
> Michael
>
> On 2/7/21 3:59 AM, Chris Evans wrote:
>> I hope this is the correct list, I _think_ you stretch to Ubuntu as well as
>> Debian (recent posts seem to say so!)
>>
>> I tried to update packages on my fallback Windows machine and got a message
>> saying "tk.h" was missing. I reinstalled Rtools: same.
>>
>> That's for another message somewhere but, perhaps pride before a fall, I
>> thought
>> "Ha, I bet it works fine in Linux" ... and it doesn't,
>> well, not for me! I tried this:
>>
>>> install.packages("tkrplot")
>
> ___
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> R-SIG-Debian@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-debian
--
Small contribution in our coronavirus rigours:
https://www.coresystemtrust.org.uk/home/free-options-to-replace-paper-core-forms-during-the-coronavirus-pandemic/
Chris Evans Visiting Professor, University of Sheffield
I do some consultation work for the University of Roehampton
and other places
but remains my main Email address. I have a work web site
at:
https://www.psyctc.org/psyctc/
and a site I manage for CORE and CORE system trust at:
http://www.coresystemtrust.org.uk/
I have "semigrated" to France, see:
https://www.psyctc.org/pelerinage2016/semigrating-to-france/
https://www.psyctc.org/pelerinage2016/register-to-get-updates-from-pelerinage2016/
If you want an Emeeting, I am trying to keep them to Thursdays and my diary is
at:
https://www.psyctc.org/pelerinage2016/ceworkdiary/
Beware: French time, generally an hour ahead of UK.
[[alternative HTML version deleted]]
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[R-sig-Debian] Problem installing tkrplot package on Ubuntu 20.04
I hope this is the correct list, I _think_ you stretch to Ubuntu as well as
Debian (recent posts seem to say so!)
I tried to update packages on my fallback Windows machine and got a message
saying "tk.h" was missing. I reinstalled Rtools: same.
That's for another message somewhere but, perhaps pride before a fall, I
thought "Ha, I bet it works fine in Linux" ... and it doesn't,
well, not for me! I tried this:
> install.packages("tkrplot")
Installing package into ‘/home/chris/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/tkrplot_0.0-25.tar.gz'
Content type 'application/x-gzip' length 39274 bytes (38 KB)
==
downloaded 38 KB
* installing *source* package ‘tkrplot’ ...
** package ‘tkrplot’ successfully unpacked and MD5 sums checked
** using staged installation
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/include/tcl8.6
-I/usr/include/tcl8.6 -fpic -g -O2
-fdebug-prefix-map=/build/r-base-8T8CYO/r-base-4.0.3=. -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c
tcltkimg.c -o tcltkimg.o
tcltkimg.c:3:10: fatal error: tk.h: No such file or directory
3 | #include
| ^~
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:172: tcltkimg.o] Error 1
ERROR: compilation failed for package ‘tkrplot’
* removing ‘/home/chris/R/x86_64-pc-linux-gnu-library/4.0/tkrplot’
The downloaded source packages are in
‘/tmp/RtmpOWOdyG/downloaded_packages’
Warning message:
In install.packages("tkrplot") :
installation of package ‘tkrplot’ had non-zero exit status
OK. So I searched and found this
(https://stat.ethz.ch/pipermail/r-sig-debian/2018-September/002956.html):
On 21 September 2018 at 20:10, Mark Leeds wrote:
| All of a sudden, I had the brilliant idea to google and the command below
| solved the problem. My apologies for noise.
|
| sudo apt-get install tk-dev
Still too difficult / laborious. Next time remember to do
apt-cache searck tkrplot # or any other search term
which would have lead you to
r-cran-tkrplot
which implies
sudo apt install r-cran-tkrplot
is all you need. No need for the ballast of two -dev packages, no need to
locally compile. There is a reason I packaged this maybe 15 years ago ...
Dirk
Fair point! So ...
chris@chris-Aether2:~/Rupdate$ sudo apt-get install r-cran-tkrplot
[sudo] password for chris:
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies.
r-cran-tkrplot : Depends: r-api-3.5
E: Unable to correct problems, you have held broken packages.
Aha, but apt-check and other things all say I don't have held or broken
packages and I think r-api-3.5 is for R 3.5 whereas I'm on 4.0.3 (courtesy
of the amazing work that people here do to package R for Debian and Ubuntu:
eternal thanks!)
So I've hit the outer edge of my IT competences and thought I should post here
before doing anything more. As I say, R is 4.0.3 and Ubuntu is
updated this more 20.04.
TIA,
Chris
--
Small contribution in our coronavirus rigours:
https://www.coresystemtrust.org.uk/home/free-options-to-replace-paper-core-forms-during-the-coronavirus-pandemic/
Chris Evans Visiting Professor, University of Sheffield
I do some consultation work for the University of Roehampton
and other places
but remains my main Email address. I have a work web site
at:
https://www.psyctc.org/psyctc/
and a site I manage for CORE and CORE system trust at:
http://www.coresystemtrust.org.uk/
I have "semigrated" to France, see:
https://www.psyctc.org/pelerinage2016/semigrating-to-france/
https://www.psyctc.org/pelerinage2016/register-to-get-updates-from-pelerinage2016/
If you want an Emeeting, I am trying to keep them to Thursdays and my diary is
at:
https://www.psyctc.org/pelerinage2016/ceworkdiary/
Beware: French time, generally an hour ahead of UK.
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Re: [R-sig-Debian] So nearly there, but can't install rJava
Thanks Sebastian, Johannes and Dirk for your inputs, I think this can be marked
[SOLVED] though I still don't understand how it started.
The answer seems to be that something sets an environment variable
JAVA.LIBRARY.PATH and this wasn't set correctly. I had never directly done
anything to set that so that's odd but what I had done that was causing the
problem (I think) is that I had used /etc/environment to set JAVA.HOME (I think
that's the spelling). I had set that correctly to point to the openjdk
directory but clearly that was causing something else to misset
JAVA.LIBRARY.PATH hence the "R CMD config JAVA" instruction not finding the
header. When I realised it was that environment variable that was at fault I
rebooted the machine to get a clean start (having deleted my /etc/environment)
and then "R CMD config JAVA" worked and then install.packages("rJava") worked
and I'm happy.
I still don't know what had caused the problem in the first place: I hadn't
directly edited anything or changed anything until I hit the first failure of
"R CMD config JAVA". After that I used synaptic to add to java related things
installed on the machine and I assume somewhere in that process I managed to do
something that messed up the environment variable. That seems surprising or
frankly unlikely but I know I didn't do anything else that might have done
this. I was going through that whole slew of installing other things using
apt-get and there was one dependency that I downloaded and compiled with the
full ./configure, make, make clean, make install sequence (began with g? can't
remember name, the HH package depended on it, I remember that much, perhaps
there was an easier way to get that). I can't see that any of that should have
hit this environment variable but clearly something I did caused it and it's
sorted now.
I can play around with the shiny server now on this local machine and be sure I
feel safe with it before I install it on my main server.
Final question to anyone who has read this far: any advice about using the open
source shiny server on a Debian stretch server? It's a fairly well equipped VM
provided by my ISP and also runs WordPress for several WP sites but nothing
much else beyond a one plain old apache site.
