Re: [R-SIG-Mac] MacTeX 2020 and TeX Live Utility (No Longer Included)
Yes, I am using Catalena. This is going way put of R territory… But if an app is not notarised, it will prmp[t you if you want to run it. If you say yes, it will never ask you again. Just to be clear - homebrew (in this case cask) is just installing the official mactex binary. The other programs are likely left overs from the older versions of mactex. But it is still working. Rainer Cheers, Rainer > On 28 Apr 2020, at 14:06, Marc Schwartz wrote: > > Rainer, > > Are you running on Catalina? > > I am not using homebrew, but if you are running on Catalina, then the > homebrew folks would have had to address the notarization issue in their > packaging independently. > > Regards, > > Marc > > >> On Apr 28, 2020, at 4:43 AM, Rainer M Krug > <mailto:rai...@krugs.de>> wrote: >> >> I just checked - I still have them. I updated (using hombrew cask) to the >> new version of MacTeX, ant all programs are still there. And TLU still works. >> >> Rainer >> >> >>> On 27 Apr 2020, at 17:44, Marc Schwartz via R-SIG-Mac >>> mailto:r-sig-mac@r-project.org>> wrote: >>> >>> Thanks for the heads up on that. >>> >>> I confirmed that tlcockpit is included in the MacTeX 2020 distribution in >>> /Library/TeX/texbin, as a symlink to the target shell script, and it is >>> actively maintained. >>> >>> Surprising that the missing apps PDF file did not mention that as an >>> alternative GUI based manager that is immediately useable. >>> >>> Regards, >>> >>> Marc >>> >>> >>>> On Apr 27, 2020, at 10:27 AM, Dr Eberhard W Lisse >>> <mailto:e...@lisse.na>> wrote: >>>> >>>> There is also the tlcockpit Java app on CTAN. >>>> >>>> el >>>> >>>> On 27/04/2020 16:07, Marc Schwartz via R-SIG-Mac wrote: >>>> [...] >>>>> One major change this year, as a result of Apple's requirement to now >>>>> use app notarization on Catalina, is that the TeX Live Utility (TLU), >>>>> as a GUI interface for updating the TeX distribution contents, is no >>>>> longer included in the MacTeX distribution. >>>> [...] >>>> >>>> >>>> -- >>>> Dr. Eberhard W. Lisse \ / Obstetrician & Gynaecologist >>>> e...@lisse.na <mailto:e...@lisse.na> / * | Telephone: >>>> +264 81 124 6733 (cell) >>>> PO Box 8421 Bachbrecht \ / If this email is signed with GPG/PGP >>>> 10007, Namibia ;/ Sect 20 of Act No. 4 of 2019 may apply >>> >>> ___ >>> R-SIG-Mac mailing list >>> R-SIG-Mac@r-project.org <mailto:R-SIG-Mac@r-project.org> >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>> <https://stat.ethz.ch/mailman/listinfo/r-sig-mac> >> >> -- >> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, >> UCT), Dipl. Phys. (Germany) >> >> Orcid ID: -0002-7490-0066 >> >> Department of Evolutionary Biology and Environmental Studies >> University of Zürich >> Office Y34-J-74 >> Winterthurerstrasse 190 >> 8075 Zürich >> Switzerland >> >> Office: +41 (0)44 635 47 64 >> Cell:+41 (0)78 630 66 57 >> email: rainer.k...@uzh.ch <mailto:rainer.k...@uzh.ch> >> rai...@krugs.de <mailto:rai...@krugs.de> >> Skype: RMkrug >> >> PGP: 0x0F52F982 >> >> >> > -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Orcid ID: -0002-7490-0066 Department of Evolutionary Biology and Environmental Studies University of Zürich Office Y34-J-74 Winterthurerstrasse 190 8075 Zürich Switzerland Office: +41 (0)44 635 47 64 Cell: +41 (0)78 630 66 57 email: rainer.k...@uzh.ch rai...@krugs.de Skype: RMkrug PGP: 0x0F52F982 [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] MacTeX 2020 and TeX Live Utility (No Longer Included)
You know why I hate java? Here it comes: ``` rof-Dumbledore:tlcockpit rainerkrug$ tlcockpit Graphics Device initialization failed for : es2, sw Error initializing QuantumRenderer: no suitable pipeline found java.lang.RuntimeException: java.lang.RuntimeException: Error initializing QuantumRenderer: no suitable pipeline found at com.sun.javafx.tk.quantum.QuantumRenderer.getInstance(QuantumRenderer.java:280) at com.sun.javafx.tk.quantum.QuantumToolkit.init(QuantumToolkit.java:244) at com.sun.javafx.tk.Toolkit.getToolkit(Toolkit.java:260) at com.sun.javafx.application.PlatformImpl.startup(PlatformImpl.java:267) at com.sun.javafx.application.PlatformImpl.startup(PlatformImpl.java:158) at com.sun.javafx.application.LauncherImpl.startToolkit(LauncherImpl.java:658) at com.sun.javafx.application.LauncherImpl.launchApplication1(LauncherImpl.java:678) at com.sun.javafx.application.LauncherImpl.lambda$launchApplication$2(LauncherImpl.java:195) at java.base/java.lang.Thread.run(Thread.java:832) Caused by: java.lang.RuntimeException: Error initializing QuantumRenderer: no suitable pipeline found at com.sun.javafx.tk.quantum.QuantumRenderer$PipelineRunnable.init(QuantumRenderer.java:94) at com.sun.javafx.tk.quantum.QuantumRenderer$PipelineRunnable.run(QuantumRenderer.java:124) ... 1 more Exception in thread "main" java.lang.RuntimeException: No toolkit found at com.sun.javafx.tk.Toolkit.getToolkit(Toolkit.java:272) at com.sun.javafx.application.PlatformImpl.startup(PlatformImpl.java:267) at com.sun.javafx.application.PlatformImpl.startup(PlatformImpl.java:158) at com.sun.javafx.application.LauncherImpl.startToolkit(LauncherImpl.java:658) at com.sun.javafx.application.LauncherImpl.launchApplication1(LauncherImpl.java:678) at com.sun.javafx.application.LauncherImpl.lambda$launchApplication$2(LauncherImpl.java:195) at java.base/java.lang.Thread.run(Thread.java:832) Prof-Dumbledore:tlcockpit rainerkrug$ ``` Cheers, Rainer > On 28 Apr 2020, at 10:43, Rainer M Krug wrote: > > I just checked - I still have them. I updated (using hombrew cask) to the new > version of MacTeX, ant all programs are still there. And TLU still works. > > Rainer > > >> On 27 Apr 2020, at 17:44, Marc Schwartz via R-SIG-Mac >> mailto:r-sig-mac@r-project.org>> wrote: >> >> Thanks for the heads up on that. >> >> I confirmed that tlcockpit is included in the MacTeX 2020 distribution in >> /Library/TeX/texbin, as a symlink to the target shell script, and it is >> actively maintained. >> >> Surprising that the missing apps PDF file did not mention that as an >> alternative GUI based manager that is immediately useable. >> >> Regards, >> >> Marc >> >> >>> On Apr 27, 2020, at 10:27 AM, Dr Eberhard W Lisse >> <mailto:e...@lisse.na>> wrote: >>> >>> There is also the tlcockpit Java app on CTAN. >>> >>> el >>> >>> On 27/04/2020 16:07, Marc Schwartz via R-SIG-Mac wrote: >>> [...] >>>> One major change this year, as a result of Apple's requirement to now >>>> use app notarization on Catalina, is that the TeX Live Utility (TLU), >>>> as a GUI interface for updating the TeX distribution contents, is no >>>> longer included in the MacTeX distribution. >>> [...] >>> >>> >>> -- >>> Dr. Eberhard W. Lisse \ / Obstetrician & Gynaecologist >>> e...@lisse.na <mailto:e...@lisse.na> / * | Telephone: >>> +264 81 124 6733 (cell) >>> PO Box 8421 Bachbrecht \ / If this email is signed with GPG/PGP >>> 10007, Namibia ;/ Sect 20 of Act No. 4 of 2019 may apply >> >> ___ >> R-SIG-Mac mailing list >> R-SIG-Mac@r-project.org <mailto:R-SIG-Mac@r-project.org> >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > -- > Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, > UCT), Dipl. Phys. (Germany) > > Orcid ID: -0002-7490-0066 > > Department of Evolutionary Biology and Environmental Studies > University of Zürich > Office Y34-J-74 > Winterthurerstrasse 190 > 8075 Zürich > Switzerland > > Office: +41 (0)44 635 47 64 > Cell: +41 (0)78 630 66 57 > email: rainer.k...@uzh.ch <mailto:rainer.k...@uzh.ch> > rai...@krugs.de <mailto:rai...@krugs.de> > Skype: RMkrug > > PGP: 0x0F52F982 > > > -- Rain