Very best all and thanks again,
Chris
- Original Message -
> From: "Sebastian Meyer"
> To: "r-sig-debian"
> Sent: Tuesday, 22 January, 2019 15:22:33
> Subject: Re: [R-sig-Debian] So nearly there, but can't install rJava
> Dear Chris,
>
> Maybe you could try debugging the error
>
>> *** Java interpreter doesn't work properly.
>
> based on the underlying javareconf script.
>
> Scrolling through
>
>> less `R RHOME`/bin/javareconf
>
> we can see that the script exits from
>
>> echo "Java interpreter : $JAVA"
>> jires=`$JAVA -classpath ${tools_classpath} getsp -test`
>> if test "$jires" != "Test1234OK"; then
>> echo "$jires"
>> echo "~*** Java interpreter doesn't work properly.~"|${SED-sed} -e 'y/~/\n/'
>> >&2
>> exit 1
>> fi
>
> From your output we can see that the Java interpreter ($JAVA) has been
> found at /usr/lib/jvm/default-java/jre/bin/java, but the subsequent call
> failed / didn't return the expected test result.
>
> You could try to run that code manually and see what you get and where
> the problem is:
>
>> JAVA=`R CMD config JAVA`
>> echo $JAVA
>> ## /usr/lib/jvm/default-java/jre/bin/java
>
>> R_SHARE_DIR=`R --slave -e 'cat(R.home("share"))'`
>> echo $R_SHARE_DIR
>> ## /usr/share/R/share
>
>> tools_classpath=${R_SHARE_DIR}/java
>> ls $tools_classpath
>> ## getsp.class README
>
>> $JAVA -classpath ${tools_classpath} getsp -test
>> ## Test1234OK
>
> NB: the variable R_SHARE_DIR is set in the `which R` script.
>
> Good luck!
>
> Sebastian
>
>
> Am 22.01.19 um 14:45 schrieb Chris Evans:
>> Thanks Dirk and Enrico,
>>
>> First clarification: I'm in this mess because I'm trying to run R 3.5.2
>> within
>> Debian stable (9/"sretch") using the stretch-cran35 repository. That uses
>> and
>> provides r-api-35 but many of the packages depend upon r-api-3. As Johannes
>> said a day or so back, the way around this is to use install.packages() in R
>> to
>> get the packages you want. That leads you into quite a lot of manual
>> identification of dependencies and I worked through all the ones I hit until
>> I
>> was left with the only packages I use that I can't install sharing just one
>> dependency: they all depend on rJava and I can't i
Re: [R-sig-Debian] So nearly there, but can't install rJava
Thanks Dirk and Enrico,
First clarification: I'm in this mess because I'm trying to run R 3.5.2 within
Debian stable (9/"sretch") using the stretch-cran35 repository. That uses and
provides r-api-35 but many of the packages depend upon r-api-3. As Johannes
said a day or so back, the way around this is to use install.packages() in R to
get the packages you want. That leads you into quite a lot of manual
identification of dependencies and I worked through all the ones I hit until I
was left with the only packages I use that I can't install sharing just one
dependency: they all depend on rJava and I can't install from the r-cran-rjava
package in the stretch-cran35 repository because that's one of the packages
that depends on r-api-3.
I thought that installing the default java and jdk Debian packages and using R
CMD javareconf (as root) would set the right variables for
install.packages("rJava") to work but no go. It fails with this information:
checking Java support in R... present:
interpreter : '/usr/lib/jvm/default-java/jre/bin/java'
archiver: '/usr/lib/jvm/default-java/bin/jar'
compiler: '/usr/lib/jvm/default-java/bin/javac'
header prep.: '/usr/lib/jvm/default-java/bin/javah'
cpp flags : ''
java libs : ''
configure: error: One or more Java configuration variables are not set.
Make sure R is configured with full Java support (including JDK). Run
R CMD javareconf
as root to add Java support to R.
If you don't have root privileges, run
R CMD javareconf -e
to set all Java-related variables and then install rJava.
ERROR: configuration failed for package ‘rJava’
* removing ‘/usr/local/lib/R/site-library/rJava’
I think the problem may be options setting where R/rJava will look for Java so
I tried:
> options(java.home="/usr/lib/jvm/java-8-openjdk-amd64/")
> options("java.home")
$java.home
[1] "/usr/lib/jvm/java-8-openjdk-amd64/"
but that doesn't change things.
As far as I can see Debian is happy with the setup of java and javac:
root@DebianAdvent:/home/chris/Downloads/gmp-6.1.2# java -version
openjdk version "1.8.0_181"
OpenJDK Runtime Environment (build 1.8.0_181-8u181-b13-2~deb9u1-b13)
OpenJDK 64-Bit Server VM (build 25.181-b13, mixed mode)
root@DebianAdvent:/home/chris/Downloads/gmp-6.1.2# javac -version
javac 1.8.0_181
root@DebianAdvent:/home/chris/Downloads/gmp-6.1.2# update-alternatives --config
javac
There is only one alternative in link group javac (providing /usr/bin/javac):
/usr/lib/jvm/java-8-openjdk-amd64/bin/javac
Nothing to configure.
root@DebianAdvent:/home/chris/Downloads/gmp-6.1.2# update-alternatives --config
java
There is only one alternative in link group java (providing /usr/bin/java):
/usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java
Nothing to configure.
root@DebianAdvent:/home/chris/Downloads/gmp-6.1.2#
And I have the full jdk not just the headless version I can see the header
files:
root@DebianAdvent:/home/chris/Downloads/gmp-6.1.2# ls -lsart
/usr/lib/jvm/java-8-openjdk-amd64/include/
total 220
80 -rw-r--r-- 1 root root 78425 Oct 22 19:05 jvmti.h
8 -rw-r--r-- 1 root root 4771 Oct 22 19:05 jvmticmlr.h
76 -rw-r--r-- 1 root root 74698 Oct 22 19:05 jni.h
8 -rw-r--r-- 1 root root 7404 Oct 22 19:05 jdwpTransport.h
12 -rw-r--r-- 1 root root 9687 Oct 22 19:05 jawt.h
24 -rw-r--r-- 1 root root 21125 Oct 22 19:05 classfile_constants.h
4 drwxr-xr-x 2 root root 4096 Jan 22 08:09 linux
4 drwxr-xr-x 3 root root 4096 Jan 22 08:09 .
4 drwxr-xr-x 8 root root 4096 Jan 22 12:55 ..
root@DebianAdvent:/home/chris/Downloads/gmp-6.1.2#
But I can't reconfigure R for Java:
root@DebianAdvent:/home/chris/Downloads/gmp-6.1.2# R CMD javareconf
*** JAVA_HOME is not a valid path, ignoring
Java interpreter : /usr/lib/jvm/default-java/jre/bin/java
/usr/lib/R/bin/javareconf: 1: /usr/lib/R/bin/javareconf:
/usr/lib/jvm/default-java/jre/bin/java: not found
*** Java interpreter doesn't work properly.
root@DebianAdvent:/home/chris/Downloads/gmp-6.1.2#
I hope this helps someone see something I can fix!
Tangential question: surely I'm not rare in running R 3.5.2 on Stretch am I?
Other tangential question: is there anything that can be done to fix the
r-api-3/r-api-3.5 issue. You can see I'm no programmer or sysadmin but if
there is anything I can do to help ...?
TIA all,
Chris
- Original Message -
> From: "Dirk Eddelbuettel"
> To: "Chris Evans"
> Cc: "r-sig-debian"
> Sent: Tuesday, 22 January, 2019 12:21:39
> Subject: Re: [R-sig-Debian] So nearly there, but can't install rJava
> On 22 January 2019 at 10:14, Chris Evans wrote:
>| root@DebianAdvent:/home/chris/Downloads/gmp-6.1.2# apt-get install
>| openjdk-8-jdk-headless
>| Reading package lists... Done
>| Building dependency tree
>| Reading state information... Done
>| openjdk-8-jdk-headless is already the newest version (8u181-b13-2~deb9u1).
>| openjdk-8-jdk
Re: [R-sig-Debian] So nearly there, but can't install rJava
As ever, I learn from this: I didn't know apt-file. Got it, installed it, used it: root@DebianAdvent:/home/chris/Downloads/gmp-6.1.2# apt-file search jni.h android-libnativehelper-dev: /usr/include/android/nativehelper/jni.h android-platform-frameworks-native-headers: /usr/include/android/android/asset_manager_jni.h android-platform-frameworks-native-headers: /usr/include/android/android/native_window_jni.h gcj-6-jdk: /usr/lib/gcc/x86_64-linux-gnu/6/include/jni.h gcj-6-jdk: /usr/lib/jvm/java-1.5.0-gcj-6-amd64/include/jni.h libavcodec-dev: /usr/include/x86_64-linux-gnu/libavcodec/jni.h libgluegen2-build-java: /usr/share/gluegen2/make/stub_includes/jni/jni.h openjdk-8-jdk-headless: /usr/lib/jvm/java-8-openjdk-amd64/include/jni.h I was 99% sure I already had that last installed. Sure enough: root@DebianAdvent:/home/chris/Downloads/gmp-6.1.2# apt-get install openjdk-8-jdk-headless Reading package lists... Done Building dependency tree Reading state information... Done openjdk-8-jdk-headless is already the newest version (8u181-b13-2~deb9u1). openjdk-8-jdk-headless set to manually installed. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Anyone else got any ideas? Chris > From: "Johannes Ranke" > To: "r-sig-debian" , "Chris Evans" > > Sent: Tuesday, 22 January, 2019 08:47:28 > Subject: Re: [R-sig-Debian] So nearly there, but can't install rJava > Am Dienstag, 22. Januar 2019, 08:27:14 CET schrieb Chris Evans: > ... > > error: jni.h: No such file or directory > > #include > > ^ > > compilation terminated. > You get a complaint that jni.h is missing. So one strategy would be to look > for > this file in the available packages: > sudo apt-file search jni.h > One of the packages returned is openjdk-8-jdk-headless (which I happen to have > installed). I think (others will know for certain) that you need a Java > Development Kit (jdk) not just a runtime environment (jre). > Cheers, > Johannes -- Chris Evans Skype: chris-psyctc Visiting Professor, University of Sheffield I do some consultation work for the University of Roehampton and other places but this remains my main Email address. I have "semigrated" to France, see: https://www.psyctc.org/pelerinage2016/semigrating-to-france/ if you want to book to talk, I am trying to keep that to Thursdays and my diary is now available at: https://www.psyctc.org/pelerinage2016/ecwd_calendar/calendar/ Beware: French time, generally an hour ahead of UK. That page will also take you to my blog which started with earlier joys in France and Spain! [[alternative HTML version deleted]] ___ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
[R-sig-Debian] So nearly there, but can't install rJava
Wow, this has amplified my respect and gratitude for the R Debian repositories. Doing all the install.packages() and following the clues about missing dependencies has taken hours! However, I have almost all the packages I want installed on this machine and Rstudio and the shiny server are installed and running fine. Bizarrely, to my mind, I am totally failing on rJava and hence a number of packages that depend on it. In R I get: checking Java support in R... present: interpreter : '/usr/lib/jvm/default-java/jre/bin/java' archiver : '' compiler : '' header prep.: '' cpp flags : '' java libs : '' configure: error: Java Development Kit (JDK) is missing or not registered in R Make sure R is configured with full Java support (including JDK). Run R CMD javareconf as root to add Java support to R. When I do R CMD javareconf I get this: root@DebianAdvent:/home/chris/Downloads/gmp-6.1.2# R CMD javareconf Java interpreter : /usr/lib/jvm/default-java/jre/bin/java Java version : 1.8.0_181 Java home path : /usr/lib/jvm/default-java Java compiler : /usr/lib/jvm/default-java/bin/javac Java headers gen.: /usr/lib/jvm/default-java/bin/javah Java archive tool: /usr/lib/jvm/default-java/bin/jar trying to compile and link a JNI program detected JNI cpp flags : detected JNI linker flags : gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/home/jranke/git/r-backports/stretch/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c conftest.c -o conftest.o conftest.c:1:17: fatal error: jni.h: No such file or directory #include ^ compilation terminated. /usr/lib/R/etc/Makeconf:162: recipe for target 'conftest.o' failed make: *** [conftest.o] Error 1 Unable to compile a JNI program JAVA_HOME : /usr/lib/jvm/default-java Java library path: JNI cpp flags : JNI linker flags : Updating Java configuration in /usr/lib/R Done. I'm pretty sure that the problem is with some missing path but I also know I'm out of my depth (again). I'm a bit puzzled because I have only installed default Debian things. Do I need particular non-default Java or Java related components? TIA (again!), Chris -- Chris Evans Skype: chris-psyctc Visiting Professor, University of Sheffield I do some consultation work for the University of Roehampton and other places but this remains my main Email address. I have "semigrated" to France, see: https://www.psyctc.org/pelerinage2016/semigrating-to-france/ if you want to book to talk, I am trying to keep that to Thursdays and my diary is now available at: https://www.psyctc.org/pelerinage2016/ecwd_calendar/calendar/ Beware: French time, generally an hour ahead of UK. That page will also take you to my blog which started with earlier joys in France and Spain! [[alternative HTML version deleted]] ___ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
Re: [R-sig-Debian] r-api-3 with R 3.5.2. on Stretch: is there a workaround?
Thanks for confirming Johannes. I take it that the "new, richer ..." option
would be a lot of work. I'm happy to let this old laptop grind through.
There's the silver lining for me that when I did this install.packages() for
pretty much the same list of packages on the server it ran through it pretty
fast so it's nice that the laptop is reminding me how fast the server is!
Very best to all,
Chris
- Original Message -
> From: "Johannes Ranke"
> To: "r-sig-debian" , "Chris Evans"
>
> Sent: Monday, 21 January, 2019 14:12:07
> Subject: Re: [R-sig-Debian] r-api-3 with R 3.5.2. on Stretch: is there a
> workaround?
> Chris,
>
> yes, the workaround is to install from within R. The alternative would be to
> increase the coverage of this repo, as currently mainly the recommended
> packages are supported. Another alternative would be to create a new, richer
> repo...