Re: [R-SIG-Mac] MacTeX 2020 and TeX Live Utility (No Longer Included)
I just checked - I still have them. I updated (using hombrew cask) to the new version of MacTeX, ant all programs are still there. And TLU still works. Rainer > On 27 Apr 2020, at 17:44, Marc Schwartz via R-SIG-Mac > wrote: > > Thanks for the heads up on that. > > I confirmed that tlcockpit is included in the MacTeX 2020 distribution in > /Library/TeX/texbin, as a symlink to the target shell script, and it is > actively maintained. > > Surprising that the missing apps PDF file did not mention that as an > alternative GUI based manager that is immediately useable. > > Regards, > > Marc > > >> On Apr 27, 2020, at 10:27 AM, Dr Eberhard W Lisse wrote: >> >> There is also the tlcockpit Java app on CTAN. >> >> el >> >> On 27/04/2020 16:07, Marc Schwartz via R-SIG-Mac wrote: >> [...] >>> One major change this year, as a result of Apple's requirement to now >>> use app notarization on Catalina, is that the TeX Live Utility (TLU), >>> as a GUI interface for updating the TeX distribution contents, is no >>> longer included in the MacTeX distribution. >> [...] >> >> >> -- >> Dr. Eberhard W. Lisse \ / Obstetrician & Gynaecologist >> e...@lisse.na / * | Telephone: +264 81 124 6733 (cell) >> PO Box 8421 Bachbrecht \ / If this email is signed with GPG/PGP >> 10007, Namibia ;/ Sect 20 of Act No. 4 of 2019 may apply > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Orcid ID: -0002-7490-0066 Department of Evolutionary Biology and Environmental Studies University of Zürich Office Y34-J-74 Winterthurerstrasse 190 8075 Zürich Switzerland Office: +41 (0)44 635 47 64 Cell: +41 (0)78 630 66 57 email: rainer.k...@uzh.ch rai...@krugs.de Skype: RMkrug PGP: 0x0F52F982 [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Homebrew [was: from Mac to LInux?]
Thanks a lot for your detailed response - it is very much appreciated. > On 2 Apr 2020, at 22:30, Simon Urbanek wrote: > > > >> On 2/04/2020, at 9:15 PM, Patrick Schratz wrote: >> >> AFAIK most people on that list would vote hard against installing R via >> homebrew for several reasons - maybe there should be a section about this on >> the R dev / CRAN page to address this topic, @Simon? Otherwise this will >> come up again and again. >> > > That main objection is that people are mixing Homebrew with CRAN and > vice-versa which leads to many problems. You cannot use packages from CRAN > when using Homebrew, period, and you have to be really careful if you want to > mix Homebrew libraries (not anything R-related) with CRAN (it is doable if > you know what you're doing). This is definitely true (and I assume, you are referring to CRAN binary packages). But I am wondering: I am always installing from the normal CRAN mirrors, and my R installation (homebrew) always installs from source. I never use `type = “source”`in the installation for packages. My question: when would I install incompatible packages (I assume, you mean binary packages for Mac) from CRAN? > > The fundamental issue is that package managers like Homebrew replace system > libraries with their own (for new features/updates that the system libraries > don't provide) which break anything that relies on the system library. Out of > all the package managers Homebrew the only one that is trying to address the > issue by trying to separate them, but even that has been diverging over time. > > The second issue is that they are increasingly replacing toolchains > (compilers) with their own builds, which makes everything incompatible in > explosive ways (things just segfault). Making sure that a compiler toolchain > is stable is actually non-trivial and many packager manager > authors/maintainers have little experience with this. That used the be the > primary reason to avoid them, because it was just normal that the released > binaries were miscompiled and things would break all the time. Fortunately, I > think that has gotten better over time. > > If you stick only with Homebrew, then you're likely ok, but you're on your > own and have to compile all packages form sources. This is true, but I did not encounter big problems. And this is, why I thought loud in suggesting to setup a (non official!) homebrew tap to install the packages, similar to how it is in linux (Debian). > Majority of our time as CRAN maintainers for the binary releases is about > providing dependent libraries for packages and making sure things "just work”. And I think everybody really appreciates this and is VErY happy about it. This is essential work! > It is doable, just a lot of work, so by using Homebrew every user has to > spend that time. Doable: definitely. lot of work: in my experience not that much more. Overall, I definitely agree, that the official distribution should stay the proper apple way. But there are circumstances, where these are delayed, or problems occur after macOS upgrades, which will delay the compilation of new ones (GRASS did not have Mac binaries for a long time due to this problem). So an alternative way of installing, community supported but approved, would be preferable. The r formula for homebrew has been installed in the last year more that 112.000 times (https://formulae.brew.sh/formula/r) so I think there is likely a rather large user base of R from homebrew. A first step in this direction, would be to either include homebrew in this list, or create a new R-sig-hoebrew list, which could become the home of these discussions. > > (FWIW I use Hombrew myself for tools, but not in /usr/local (I'm using > /opt/brew) and I only put it on the PATH for the tools that I need, never to > compile anything "native" against it.) Than you are completely in the cold and without support from homebrew… As far as I heard, in this case, everything is locally compiled and not using the binaries - correct? Cheers, and thanks again for your very useful clarifications, Rainer > > Cheers, > Simon > > > >> Anyhow, this is also not relating to the initial topic of that thread and >> should probably discussed separately. >> On 2. Apr 2020, 10:04 +0200, Rainer M Krug , wrote: >>> I am using Homebrew on a Mac (two Macs - one at home, one at work) instead >>> of the official R package, and I did not have any problems after upgrades - >>> maybe I am lucky, maybe not as picky in defining “problem”, but my >>> suggestion would be to try R from homebrew to install R. >>> >>> OK - no support from here - I know. >>> >>> And home
Re: [R-SIG-Mac] Homebrew
> On 2 Apr 2020, at 12:56, Hervé Pagès wrote:
>
> Just for a minute let's ignore the fact that installing R via Homebrew is not
> considered a good option by the competent authorities (which sounds like a
> good enough reason to stay away from it). I'm still wondering: what's the
> benefit vs installing the official CRAN binary? Just curious.