>
> Kind regards,
>
> Johannes
>
> Am Montag, 21. Januar 2019, 13:45:52 CET schrieb Chris Evans:
>> Now that I am at least mapping the right repository to my Debian version
>> (doh!) I have another question. In the installation page at
>> https://cran.r-project.org/bin/linux/debian/#debian-stretch-stable there is
>> the line:
>>
>> "Please note that R packages from the Debian stretch distribution are not
>> compatible with R 3.5.x, as it provides r-api-3.5, while the stretch
>> packages depend on r-api-3."
>>
>> Certainly a number of packages won't install with Synaptic giving the
>> complaint about depending on r-api-3 and not having it, exactly as that
>> line says. It seems that one package that gives this error, car, builds
>> fine in R with the usual install.packages("car") (after dealing with the
>> curl library dependency).
>>
>> Am I right that the workaround is to install all the affected packages
>> within R? On the very slow old laptop I'm using for this work that is
>> taking ages and I'm guessing that had I been able to install the debs the
>> installation would have been much faster.
>>
>> Is there a workaround or am I right that installing within R _is_ the
>> workaround?
>>
>> TIA (again),
>>
>> Chris
>
>
> --
> Johannes Ranke
> Wissenschaftlicher Berater
> https://jrwb.de/contact
--
Chris Evans Skype: chris-psyctc
Visiting Professor, University of Sheffield
I do some consultation work for the University of Roehampton
and other places but this
remains my main Email address.
I have "semigrated" to France, see:
https://www.psyctc.org/pelerinage2016/semigrating-to-france/ if you want to
book to talk, I am trying to keep that to Thursdays and my diary is now
available at: https://www.psyctc.org/pelerinage2016/ecwd_calendar/calendar/
Beware: French time, generally an hour ahead of UK. That page will also take
you to my blog which started with earlier joys in France and Spain!
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[R-sig-Debian] r-api-3 with R 3.5.2. on Stretch: is there a workaround?
Now that I am at least mapping the right repository to my Debian version (doh!)
I have another question. In the installation page at
https://cran.r-project.org/bin/linux/debian/#debian-stretch-stable there is the
line:
"Please note that R packages from the Debian stretch distribution are not
compatible with R 3.5.x, as it provides r-api-3.5, while the stretch packages
depend on r-api-3."
Certainly a number of packages won't install with Synaptic giving the complaint
about depending on r-api-3 and not having it, exactly as that line says. It
seems that one package that gives this error, car, builds fine in R with the
usual install.packages("car") (after dealing with the curl library dependency).
Am I right that the workaround is to install all the affected packages within
R? On the very slow old laptop I'm using for this work that is taking ages and
I'm guessing that had I been able to install the debs the installation would
have been much faster.
Is there a workaround or am I right that installing within R _is_ the
workaround?
TIA (again),
Chris
--
Chris Evans Skype: chris-psyctc
Visiting Professor, University of Sheffield
I do some consultation work for the University of Roehampton
and other places but this
remains my main Email address.
I have "semigrated" to France, see:
https://www.psyctc.org/pelerinage2016/semigrating-to-france/ if you want to
book to talk, I am trying to keep that to Thursdays and my diary is now
available at: https://www.psyctc.org/pelerinage2016/ecwd_calendar/calendar/
Beware: French time, generally an hour ahead of UK. That page will also take
you to my blog which started with earlier joys in France and Spain!
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[R-sig-Debian] Still hitting odd problems trying to install R 3.5.2 on Debian amd64 machine
iecran.0) but it is not going to be installed Depends: r-recommended (= 3.5.2-1~jessiecran.0) but it is not going to be installed Recommends: r-base-html but it is not going to be installed E: Unable to correct problems, you have held broken packages. root@DebianAdvent:/etc/apt# apt-get install r-base-core Reading package lists... Done Building dependency tree Reading state information... Done Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies: r-base-core : Depends: libicu52 (>= 52~m1-1~) but it is not installable Depends: libpng12-0 (>= 1.2.13-4) but it is not installable Depends: libreadline6 (>= 6.0) but it is not installable Recommends: r-recommended but it is not going to be installed Recommends: r-base-dev but it is not going to be installed Recommends: r-doc-html but it is not going to be installed E: Unable to correct problems, you have held broken packages. root@DebianAdvent:/etc/apt# r-base-core: Depends: libicu52 (>=52~m1-1~) but it is not installable Depends: libpng12-0 (>=1.2.13-4) but it is not installable Depends: libreadline6 (>=6.0) but it is not installable Recommends: r-recommended but it is not going to be installed Recommends: r-base-dev but it is not going to be installed At this point, before trying anything more under my own, perhaps inept, steam, I decided to stop and ask the list if someone can see from those messages what I'm doing wrong. Here is my current sources.list: chris@DebianAdvent:~$ cd /etc/apt chris@DebianAdvent:/etc/apt$ cat sources.list # deb cdrom:[Debian GNU/Linux 9.6.0 _Stretch_ - Official amd64 NETINST 20181110-11:34]/ stretch main # deb cdrom:[Debian GNU/Linux 9.6.0 _Stretch_ - Official amd64 NETINST 20181110-11:34]/ stretch main deb http://mirror.mythic-beasts.com/debian/ stretch main contrib non-free deb-src http://mirror.mythic-beasts.com/debian/ stretch contrib main non-free deb http://security.debian.org/debian-security/ stretch/updates main deb-src http://security.debian.org/debian-security/ stretch/updates main # stretch-updates, previously known as 'volatile' deb http://mirror.mythic-beasts.com/debian/ stretch-updates main deb-src http://mirror.mythic-beasts.com/debian/ stretch-updates main ### that was where I'd gotten to with synaptic ### this is for CRAN for Debian deb http://cran.ma.imperial.ac.uk/bin/linux/debian jessie-cran35/ deb-src http://cran.ma.imperial.ac.uk/bin/linux/debian jessie-cran35/ chris@DebianAdvent:/etc/apt$ TIA, Chris -- Chris Evans Skype: chris-psyctc Visiting Professor, University of Sheffield I do some consultation work for the University of Roehampton and other places but this remains my main Email address. I have "semigrated" to France, see: https://www.psyctc.org/pelerinage2016/semigrating-to-france/ if you want to book to talk, I am trying to keep that to Thursdays and my diary is now available at: https://www.psyctc.org/pelerinage2016/ecwd_calendar/calendar/ Beware: French time, generally an hour ahead of UK. That page will also take you to my blog which started with earlier joys in France and Spain! ___ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
Re: [R-sig-Debian] Installing Rstudio and shiny free server on Debian
- Original Message - > From: "Dirk Eddelbuettel" > To: "Chris Evans" > Cc: "r-sig-debian" > Sent: Saturday, 12 January, 2019 21:23:46 > Subject: Re: [R-sig-Debian] Installing Rstudio and shiny free server on Debian > On 12 January 2019 at 20:30, Chris Evans wrote: >| I wonder if I'm hitting problems you're not seeing not only because of >running >| stretch/stable but also because of running the i386 version. I suspect most >| people are on 64 bit systems now. > > Cannot speak to i386. I gave up on it relatively late given that I always had > lower-memory laptops. It may be time to let that one go. Yes! Surreal oddity of the Toshiba that it won't accept amd64 of either Debian or Ubuntu. I never liked it and I don't think they have a great record of sympathy with FLOSS. I'll find another machine that will take amd64 and relegate this to a curiosity, or recycle it! > I can only speak to amd64. Which works *great* and very reliably. I had assumed so and believe you completely. Always been true on my various www server machines over the years, i386 and then, latterly, amd64. I was working with R, Emacs and ESS on those though, not Rstudio. Now do almost all my R work through Rstudio and, sadly, for now, on Windoze laptops. About to try to change that, but that's another story! >| root@Toshiba-L750-Stretchi386:/etc/apt# apt-get install rstudio > > Your thinko. Dont' understand "thinko"! > I have known JJ Nor do I understand "JJ"! > for nearly ten years, and I have complained > nearly all that time that they need an apt-get'able repo. If you mean Rstudio.com, for Rstudio and the free server then I agree completely and it seems daft they don't, particularly as they offer a CRAN mirror. (If I understand your "JJ" correctly.) > Which they don't have, so you read the instructions wrong. Download, then > 'sudo dpkg -i' (or do 'sudo gdebi ...' per their instructions). I had downloaded, and I was in a root session, hence no "sudo". I think that's OK (though I know some people, Knoppixers particularly, think people like me who still use "su" and open root sessions are dark shapeshifters who should be burned at the stake!) >| Has anyone been able to download and install the server on a 64bit Debian >| stretch system? > > Easily by manual downloads first. Great. Now to find an old machine that _will_ host amd64 stretch and follow your example! Then on to the actual server!! Many thanks again, Chris > Dirk > > -- > http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org -- Chris Evans Skype: chris-psyctc Visiting Professor, University of Sheffield I do some consultation work for the University of Roehampton and other places but this remains my main Email address. I have "semigrated" to France, see: https://www.psyctc.org/pelerinage2016/semigrating-to-france/ if you want to book to talk, I am trying to keep that to Thursdays and my diary is now available at: https://www.psyctc.org/pelerinage2016/ecwd_calendar/calendar/ Beware: French time, generally an hour ahead of UK. That page will also take you to my blog which started with earlier joys in France and Spain! ___ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
Re: [R-sig-Debian] Installing Rstudio and shiny free server on Debian
Thanks Dirk, I wonder if I'm hitting problems you're not seeing not only because of running stretch/stable but also because of running the i386 version. I suspect most people are on 64 bit systems now. Anyway, I have managed to install Rstudio OK by going up to stretch-cran35. Rstudio wouldn't install from there: root@Toshiba-L750-Stretchi386:/etc/apt# apt-get install rstudio Reading package lists... Done Building dependency tree Reading state information... Done Package rstudio is not available, but is referred to by another package. This may mean that the package is missing, has been obsoleted, or is only available from another source E: Package 'rstudio' has no installation candidate But pulling the i386 deb from https://download2.rstudio.org/rstudio-server-1.1.463-i386.deb got me the complaint about libgstreamer: root@Toshiba-L750-Stretchi386:/home/chris/Downloads# gdebi rstudio-1.1.463-i386.deb Reading package lists... Done Building dependency tree Reading state information... Done Reading state information... Done This package is uninstallable Dependency is not satisfiable: libgstreamer0.10-0 But I then found https://unix.stackexchange.com/questions/277238/is-it-possible-to-install-both-gstreamer-0-10-and-gstreamer-1-0-at-the-same-time and followed the advice there: "I managed to get processing-video 2.2.1 to work, installing the corresponding Debian Jessie .deb files downloaded via https://pkgs.org: gstreamer-0.10-gconf gstreamer-0.10-plugins-base libgstreamer0.10-0 libgstreamer-plugins-base0.10-0" I pulled down those last two, installed them with dpkg -i, and now Rstudio has installed from the Rstudio deb I had pulled down and, on a cursory check, it seems to work fine. The rstudio-server-1.1.463-i386.deb also says it's installed but is, not to my surprise, giving error messages rather than starting up: root@Toshiba-L750-Stretchi386:/home/chris/Downloads# dpkg -i rstudio-server-1.1.463-i386.deb Selecting previously unselected package rstudio-server. (Reading database ... 174017 files and directories currently installed.) Preparing to unpack rstudio-server-1.1.463-i386.deb ... Unpacking rstudio-server (1.1.463) ... Setting up rstudio-server (1.1.463) ... groupadd: group 'rstudio-server' already exists rsession: no process found Created symlink /etc/systemd/system/multi-user.target.wants/rstudio-server.service → /etc/systemd/system/rstudio-server.service. Job for rstudio-server.service failed because the control process exited with error code. See "systemctl status rstudio-server.service" and "journalctl -xe" for details. ● rstudio-server.service - RStudio Server Loaded: loaded (/etc/systemd/system/rstudio-server.service; enabled; vendor preset: enabled) Active: activating (auto-restart) (Result: exit-code) since Sat 2019-01-12 19:54:34 GMT; 29ms ago Process: 4107 ExecStart=/usr/lib/rstudio-server/bin/rserver (code=exited, status=127) Jan 12 19:54:34 Toshiba-L750-Stretchi386 systemd[1]: Failed to start RStudio Server. Jan 12 19:54:34 Toshiba-L750-Stretchi386 systemd[1]: rstudio-server.service: Unit entered failed state. Jan 12 19:54:34 Toshiba-L750-Stretchi386 systemd[1]: rstudio-server.service: Failed with result 'exit-code'. I will do some more sleuthing around to see if I can get beyond that but from what I'm seeing in https://www.rstudio.com/products/rstudio/download-server/ I may be at a dead end here as I think the deb that I am trying to install there is the one for Debian 8 and it looks as if they've only rolled a deb for amd64 for Debian "9+" Last question, to everyone, for tonight: Has anyone been able to download and install the server on a 64bit Debian stretch system? TIA, Chris - Original Message ----- > From: "Dirk Eddelbuettel" > To: "Chris Evans" > Cc: "r-sig-debian" > Sent: Saturday, 12 January, 2019 14:58:10 > Subject: Re: [R-sig-Debian] Installing Rstudio and shiny free server on Debian > Chris, > > I fear you may be overcomplicating things. RStudio tends to just work; the > .deb files are also large and "mostly self-contained" -- so that generally > only require one or two other packages you should find without trouble. Of > course I cannot fully speak to your experience as I do not run Debian stable > (mostly current Debian (ie "testing") or Ubuntu (ie now 18.10) for me), as > well as Docker rather than VMs. > > The README at the RStudio site also tends to cover what you need. And no, I > don't think I know a single person who'd recommend compiling from source. > > So I would say just try it and if something comes up come back here, and we > will try to help. Lastly, recall that installations of packages should be > fully reversible (unless you do unspeakable things). So if for whatever > reason the .deb does not install,
[R-sig-Debian] Installing Rstudio and shiny free server on Debian