Arguments against homebrew:
Not an official response, but in the past, homebrew was compiling everything on
the local machine. This is not the case anymore, and the default installation
in homebrew, installs a binary.
All packages need to be installed from source. This takes time, but I had no
problems with any of the packages I use.
Just some tidbits from previous discussions.
But I would like to also hear the official reason (no resources would be a good
enough justification as well).
Arguments for homebrew:
it is more Linux like, in the way that you have more control over the tools
used. e.g. when still using the official R installation, I regularly used
different versions of GDAL in R, GRASS, …, which can cause inconsistencies.
The installation is done without requiring root privileges, which is a big
advantage (as I see it).
Cheers,
Rainer
>
> Thanks,
> H.
>
> On 4/2/20 03:43, Rainer M Krug wrote:
>>> On 2 Apr 2020, at 12:17, Duncan Murdoch wrote:
>>>
>>> On 02/04/2020 5:58 a.m., Dr Eberhard W Lisse wrote:
>>>> New thread :-)-O
>>>> I am wondering if I should not try to figure out how automate this.
>>>> Is there a way of (only) listing all user installed (additional)
>>>> packages, ie not the ones that come with R?
>> I had something similar in mind - here is my repo which collects ides (no
>> code yet)
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_rkrug_install=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=uDuycJflTWje5wqLzrbP7zBZojiWq6DmyxGuwakypr0=ZUWEqptXXn0kw7PX-ToEnYb7DtfXGUcOn5PzyQVfVG8=
>> If you are interested, we could get this going.
>> If I understand correctly, this would be very useful in many cases.
>>>
>>> Look at the "Priority" column in installed.packages(). "base" is part of
>>> R, "recommended" is normally distributed with R. "recommended" packages can
>>> be updated after R is installed, "base" packages can't.
>> That is a good idea. We should take this forward.
>>>
>>> If you just copy all the packages to the new library that aren't already
>>> there, and run update.packages(checkBuilt = TRUE) R will re-install
>>> everything that was originally installed under an earlier version.
>> Cheers,
>> Rainer
>>>
>>> Duncan Murdoch
>>>> I could then construct the below file automagically, and if I was
>>>> really bothered and bored find out how to make Homebrew pre/post
>>>> install scripts to automate this :-)-O
>>>> And, for the record, other than that, I can only recall one serious
>>>> issue, when the openblas library got lost recently which was however
>>>> fixed quite quickly.
>>>> greetings, el
>>>> On 02/04/2020 10:17, Dr Eberhard W Lisse wrote:
>>>>>
>>>>> I do same, including Rstudio (Cask).
>>>>>
>>>>> Once in a while after major updates I need to reinstall all my extra
>>>>> packages, so I have written me a little script along the lines of
>>>>>
>>>>> #!/usr/local/bin/Rscript
>>>>> local({
>>>>> r <- getOption("repos")
>>>>> r["CRAN"] <-
>>>>> "https://urldefense.proofpoint.com/v2/url?u=https-3A__cloud.r-2Dproject.org_=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=uDuycJflTWje5wqLzrbP7zBZojiWq6DmyxGuwakypr0=rnzs7MN3dX-WT08dEbSoFz0AVBgX-xNNlW9keQhr0jg=
>>>>> "
>>>>> options(repos = r)
>>>>> })
>>>>> install.packages(c(
>>>>> "RMariaDB", "rstudioapi"
>>>>> ))
>>>>>
>>>>> made it 0755 and can run it from the command line. Put it in my
>>>>> handbook so I don't forget and never looked back.
>>>>>
>>>>>
>>>>> greetings, el
>>>>>
>>>>> On 02/04/2020 10:03 am, Rainer M Krug wrote:
>>>>>> I am using Homebrew on a Mac (two Macs - one at home, one at work)
>>>>>> instead of the official R package, and I did not have any pro
Re: [R-SIG-Mac] Homebrew
> On 2 Apr 2020, at 12:17, Duncan Murdoch wrote:
>
> On 02/04/2020 5:58 a.m., Dr Eberhard W Lisse wrote:
>> New thread :-)-O
>> I am wondering if I should not try to figure out how automate this.
>> Is there a way of (only) listing all user installed (additional)
>> packages, ie not the ones that come with R?
I had something similar in mind - here is my repo which collects ides (no code
yet) https://github.com/rkrug/install
If you are interested, we could get this going.
If I understand correctly, this would be very useful in many cases.
>
> Look at the "Priority" column in installed.packages(). "base" is part of R,
> "recommended" is normally distributed with R. "recommended" packages can be
> updated after R is installed, "base" packages can't.
That is a good idea. We should take this forward.
>
> If you just copy all the packages to the new library that aren't already
> there, and run update.packages(checkBuilt = TRUE) R will re-install
> everything that was originally installed under an earlier version.
Cheers,
Rainer
>
> Duncan Murdoch
>> I could then construct the below file automagically, and if I was
>> really bothered and bored find out how to make Homebrew pre/post
>> install scripts to automate this :-)-O
>> And, for the record, other than that, I can only recall one serious
>> issue, when the openblas library got lost recently which was however
>> fixed quite quickly.
>> greetings, el
>> On 02/04/2020 10:17, Dr Eberhard W Lisse wrote:
>>>
>>> I do same, including Rstudio (Cask).
>>>
>>> Once in a while after major updates I need to reinstall all my extra
>>> packages, so I have written me a little script along the lines of
>>>
>>> #!/usr/local/bin/Rscript
>>> local({
>>> r <- getOption("repos")
>>> r["CRAN"] <- "https://cloud.r-project.org/;
>>> options(repos = r)
>>> })
>>> install.packages(c(
>>> "RMariaDB", "rstudioapi"
>>> ))
>>>
>>> made it 0755 and can run it from the command line. Put it in my
>>> handbook so I don't forget and never looked back.
>>>
>>>
>>> greetings, el
>>>
>>> On 02/04/2020 10:03 am, Rainer M Krug wrote:
>>>> I am using Homebrew on a Mac (two Macs - one at home, one at work)
>>>> instead of the official R package, and I did not have any problems
>>>> after upgrades - maybe I am lucky, maybe not as picky in defining
>>>> “problem”, but my suggestion would be to try R from homebrew to
>>>> install R.
>>>>
>>>> OK - no support from here - I know.
>>>>
>>>> And homebrew has also binary versions. What is missing, is a hombrew
>>>> R package repository. Maybe an idea to create one?
>>>>
>>>>
>>>> Cheers,
>>>>
>>>> Rainer
>>
>
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology,
UCT), Dipl. Phys. (Germany)
Orcid ID: -0002-7490-0066
Department of Evolutionary Biology and Environmental Studies
University of Zürich
Office Y34-J-74
Winterthurerstrasse 190
8075 Zürich
Switzerland
Office: +41 (0)44 635 47 64
Cell: +41 (0)78 630 66 57
email: rainer.k...@uzh.ch
rai...@krugs.de
Skype: RMkrug
PGP: 0x0F52F982
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Re: [R-SIG-Mac] Transitioning from Mac to LInux?
I am using Homebrew on a Mac (two Macs - one at home, one at work) instead of the official R package, and I did not have any problems after upgrades - maybe I am lucky, maybe not as picky in defining “problem”, but my suggestion would be to try R from homebrew to install R. OK - no support from here - I know. And homebrew has also binary versions. What is missing, is a hombrew R package repository. Maybe an idea to create one? Cheers, Rainer > On 2 Apr 2020, at 02:37, Duncan Murdoch wrote: > > On 01/04/2020 2:48 p.m., Carl Witthoft wrote: >> If I should ask over at r-sig-debian instead of here, please tell me. >> I don't wish to clog r-sig-mac with off-topic stuff. >> I've been watching the massive headaches people are dealing with trying >> to keep R fully compatible with each MacOS X upgrade, I'm wondering >> whether replacing my iMac (2009) with a new Mac really makes sense from >> an R - user point of view, as opposed to getting some inexpensive >> desktop and installing Linux. I know I can run R and RStudio under >> Linux, for example, but don't know what limitations, if any there are >> when it comes to building packages from source, getting compatible >> compilers, and so on. >> What have some of you 'power R users' discovered when/if you tried to >> build , or incorporate Bioconductor or other repository's packages under >> Linux? > > If your iMac is still working, try installing Ubuntu or some other Linux on > it. I think at that age Apple is no longer providing upgrades, but I just > put Ubuntu on a 2008 iMac, and it works well. (I needed to upgrade the > memory, but that just cost $40 for 4 GB.) > > So I got a $40 desktop, with a nice screen. > > Duncan Murdoch > > _______ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Orcid ID: -0002-7490-0066 Department of Evolutionary Biology and Environmental Studies University of Zürich Office Y34-J-74 Winterthurerstrasse 190 8075 Zürich Switzerland Office: +41 (0)44 635 47 64 Cell: +41 (0)78 630 66 57 email: rainer.k...@uzh.ch rai...@krugs.de Skype: RMkrug PGP: 0x0F52F982 [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Please test R 4.0.0 pre-releases!
> On 1 Apr 2020, at 16:07, Patrick Schratz wrote: > > The same goes here regarding support. > > I am (co-)maintaining a package on ropensci focusing on provider-agnostic CI > approaches for R (tic) and have quite some experience with all the little > culprits there. > > Since you mentioned Travis: Be aware that the R community is (slowly but > actively) moving away from Travis for a few reasons. > Also on GitHub Actions you can only build on 10.15 (Catalina) right now. So where is the R community moving too? Rainer > > Best, Patrick > On 1. Apr 2020, 15:41 +0200, Bob Rudis , wrote: >> I shall pile on with an additional offer of assistance, Simon and a huge #ty >> for this and all the work you do. >> >>> On Apr 1, 2020, at 09:30, Balamuta, James Joseph >>> wrote: >>> >>> Simon, >>> >>> Thanks for the overview! A few quick questions: >>> >>> 1. Compiler-wise, the external clang compiler requirement was removed and, >>> so, there is no guarantee of OpenMP on macOS again? >>> 2. Why was 10.13 chosen as the oldest system instead of 10.14 given the new >>> push for increased security by Apple? >>> 3. How likely is the oldest system requirement to be bumped in a patch >>> release? >>> >>> Also, if you need help with mac-builder, Travis, or GitHub Actions, I'm >>> more than happy to help! >>> >>> Best, >>> >>> JJB >>> >>> On 3/31/20, 11:59 PM, "R-SIG-Mac on behalf of Simon Urbanek" >>> >>> wrote: >>> >>> Dear Mac users, >>> >>> R 4.0.0 will be using an entirely new toolchain, entirely new build system >>> on entirely new macOS version and hardware. Therefore I would like to ask >>> you kindly to test the binaries from >>> >>> https://mac.R-project.org >>> >>> before the release as much as you can. Raising any issues after the release >>> is too late! So please, please, test the pre-releases. Report any issues >>> either directly to me or this mailing list. >>> >>> The nightly builds are signed, but not necessarily notarized. However, the >>> build fulfils Apple's conditions and is known to pass notarization (in fact >>> the the package available for download today is actually notarized) so it >>> should be a good test for the release which will be notarized and should >>> work on Catalina. >>> >>> For those that want to replicate our setup - technical details: we are now >>> building with macOS 10.13 (High Sierra) as target (i.e. the oldest >>> supported system), regular Apple Xcode/command line tools and GNU Fortran >>> 8.2. R builds are running on macOS 10.15 (Catalina) with Xcode 11.4 using >>> macOS 10.13 target. Packages are built on macOS 10.13 VMs with just Apple >>> command line tools (this should make it easy to replicate the setup using >>> Travis, for example). All 3rd party libraries that CRAN uses are available >>> in http://mac.r-project.org/libs-4/ >>> >>> The new R build system is in >>> https://svn.r-project.org/R-dev-web/trunk/QA/Simon/R4 >>> Packages build system has not changed and is in >>> https://svn.r-project.org/R-dev-web/trunk/QA/Simon/packages >>> >>> We also plan to have a mac-builder available with similar function as the >>> win-builder where pre-submission tests can be performed and potentially a >>> Travis template. >>> >>> Please test R pre-releases and provide feedback! >>> >>> Thanks, >>> Simon >>> >>> _______ >>> R-SIG-Mac mailing list >>> R-SIG-Mac@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>> >>> >>> ___ >>> R-SIG-Mac mailing list >>> R-SIG-Mac@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> >> ___ >> R-SIG-Mac mailing list >> R-SIG-Mac@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > [[alternative HTML version deleted]] > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Orcid ID: -0002-7490-0066 Department of Evolutionary Biology and Environmental Studies University of Zürich Office Y34-J-74 Winterthurerstrasse 190 8075 Zürich Switzerland Office: +41 (0)44 635 47 64 Cell: +41 (0)78 630 66 57 email: rainer.k...@uzh.ch rai...@krugs.de Skype: RMkrug PGP: 0x0F52F982 [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Install r-devel with homebrew?