First, as I'm here and owe it: huge thanks to Dirk and others who maintain the Debian packaging. Second: I realise these questions are not right on topic here and I will go to the rstudio community support next but I'm failing to find answers elsewhere on the web which makes me suspect they haven't come up there and might well be Debian specific so I suspect that if the expertise I'm looking for is anywhere, it will be here. Context: I've run an internet server on Debian systems for about 15 years and Debian is the only distro I've ever used. I'm in the process of moving some ancient, interactive forms that do simple things using CGIwithR to Shiny apps as it'll clearly be way easier for me to create new ones and update existing ones using shiny rather than CGIwithR. I'm starting off using shinyapps.io but I'll have to install the free shiny server in the near future as I can't afford the level at shinyapps.io I will need when I have all the apps I want up and running. My server is a VM set up by the excellent ISP, Mythic Beasts running: 4.9.0-7-amd64 #1 SMP Debian 4.9.110-3+deb9u2 (2018-08-13) x86_64 GNU/Linux I don't want to do what can clearly be a challenging install on that machine for fear of breaking things there so I've turned an old laptop (Toshiba L-750) into a Debian machine but find I can only install i386 on it (neither amd64 Stretch or Ubuntu install on it, they just hang very shortly after starting the install). So here I am having a dry run on that i386 stretch. For now I've got R up to 3.4.4 and pulled the shiny server down from https://download2.rstudio.org/rstudio-server-1.1.463-i386.deb as per https://www.rstudio.com/products/rstudio/download-server/ | https://www.rstudio.com/products/rstudio/download-server/ and I've tried installing it but it fails on a dependency on libgstreamer0.10-0 and on libgstreamer-plugins-base0.10-0 and installing Rstudio seems to fail on the first dependency. Clearly I could start testing out the route of compiling both from source, or I assume I could for the shiny server at least as the instructions seem to be fairly clear. However, I thought I'd ask here if anyone had any experience of installing Rstudio and the free shiny server on Stretch. Meanwhile, I'll go hunting around a couple of other old machines I have around to see if I can find one that'll install amd64 Stretch! TIA, Chris -- Chris Evans Skype: chris-psyctc Visiting Professor, University of Sheffield I do some consultation work for the University of Roehampton and other places but this remains my main Email address. I have "semigrated" to France, see: https://www.psyctc.org/pelerinage2016/semigrating-to-france/ if you want to book to talk, I am trying to keep that to Thursdays and my diary is now available at: https://www.psyctc.org/pelerinage2016/ecwd_calendar/calendar/ Beware: French time, generally an hour ahead of UK. That page will also take you to my blog which started with earlier joys in France and Spain! ___ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
Re: [R-sig-Debian] R 3 and Debian Testing
I think that only gets us R = 3.0.0 if the full line is http://cran.r-project.org/bin/linux/debian/ squeeze-cran3/ I had squeeze-cran/ not squeeze-cran3/ so I wasn't getting the update to 3.0.0. I think I must have been missing some Emails alerting us. Very best all and many, many thanks to the stars who make all this work for lusers like myself. Chris - Original Message - From: Dirk Eddelbuettel e...@debian.org To: Lorenzo Isella lorenzo.ise...@gmail.com Cc: r-sig-debian@r-project.org Sent: Tuesday, 7 May, 2013 5:53:32 PM Subject: Re: [R-sig-Debian] R 3 and Debian Testing On 7 May 2013 at 18:33, Lorenzo Isella wrote: | Dear All, | I am using Debian testing on multiple machine machines at home. | This is my source list | | deb http://ftp.ch.debian.org/debian/ testing main contrib | non-free | deb-src http://ftp.ch.debian.org/debian/ testing main non-free | contrib | | deb http://security.debian.org/ testing/updates main contrib | non-free | deb-src http://security.debian.org/ testing/updates main contrib | non-free | | So, my repositories always point to the latest Debian testing, even | now | after the new release of Debian 7. | I am wondering if, after the new release of Debian 7, R 3 will | become | routinely available to me, without the need to add any specific | repository. The repository mirrored at every CRAN mirror with base page at http://cran.r-project.org/bin/linux/debian/ has been at your disposal for at least half a decade. Thanks to Johannes, R 3.0.0 is only one apt-get update away, and so will R 3.0.1 come May 16 (plus a few days for compiling and mirroring) just like dozens of releases before this one. Dirk -- Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com ___ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian -- Chris Evans ch...@psyctc.org Skype: chris-psyctc Consultant Psychiatrist in Psychotherapy, Notts. PDD network; Professor, Psychotherapy, Nottingham University *If I am writing from one of those roles, it will be clear. Otherwise* *my views are my own and not representative of those institutions* If you have difficulty Emailing me on this address or getting a reply, send again but cc to: chris dot evans at nottshc dot nhs dot uk and to: c dot evans at nottingham dot ac dot uk -- Chris Evans ch...@psyctc.org Skype: chris-psyctc Consultant Psychiatrist in Psychotherapy, Notts. PDD network; Professor, Psychotherapy, Nottingham University *If I am writing from one of those roles, it will be clear. Otherwise* *my views are my own and not representative of those institutions* If you have difficulty Emailing me on this address or getting a reply, send again but cc to: chris dot evans at nottshc dot nhs dot uk and to: c dot evans at nottingham dot ac dot uk ___ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
Re: [R-sig-Debian] Problem updating packages in 2.15.1 on Ubuntu 12.04: updating options
every package and stay up to date. By 2003, I noticed that the R package update would start at 5pm and still be going when I came for work. After that, I had to drop my build everything commitment and started a list of packages I'll always install. Thanks again Paul and John, Chris -- Chris Evans ch...@psyctc.org Skype: chris-psyctc Consultant Psychiatrist in Psychotherapy, Notts. PDD network; Professor, Psychotherapy, Nottingham University *If I am writing from one of those roles, it will be clear. Otherwise* *my views are my own and not representative of those institutions* If you have difficulty Emailing me on this address or getting a reply, send again but cc to: chris dot evans at nottshc dot nhs dot uk and to: c dot evans at nottingham dot ac dot uk ___ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian -- Chris Evans ch...@psyctc.org Skype: chris-psyctc Consultant Psychiatrist in Psychotherapy, Notts. PDD network; Professor, Psychotherapy, Nottingham University *If I am writing from one of those roles, it will be clear. Otherwise* *my views are my own and not representative of those institutions* If you have difficulty Emailing me on this address or getting a reply, send again but cc to: chris dot evans at nottshc dot nhs dot uk and to: c dot evans at nottingham dot ac dot uk ___ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
Re: [R-sig-Debian] Problem updating packages in 2.15.1 on Ubuntu 12.04
[Sorry to those who know all of this, just delete, I think it's worth it getting in the list archives and hence the googleSphere.] Paul Johnson sent the following at 02/08/12 18:39: Greetings On Thu, Aug 2, 2012 at 4:55 AM, Chris Evans chrish...@psyctc.org wrote: Paul Johnson sent the following at 01/08/12 16:01: On Wed, Aug 1, 2012 at 1:02 AM, Chris Evans chrish...