Thanks Patrick. This is working, and I can start r-devel. I am aware that some say that there are problems with homebrew, but I have never experienced any. Thanks, Rainer > On 23 Mar 2020, at 15:24, Patrick Schratz wrote: > > Rainer, > > Be aware that the homebrew build of R used a different underlying C standard > (if that is the correct way to name it?) which may cause issues when > compiling certain packages from source. > I think most people in this mailing list do not recommend it. > In addition, you might want to change your compiler to an openmp enabled > clang one. > > I use a small script which installs R-dev: > > wget > https://mac.r-project.org/el-capitan/R-devel/R-devel-el-capitan-sa-x86_64.tar.gz > > <https://mac.r-project.org/el-capitan/R-devel/R-devel-el-capitan-sa-x86_64.tar.gz> > sudo tar fvxz R*.tar.gz -C / > rm R-devel-el-capitan-sa-x86_64.tar.gz > > Cheers, Patrick > On 23. Mar 2020, 15:09 +0100, Balamuta, James Joseph , > wrote: >> Rainer, >> >> Download the R-devel build from http://mac.r-project.org >> >> The build is available under "Universal nightly builds for Mac OS X (10.6+ >> and 10.9+)" table. >> >> R-devel-el-capitan-sa-x86_64.tar.gz (67Mb) >> http://mac.r-project.org/el-capitan/R-devel/R-devel-el-capitan-sa-x86_64.tar.gz >> >> R-devel-el-capitan-signed.pkg (77Mb, installer incl. GUI) >> http://mac.r-project.org/el-capitan/R-devel/R-devel-el-capitan-signed.pkg >> >> Best, >> >> JJB >> >> On 3/23/20, 9:06 AM, "R-SIG-Mac on behalf of Rainer M Krug" >> wrote: >> >> Hi >> >> I know - homebrew is not a supported installation approach to R, but I am >> asking anyway: >> >> Is there a way of installing r-devel via homebrew? Otherwise, what is the >> easiest way of getting r-devel on my Mac, without interfering with the >> homebrew install? >> >> Thanks, >> >> Rainer >> >> >> -- >> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, >> UCT), Dipl. Phys. (Germany) >> >> Orcid ID: -0002-7490-0066 >> >> Department of Evolutionary Biology and Environmental Studies >> University of Zürich >> Office Y34-J-74 >> Winterthurerstrasse 190 >> 8075 Zürich >> Switzerland >> >> Office: +41 (0)44 635 47 64 >> Cell: +41 (0)78 630 66 57 >> email: rainer.k...@uzh.ch >> rai...@krugs.de >> Skype: RMkrug >> >> PGP: 0x0F52F982 >> >> ___ >> R-SIG-Mac mailing list >> R-SIG-Mac@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> >> >> ___ >> R-SIG-Mac mailing list >> R-SIG-Mac@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Orcid ID: -0002-7490-0066 Department of Evolutionary Biology and Environmental Studies University of Zürich Office Y34-J-74 Winterthurerstrasse 190 8075 Zürich Switzerland Office: +41 (0)44 635 47 64 Cell: +41 (0)78 630 66 57 email: rainer.k...@uzh.ch rai...@krugs.de Skype: RMkrug PGP: 0x0F52F982 [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Install r-devel with homebrew?
Thanks - done this (the tar.gz, as I don’t want to install it and run it from the downloaded location). But how can I run R? I have the command R, but I get the message "“R.framework” cannot be opened because the developer cannot be verified." Any suggestions? Rainer > On 23 Mar 2020, at 15:09, Balamuta, James Joseph > wrote: > > Rainer, > > Download the R-devel build from http://mac.r-project.org > > The build is available under "Universal nightly builds for Mac OS X (10.6+ > and 10.9+)" table. > > R-devel-el-capitan-sa-x86_64.tar.gz (67Mb) > http://mac.r-project.org/el-capitan/R-devel/R-devel-el-capitan-sa-x86_64.tar.gz > > > R-devel-el-capitan-signed.pkg (77Mb, installer incl. GUI) > http://mac.r-project.org/el-capitan/R-devel/R-devel-el-capitan-signed.pkg > > Best, > > JJB > > On 3/23/20, 9:06 AM, "R-SIG-Mac on behalf of Rainer M Krug" > wrote: > >Hi > >I know - homebrew is not a supported installation approach to R, but I am > asking anyway: > >Is there a way of installing r-devel via homebrew? Otherwise, what is the > easiest way of getting r-devel on my Mac, without interfering with the > homebrew install? > >Thanks, > >Rainer > > >-- >Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation > Biology, UCT), Dipl. Phys. (Germany) > >Orcid ID: -0002-7490-0066 > >Department of Evolutionary Biology and Environmental Studies >University of Zürich >Office Y34-J-74 >Winterthurerstrasse 190 >8075 Zürich >Switzerland > >Office:+41 (0)44 635 47 64 >Cell: +41 (0)78 630 66 57 >email: rainer.k...@uzh.ch > rai...@krugs.de >Skype: RMkrug > > PGP: 0x0F52F982 > >___ >R-SIG-Mac mailing list >R-SIG-Mac@r-project.org >https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Orcid ID: -0002-7490-0066 Department of Evolutionary Biology and Environmental Studies University of Zürich Office Y34-J-74 Winterthurerstrasse 190 8075 Zürich Switzerland Office: +41 (0)44 635 47 64 Cell: +41 (0)78 630 66 57 email: rainer.k...@uzh.ch rai...@krugs.de Skype: RMkrug PGP: 0x0F52F982 [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] Install r-devel with homebrew?
Hi I know - homebrew is not a supported installation approach to R, but I am asking anyway: Is there a way of installing r-devel via homebrew? Otherwise, what is the easiest way of getting r-devel on my Mac, without interfering with the homebrew install? Thanks, Rainer -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Orcid ID: -0002-7490-0066 Department of Evolutionary Biology and Environmental Studies University of Zürich Office Y34-J-74 Winterthurerstrasse 190 8075 Zürich Switzerland Office: +41 (0)44 635 47 64 Cell: +41 (0)78 630 66 57 email: rainer.k...@uzh.ch rai...@krugs.de Skype: RMkrug PGP: 0x0F52F982 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] damned Catalina
Just works out of the box, i.e. the cloud repo. PS: please CC the list in - thanks > On 18 Dec 2019, at 14:34, bruno apolloni wrote: > > I tried from many repo: > > https://cran.r-project.org <https://cran.r-project.org/> > https://pbil.univ-lyon1.fr/CRAN/ <https://pbil.univ-lyon1.fr/CRAN/> > https://cran.stat.unipd.it <https://cran.stat.unipd.it/> > http://cran.mirror.garr.it/mirrors/CRAN/ > <http://cran.mirror.garr.it/mirrors/CRAN/> > > always with the same answer: > > package ‘regtools’ is not available (for R version 3.6.2) . > > Which URL you refer to? The above links are opened in Safari. > > Thanks for your cooperation > > Bruno > >> Il giorno 18 dic 2019, alle ore 13:41, Rainer M Krug > <mailto:rai...@krugs.de>> ha scritto: >> >> Also on Catalena: I can install without problems. Try a different repo? Can >> you open the URL in Safari? >> >> >> Cheers, >> >> Rainer >> >>> On 18 Dec 2019, at 13:32, bruno apolloni >> <mailto:apoll...@di.unimi.it>> wrote: >>> >>> Any help after the Ken answer? >>> >>> Thanks a lot >>> Bruno >>> >>>> Inizio messaggio inoltrato: >>>> >>>> Da: bruno apolloni mailto:apoll...@di.unimi.it>> >>>> Oggetto: Re: [R-SIG-Mac] damned Catalina >>>> Data: 18 dicembre 2019 13:30:54 CET >>>> A: Ken Beath mailto:k...@kjbeath.com.au>> >>>> >>>> Actually, in https://cran.r-project.org/bin/macosx/ >>>> <https://cran.r-project.org/bin/macosx/> >>>> <https://cran.r-project.org/bin/macosx/ >>>> <https://cran.r-project.org/bin/macosx/>> I read; >>>> >>>> For discussion of Mac-related topics and reporting Mac-specific bugs, >>>> please use the R-SIG-Mac <https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>>> <https://stat.ethz.ch/mailman/listinfo/r-sig-mac>> mailing list. >>>> >>>> Did something went wrong? Should I remove the first line of my mail? >>>> Actually, what I need is to run “regtools” on Cran R insalled on my >>>> computer. Thanks for your unsderstanding, all the best >>>> >>>> Bruno >>>> >>>> Bruno Apolloni >>>> (Full Professor ) >>>> Dipartimento di Informatica >>>> University of Milano >>>> Via Comelico 39 >>>> 20135 Milano (Italy) >>>> Tel. +39(0)2-50316284 >>>> Fax. +39(0)2-50316228 >>>> Mobile +39 333 7469878 >>>> e-mail: apoll...@di.unimi.it <mailto:apoll...@di.unimi.it> >>>> <mailto:apoll...@di.unimi.it <mailto:apoll...@di.unimi.it>> >>>> http://homes.di.unimi.it/apolloni <http://homes.di.unimi.it/apolloni> >>>> <http://homes.di.unimi.it/apolloni <http://homes.di.unimi.it/apolloni>> >>>> >>>> >>>>> Il giorno 18 dic 2019, alle ore 13:08, Ken Beath >>>> <mailto:k...@kjbeath.com.au> <mailto:k...@kjbeath.com.au >>>>> <mailto:k...@kjbeath.com.au>>> ha scritto: >>>>> >>>>> Try another repository. It works fine with the main CRAN and teh RStudio >>>>> repositories. >>>>> >>>>> Ken >>>>> >>>>>> On 18 Dec 2019, at 10:50 pm, bruno apolloni >>>>> <mailto:apoll...@di.unimi.it> <mailto:apoll...@di.unimi.it >>>>>> <mailto:apoll...@di.unimi.it>>> wrote: >>>>>> >>>>>> Dear All >>>>>> >>>>>> among disasters of the new operating system Catalina, this one concerns >>>>>> R. >>>>>> >>>>>> Trying to install “regtools" the answer by Crane R consolle is >>>>>> >>>>>> unable to access index for repository >>>>>> https://cran.stat.unipd.it/bin/macosx/el-capitan/contrib/3.6 >>>>>> <https://cran.stat.unipd.it/bin/macosx/el-capitan/contrib/3.6> >>>>>> <https://cran.stat.unipd.it/bin/macosx/el-capitan/contrib/3.6 >>>>>> <https://cran.stat.unipd.it/bin/macosx/el-capitan/contrib/3.6>> >>>>>> <https://cran.stat.unipd.it/bin/macosx/el-capitan/contrib/3.6 >>>>>> <https://cran.stat.unipd.it/bin/macosx/el-capitan/contrib/3.6> >>>>>> <https://cran.stat.unipd.it/bin/m
Re: [R-SIG-Mac] damned Catalina
Also on Catalena: I can install without problems. Try a different repo? Can you open the URL in Safari? Cheers, Rainer > On 18 Dec 2019, at 13:32, bruno apolloni wrote: > > Any help after the Ken answer? > > Thanks a lot > Bruno > >> Inizio messaggio inoltrato: >> >> Da: bruno apolloni >> Oggetto: Re: [R-SIG-Mac] damned Catalina >> Data: 18 dicembre 2019 13:30:54 CET >> A: Ken Beath >> >> Actually, in https://cran.r-project.org/bin/macosx/ >> <https://cran.r-project.org/bin/macosx/> I read; >> >> For discussion of Mac-related topics and reporting Mac-specific bugs, please >> use the R-SIG-Mac <https://stat.ethz.ch/mailman/listinfo/r-sig-mac> mailing >> list. >> >> Did something went wrong? Should I remove the first line of my mail? >> Actually, what I need is to run “regtools” on Cran R insalled on my >> computer. Thanks for your unsderstanding, all the best >> >> Bruno >> >> Bruno Apolloni >> (Full Professor ) >> Dipartimento di Informatica >> University of Milano >> Via Comelico 39 >> 20135 Milano (Italy) >> Tel. +39(0)2-50316284 >> Fax. +39(0)2-50316228 >> Mobile +39 333 7469878 >> e-mail: apoll...@di.unimi.it <mailto:apoll...@di.unimi.it> >> http://homes.di.unimi.it/apolloni <http://homes.di.unimi.it/apolloni> >> >> >>> Il giorno 18 dic 2019, alle ore 13:08, Ken Beath >> <mailto:k...@kjbeath.com.au>> ha scritto: >>> >>> Try another repository. It works fine with the main CRAN and teh RStudio >>> repositories. >>> >>> Ken >>> >>>> On 18 Dec 2019, at 10:50 pm, bruno apolloni >>> <mailto:apoll...