@psyctc.org wrote: The specific message is: Warning: package 'spatial' in library '/usr/lib/R/library' will not be updated and the number of libraries about which that's the complaint is now increasingly almost daily so clearly something is wrong. Yes, the something wrong is the system administrator :) Sweet of you to confirm what I myself said (Clearly I don't understand something and am doing something wrong. Please can someone enlighten me?) However, I am only as good as the information I can find and I honestly don't think that's very clear but let's move on from that bit of who's the wrong one. People often say I'm sweet :) !! Please remember that you have a choice of installing R packages from the R repositories using install.packages (or update.packages). That downloads source code, compiles and installs. Generally, on Debian, it will install to /usr/local/lib/R/site-library. But you may also install them as Debian packages that have been built on somebody else's system and wrapped up for your usage. Those generally install into /usr/lib/R/site-library. Are these mutually exclusive ways of doing things? If so, I think we should have a much clearer statement to that effect somewhere. If not, and I had assumed they were not, it would be useful to be told why the two different library locations are used and how R handles things when it may find copies of the same library in different library locations. This is a decision made by the R packager of your Linux distribution, not by the R team. This pattern you are looking at is unique to Debian, although I noticed what Dirk was doing on Debian and thought it was really good, and I explained it to the RedHat packager, and they are doing something similar now. It is a convenient policy, to use /usr/lib/R/library for the packages distributed with R, /usr/lib/R/site-library for the packages built as Debian packages, and then encourage users who install their own to use /usr/loca/lib/R/site-library or ~/R. I don't use Debian packages very often because I, like you, want to compile my own. In order to diagnose your trouble, please lets concentrate on one problem at a time. Do what I do now. Open a terminal. You run $ sudo R and then inside R, run this install.packages(spatial, dep=T, repos=http://rweb.quant.ku.edu/cran;) I put my repos there because I'm reasonably sure it does not suck. I can't speak to other servers. I us install.packages because it gives us a clear avenue to track what's going on. That worked and got me this: chris@chris-tosh:~$ sudo R [sudo] password for chris: R version 2.15.1 (2012-06-22) -- Roasted Marshmallows Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: i686-pc-linux-gnu (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. [Previously saved workspace restored] install.packages(spatial, dep=T, repos=http://rweb.quant.ku.edu/cran;) Installing package(s) into ‘/home/chris/R/i686-pc-linux-gnu-library/2.15’ (as ‘lib’ is unspecified) trying URL 'http://rweb.quant.ku.edu/cran/src/contrib/spatial_7.3-4.tar.gz' Content type 'application/x-gzip' length 44360 bytes (43 Kb) opened URL == downloaded 43 Kb * installing *source* package ‘spatial’ ... ** package ‘spatial’ successfully unpacked and MD5 sums checked ** libs gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c init.c -o init.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c krc.c -o krc.o gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe -g -c pps.c -o pps.o gcc -std=gnu99 -shared -o spatial.so init.o krc.o pps.o -L/usr/lib/R/lib -lR installing to /home/chris/R/i686-pc-linux-gnu-library/2.15/spatial/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (spatial) The downloaded source packages are in ‘/tmp/RtmpPatSiy/downloaded_packages’ So that (to me) is interesting
Re: [R-sig-Debian] Problem updating packages in 2.15.1 on Ubuntu 12.04: updating options
I have changed the subject line to reflect a thread split. Paul Johnson sent the following at 02/08/12 18:39: ... much snipped that was continued in my last posting ... I'm not an unkind person, I'm not trying to insult you by ignoring the rest of your message. Lets fix one thing at a time. As for your complaint that nobody has written out all the details of why things work this way in Debian, well, I suppose you could be the one to write it all out :). If you get a handle on how this works, you could post a blog explanation and we'd all benefit by being able to refer users to it. That's how stuff gets done. Agreed. That way and by google and other search systems picking these things up on archives of lists like these. I'm happy to try to write this up as a bloggish thing but one thing I've become very wary of is such stuff cluttering up the internet long after the open source package in question has moved on. Nowadays I tend to use the time limited searches in Google to restrict things to try to find out if things are recent. I might commit to trying to write an idiots' guide to running R on Ubuntu and Debian and using update.packages() to keep libraries/packages up to date ... but only if I feel confident that I'll find time to keep it current. How did I learn about this packaging policy? I'm pretty sure I asked in this list, and was told the information is in the file that is distributed with the Debian package r-base-core, /usr/share/doc/r-base-core/changelog.Debian.gz, * debian/rules: Add R_LIBS setting to /etc/R/Renviron such that user-installed packages will be in /usr/local/lib/R/site-library, Debian packages will install into /usr/lib/R/site-library and the r-base-core and r-recommended packages will use the standard /usr/lib/R/library directory I know for sure from previous debates here that the Debian packagers expect you to use the packages they provide, and they don't think ordinary users should bother trying to compile packages. OK. Is that true packagers? I've had that impression at times but at other times it has also seemed that the packaging is designed to sit alongside the CRAN repositories simply making it much easier to get the bases of a minimal or a really nearly complete R system easily through the Debian or Ubuntu upgrade systems. However, when I find I'm reading things that way I find myself believing that update.packages() ought to remain a non-deprecated option. That does not speak to the fact that you may not have access to an up-to-date repository for packages for your particular system. John Nash pointed you at one that will work for you. OK. Let's see if I've got this right or wrong. I think there are three repositories that a Ubuntu system can use to update R: 1) CRAN: challenging for raw installation but might be best way to do daily updates using update.packages() and believing that the majority of packages will give error messages explaining why that doesn't work when it doesn't (and to be fair, I think that Rgtk2 and rggobi do give such messages, I just haven't yet been able to spend time nailing down what I might have to do to get them what they want ... or to decided that that's not possible on Ubuntu 12.04) 2) the Debian/Ubuntu repositories that are linked with CRAN mirrors. In my /etc/apt/sources.list these are: deb http://www.stats.bris.ac.uk/R/bin/linux/ubuntu precise/ deb-src http://www.stats.bris.ac.uk/R/bin/linux/ubuntu precise/ These are much more likely than #1 to have all the dependencies already dealt with to provide a compiled library so you should (probably) never have to update other things in your system to get things working if you go this way. However, they may not update as often as #1 and they may lack a few libraries that are in #1 (but if so, it may be because those libraries are a real challenge to compile for Debian/Ubuntu?) 3) Specific Ubuntu ppa repositories which John C Nash makes available at: https://launchpad.net/~marutter/+archive/rrutter I'm not really very clearly how this differs markedly from #2 but it sounds as if it might update more often. As I understand it, I would use update.packages() within R (sudo R) to update using #1 but #2 and #3 will update using synaptic or the Ubuntu package update system. I am very unclear whether any of these systems is supposed to exclude or deprecate using the other. OK. Can people help clarify this? Thanks again Paul and John, Chris -- Chris Evans ch...@psyctc.org Skype: chris-psyctc Consultant Psychiatrist in Psychotherapy, Notts. PDD network; Professor, Psychotherapy, Nottingham University *If I am writing from one of those roles, it will be clear. Otherwise* *my views are my own and not representative of those institutions* If you have difficulty Emailing me on this address or getting a reply, send again but cc to: chris dot evans at nottshc dot nhs dot uk and to: c dot evans at nottingham
Re: [R-sig-Debian] Problem updating packages in 2.15.1 on Ubuntu 12.04