@di.unimi.it>> wrote: >>>> >>>> Dear All >>>> >>>> among disasters of the new operating system Catalina, this one concerns R. >>>> >>>> Trying to install “regtools" the answer by Crane R consolle is >>>> >>>> unable to access index for repository >>>> https://cran.stat.unipd.it/bin/macosx/el-capitan/contrib/3.6 >>>> <https://cran.stat.unipd.it/bin/macosx/el-capitan/contrib/3.6> >>>> <https://cran.stat.unipd.it/bin/macosx/el-capitan/contrib/3.6 >>>> <https://cran.stat.unipd.it/bin/macosx/el-capitan/contrib/3.6>> >>>> >>>> The same for “devtools”. This happens on my Mac with Catalina OS. The >>>> same installation on same Crane R but on a laptop of colleauge of mine >>>> endowed with previous OS (el captain) succeeds without any problem. >>>> >>>> Any remedy to suggest? >>>> >>>> Thanks a lot >>>> >>>> Bruno >>>>[[alternative HTML version deleted]] >>>> >>>> ___ >>>> R-SIG-Mac mailing list >>>> R-SIG-Mac@r-project.org <mailto:R-SIG-Mac@r-project.org> >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>>> >>> >> >> >> >> >> >> >> >> >> >> >> > > > [[alternative HTML version deleted]] > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Orcid ID: -0002-7490-0066 Department of Evolutionary Biology and Environmental Studies University of Zürich Office Y34-J-74 Winterthurerstrasse 190 8075 Zürich Switzerland Office: +41 (0)44 635 47 64 Cell: +41 (0)78 630 66 57 email: rainer.k...@uzh.ch rai...@krugs.de Skype: RMkrug PGP: 0x0F52F982 [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] R crashes after installing certain packages
loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
| 6: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
| 7: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
| 8: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck =
vI[[j]])
| 9: asNamespace(ns)
| 10: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
| 11: loadNamespace(package, lib.loc, keep.source, partial = TRUE)
| 12: withCallingHandlers(expr, packageStartupMessage = function(c)
invokeRestart("muffleMessage"))
| 13: suppressPackageStartupMessages(loadNamespace(package, lib.loc,
keep.source, partial = TRUE))
| 14: code2LazyLoadDB(package, lib.loc = lib.loc, keep.source = keep.source,
compress = compress)
| 15: makeLazyLoading(pkg_name, lib, keep.source = keep.source)
| 16: doTryCatch(return(expr), name, parentenv, handler)
| 17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
| 18: tryCatchList(expr, classes, parentenv, handlers)
| 19: tryCatch(expr, error = function(e) {call <- conditionCall(e)if
(!is.null(call)) {if (identical(call[[1L]], quote(doTryCatch)))
call <- sys.call(-4L)dcall <- deparse(call)[1L]prefix <-
paste("Error in", dcall, ": ")LONG <- 75Lmsg <-
conditionMessage(e)sm <- strsplit(msg, "\n")[[1L]]w <- 14L +
nchar(dcall, type = "w") + nchar(sm[1L], type = "w")if (is.na(w))
w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type
= "b")if (w > LONG) prefix <- paste0(prefix, "\n ")}
else prefix <- "Error : "msg <- paste0(prefix, conditionMessage(e), "\n")
.Internal(seterrmessage(msg[1L]))if (!silent &&
identical(getOption("show.error.messages"), TRUE)) {cat(msg,
file = stderr()).Internal(printDeferredWarnings())}
invisible(structure(msg, class = "try-error", condition = e))})
| 20: try({suppressPackageStartupMessages(.getRequiredPackages(quietly =
TRUE))makeLazyLoading(pkg_name, lib, keep.source = keep.source)})
| 21: do_install_source(pkg_name, instdir, pkg, desc)
| 22: do_install(pkg)
| 23: tools:::.install_packages()
| The downloaded source packages are in
|
‘/private/var/folders/50/wcr5bjwn75q595n6x82gxj28gn/T/RtmpK6Dn5L/downloaded_packages’
|
| An irrecoverable exception occurred. R is aborting now ...
| Warning message:
| In install.packages("car") :
| installation of package ‘car’ had non-zero exit status
| /usr/local/Cellar/r/3.3.2/R.framework/Resources/bin/INSTALL: line 34: 64396
Doneecho 'tools:::.install_packages()'
| 64397 Segmentation fault: 11 | R_DEFAULT_PACKAGES= LC_COLLATE=C
"${R_HOME}/bin/R" $myArgs --slave --args ${args}
| >
`
So something is not proper here.
In general: trying to load a package which is not present results in a
segfault:
,
| > library(fff)
| Error in library(fff) : there is no package called ‘fff’
|
| *** caught segfault ***
| address 0x18, cause 'memory not mapped'
|
| Possible actions:
| 1: abort (with core dump, if enabled)
| 2: normal R exit
| 3: exit R without saving workspace
| 4: exit R saving workspace
| Selection:
`
R, R-GUI, and RStudio are all installed using homebrew.
I can do further tests if needed.
Cheers,
Rainer
>
> Note: I’m not very technically sound in these issues and a solution
> explained in a layman language will be much appreciated.
>
> Thanks,
> Chaitanya
> Graduate student
> MS in Business Analytics
> University of Texas at Dallas
>
> [[alternative HTML version deleted]]
>
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
--
Rainer M. Krug
email: Rainerkrugsde
PGP: 0x0F52F982
signature.asc
Description: PGP signature
___
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Re: [R-SIG-Mac] Lost Library ?
Roger Koenker <rkoen...@illinois.edu> writes: >> On Sep 7, 2016, at 2:13 AM, Rainer M Krug <rai...@krugs.de> wrote: >> >> Roger Koenker <rkoen...@illinois.edu> writes: >> >> >> This indicates, that you installed gurobi using homebrew? > > No, I don’t use homebrew, it was installed from the dmg downloaded > from the gurobi website. In that case you should contact their support. Rainer >> >> How did you install the R package? Did you install it as a binary? If >> yes, then install it type="source" so that it is compiled with the >> correct library paths. > > The gurobi download includes a mac binary and I installed that — as > far as I can tell there is no publicly available source version. >> >> If both assumptions are wrong: how did you install R, gurobi and the R >> packages? >> >> Cheers, >> >> Rainer >> > -- Rainer M. Krug email: Rainerkrugsde PGP: 0x0F52F982 signature.asc Description: PGP signature ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Lost Library ?