John C Nash sent the following at 01/08/12 15:30: The PPA for latest Ubuntu packages doesn't seem to be in the sources list. https://launchpad.net/~marutter/+archive/rrutter Aha. OK. Fixed that. That seems to have meant that cran, coda and spatial have now been updated (by apt-get update). Interestingly, I'm still getting the comment that coda won't be updated even after that. I suspect that means that the main cran repository has a version of coda even more recent than the one in rrutter. Also see the CRAN page (I've used the probability.ca mirror) http://probability.ca/cran/bin/linux/ubuntu/ I have and thought I was pretty compliant with that. Only thing I've not followed is the backports bit. Many thanks, C Best, JN On 08/01/2012 02:02 AM, Chris Evans wrote: The specific message is: Warning: package 'spatial' in library '/usr/lib/R/library' will not be updated and the number of libraries about which that's the complaint is now increasingly almost daily so clearly something is wrong. I'm working on a laptop on which I do the recommended Ubuntu updates daily. I done a standard installation of R 2.15.1 using synaptic with: deb http://www.stats.bris.ac.uk/R/bin/linux/ubuntu precise/ deb-src http://www.stats.bris.ac.uk/R/bin/linux/ubuntu precise/ in /etc/apt/sources.list and I added most of the optional packages that are packaged at that source. I have been updating going into R through sudo R in my home directory and then using update.packages(instlib=.libPaths()[1],ask=FALSE) However, that gets these complaints about not updating. I get the same message if I use: update.packages(ask=FALSE) I get the same if I use su rather than sudo and if I update as an ordinary user and if I point to a different mirror repository (I have been using Switzerland as Bristol seemed to be lagging behind Switzerland a lot). I was doing to that without a personal library but tried updating as an ordinary user and created a personal library as prompted but that still gets the same but that means that my .libPaths() is now: .libPaths() [1] /home/chris/R/i686-pc-linux-gnu-library/2.15 [2] /usr/local/lib/R/site-library [3] /usr/lib/R/site-library [4] /usr/lib/R/library I think I've read and understood umpteen questions about the different ways of updating libraries on this list. I would like to update to the latest library versions regularly (as 2.15.1 for Windoze in a VM box on this machine does fine). Clearly I don't understand something and am doing something wrong. Please can someone enlighten me? Thanks in advance, Chris -- Chris Evans ch...@psyctc.org Skype: chris-psyctc Consultant Psychiatrist in Psychotherapy, Notts. PDD network; Professor, Psychotherapy, Nottingham University *If I am writing from one of those roles, it will be clear. Otherwise* *my views are my own and not representative of those institutions* If you have difficulty Emailing me on this address or getting a reply, send again but cc to: chris dot evans at nottshc dot nhs dot uk and to: c dot evans at nottingham dot ac dot uk ___ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian
Re: [R-sig-Debian] update.packages() as ordinary user, /usr/lib/R/site-library is not writable
Huge thanks to Johannes (sorry, Johannes, I think I implied that Dirk
was doing all the hard work in rolling things in my earlier reply, the
you is plural!)
What I've done:
A) removed r-cran-rgl and r-cran-xml using synaptic as root
B) re-entered new R session as user chris, confirmed that the packages
had gone using installed.packages() and grep()!
C) ran adduser chris staff as root
D) logged off gnome session (ah, that bit's a pain when making group
membership changes which won't otherwise propagate to current session!)
E) logged back in!
F) checked I was now member of staff: yes!
G) checked I can write to /usr/local/lib/R/site-library: yes!
H) ran R as user chris ... now it gets interesting and frustrating:
no damn joy, update.packages and selecting only abind to update
without specifying instlib says it runs fine but next time I run
update.packages it still shows the old version and wants to do the
update again so I
I) (and this was a debugging mistake for which I apologise) did the same
but specifying instlib as /usr/local ... and it runs fine again (this
time I checked that it had updated in /usr/local/... and there it was in
solitary splendour as my first updated library/package there) ... but ...
J) that hasn't gained me anything (I suspect the previous update without
the instlib= may have been fine too) as update.packages still wants to
update it ...
K) so I get thoughtful: clearly update.packages is reading from /usr/lib
not /usr/local ...
L) so I check .libPaths():
.libPaths()
[1] /home/chris/R/i486-pc-linux-gnu-library/2.13
[2] /usr/local/lib/R/site-library
[3] /usr/lib/R/site-library
[4] /usr/lib/R/library
M) Hm. Looks good to me but I see Dirk is telling me /usr/local/...
should be first so I go to /etc/R/Renviron and I find:
R_LIBS_SITE=${R_LIBS_SITE-'/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library'}
and nothing I can see in Renviron.site that would override that.
I _THINK_ I see a logic: installation is happening first come, first
used on the libPaths but update.packages() is reading from all the
library locations and the later are overriting the earlier ... that
would explain things but surely it would mean that no-one, including
Dirk, would be able to run update.packages() successfully as a non-root
user.
So now I'm baffled as to how to be friendly with R and linux/Debian on
this machine!
Perhaps I should say that I would like to work by:
1) having the cran deb line in /etc/apt/sources.list and doing basic
installation of R from there as my understanding is that that will get
me the latest R for Debian when you (plural) have rolled it and put it
on CRAN getting me round the downloading and replacing I used to do on
windoze and also making it pretty likely that you'll have sorted out
dependency problems etc.
2) would like then to rely on update.packages() from within R
3) but running as local user as I can see the logic of that
#1 and #2 are what I've always done on my Debian web server (where I was
running some cgi-bin scripts invoking R) but I always did the
update.packages() as root. I've now moved that server to a shell
account at mythic-beasts (great guys) so I'll have to do #3 for that too
in future and though I could update as root on this laptop I do see the
logic of not doing that and clearly you both and presumably many others
on this list do #1, #2 and #3 so why is it not working for me?!
Suggestions gratefully received!
Very best karma to all,
Chris
Dirk Eddelbuettel sent the following at 21/09/11 13:49:
Hi Chris,
Thanks for patient follow-up even after I (as Johannes noted) evidently
overlooked key parts of your first email.
On 21 September 2011 at 07:49, Chris Evans wrote:
| I ran synaptic from the Debian application menu which defaults to root
| after askling for the root password the first time I invoke it after a
| reboot. (I probably should have said that I've been using Debian for my
| internet server work for about 15 years: I'm not a Debian/linux newbie,
| just someone finally throwing away the reins from M$ to have a laptop
| running Debian as well!)
Perfect.
| I get that from invoking update.packages() in an R session launched from
| a user (chris) terminal session. Before that I had done an install of
I do that too, as well as calling the 'install.r' helper script from littler
(in its examples/ diretory, if interested).
This requires that you make /usr/local/lib/R/site-library/ writable for _you_
as user chris, else you cannot.
[ It also assumes that the Renviron setting mentioned last time is still
valid, do this:
edd@max:~$ R -q -e 'print(.libPaths())'
R print(.libPaths())
[1] /usr/local/lib/R/site-library /usr/lib/R/site-library
/usr/lib/R/library
R
R
It _must_ be first as here. ]
Now, /usr/local/lib/R/site-library/ comes shipped from the r-base-core
package as owned by group 'staff' so one solution is to add yourself to group
staff:
edd@max:~$ ls -ld /usr