Roger Koenker <rkoen...@illinois.edu> writes: > This is a question about how to find a lost library needed for the gurobi R > package. > Gurobi is a optimization system with various frontends including to R. > Even though I realize that few of you use, or may even know about, gurobi I > hope > that there may be some generic advice — my first dubious attempts, contrary > to Simon’s > periodic advice that use of DYLD_LIBRARY_PATH is frowned upon, have proven > futile. > Here is the basic story: I just saw that gurobi is a commercial package which comes with their own R interface - I would ask on their mailing list. Cheers, Rainer > > I've installed gurobi and its license file and this seems to work on a test > problem from the command line, > but I would like to use the R package interface and have installed the R > binary package that comes with > the gurobi download on a R 3.3.0 system on an osx 10.11.5 machine, As far > as I can see there is no > source version of the R package available. The package “seems to” install, > but I now see in R: > >> library(gurobi) > Loading required package: gurobi > Loading required package: slam > Error in dyn.load(file, DLLpath = DLLpath, ...) : > unable to load shared object > '/Library/Frameworks/R.framework/Versions/3.3/Resources/library/gurobi/libs/gurobi.so': > > dlopen(/Library/Frameworks/R.framework/Versions/3.3/Resources/library/gurobi/libs/gurobi.so, > 6): Library not loaded: libgurobi65.so > Referenced from: > /Library/Frameworks/R.framework/Versions/3.3/Resources/library/gurobi/libs/gurobi.so > Reason: image not found > > the library libgurobi65.so is sitting in /usr/local/lib so I don't understand > why the > R process can't find it -- this is what the R package library thinks: > > yzzy: otool -L g* > > gurobi.so: > gurobi.so (compatibility version 0.0.0, current version 0.0.0) > libgurobi65.so (compatibility version 6.5.0, current version 6.5.2) > /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current > version 1197.1.1) > /Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libR.dylib > (compatibility version 3.2.0, current version 3.2.2) > > /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation > (compatibility version 150.0.0, current version 855.17.0) > > Many thanks for your help, > Roger > > url:www.econ.uiuc.edu/~rogerRoger Koenker > emailrkoen...@uiuc.eduDepartment of Economics > vox: 217-333-4558University of Illinois > fax: 217-244-6678 Urbana, IL 61801 > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Rainer M. Krug email: Rainerkrugsde PGP: 0x0F52F982 signature.asc Description: PGP signature ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Lost Library ?
Roger Koenker <rkoen...@illinois.edu> writes: > This is a question about how to find a lost library needed for the gurobi R > package. > Gurobi is a optimization system with various frontends including to R. > Even though I realize that few of you use, or may even know about, gurobi I > hope > that there may be some generic advice — my first dubious attempts, contrary > to Simon’s > periodic advice that use of DYLD_LIBRARY_PATH is frowned upon, have proven > futile. > Here is the basic story: > > I've installed gurobi and its license file and this seems to work on a test > problem from the command line, > but I would like to use the R package interface and have installed the R > binary package that comes with > the gurobi download on a R 3.3.0 system on an osx 10.11.5 machine, As far > as I can see there is no > source version of the R package available. The package “seems to” install, > but I now see in R: > >> library(gurobi) > Loading required package: gurobi > Loading required package: slam > Error in dyn.load(file, DLLpath = DLLpath, ...) : > unable to load shared object > '/Library/Frameworks/R.framework/Versions/3.3/Resources/library/gurobi/libs/gurobi.so': > > dlopen(/Library/Frameworks/R.framework/Versions/3.3/Resources/library/gurobi/libs/gurobi.so, > 6): Library not loaded: libgurobi65.so > Referenced from: > /Library/Frameworks/R.framework/Versions/3.3/Resources/library/gurobi/libs/gurobi.so > Reason: image not found > > the library libgurobi65.so is sitting in /usr/local/lib so I don't understand > why the > R process can't find it -- this is what the R package library thinks: This indicates, that you installed gurobi using homebrew? How did you install the R package? Did you install it as a binary? If yes, then install it type="source" so that it is compiled with the correct library paths. If both assumptions are wrong: how did you install R, gurobi and the R packages? Cheers, Rainer > > yzzy: otool -L g* > > gurobi.so: > gurobi.so (compatibility version 0.0.0, current version 0.0.0) > libgurobi65.so (compatibility version 6.5.0, current version 6.5.2) > /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current > version 1197.1.1) > /Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libR.dylib > (compatibility version 3.2.0, current version 3.2.2) > > /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation > (compatibility version 150.0.0, current version 855.17.0) > > Many thanks for your help, > Roger > > url:www.econ.uiuc.edu/~rogerRoger Koenker > emailrkoen...@uiuc.eduDepartment of Economics > vox: 217-333-4558University of Illinois > fax: 217-244-6678 Urbana, IL 61801 > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Rainer M. Krug email: Rainerkrugsde PGP: 0x0F52F982 signature.asc Description: PGP signature ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] Setting locale for running R in emacs / ess
Hi I installed R via homebrew, but it should be the same for the normal R installation. When I start R in emacs, I get these unset locale warnings: , | During startup - Warning messages: | 1: Setting LC_CTYPE failed, using "C" | 2: Setting LC_COLLATE failed, using "C" | 3: Setting LC_TIME failed, using "C" | 4: Setting LC_MESSAGES failed, using "C" | 5: Setting LC_MONETARY failed, using "C" | > > options(STERM='iESS', str.dendrogram.last="'", editor='emacsclient', show.error.locations=TRUE) | > sessionInfo() | R version 3.2.2 (2015-08-14) | Platform: x86_64-apple-darwin14.5.0 (64-bit) | Running under: OS X 10.11 (El Capitan) | | locale: | [1] C | | attached base packages: | [1] stats graphics grDevices utils datasets methods base | > version |_ | platform x86_64-apple-darwin14.5.0 | arch x86_64 | os darwin14.5.0 | system x86_64, darwin14.5.0 | status | major 3 | minor 2.2 | year 2015 | month 08 | day14 | svn rev69053 | language R | version.string R version 3.2.2 (2015-08-14) | nickname Fire Safety | > ` But I have the following in my .emacs file which should set the locales (as far as I know) , | (setq utf-translate-cjk-mode nil) ; disable CJK coding/encoding (Chinese/Japanese/Korean characters) | (set-language-environment 'utf-8) | ;; (set-keyboard-coding-system 'utf-8-mac) ; For old Carbon emacs on OS X only | (setq locale-coding-system 'utf-8) | (set-default-coding-systems 'utf-8) | (set-terminal-coding-system 'utf-8) | (unless (eq system-type 'windows-nt) | (set-selection-coding-system 'utf-8)) | (prefer-coding-system 'utf-8) ` which apparently does not work. Do I have to resort to setting the locales as described at http://stackoverflow.com/questions/30264526/why-does-my-ess-r-session-fall-back-to-c-locale or am I missing something? Thanks, Rainer -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Stellenbosch University South Africa Tel : +33 - (0)9 53 10 27 44 Cell: +33 - (0)6 85 62 59 98 Fax : +33 - (0)9 58 10 27 44 Fax (D):+49 - (0)3 21 21 25 22 44 email: rai...@krugs.de Skype: RMkrug PGP: 0x0F52F982 signature.asc Description: PGP signature ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Setting locale for running R in emacs / ess
Marc Schwartz <marc_schwa...@me.com> writes: >> On Oct 23, 2015, at 5:33 AM, Rainer M Krug <rai...@krugs.de> wrote: >> >> Hi >> >> I installed R via homebrew, but it should be the same for the normal R >> installation. >> >> When I start R in emacs, I get these unset locale warnings: >> >> , >> | During startup - Warning messages: >> | 1: Setting LC_CTYPE failed, using "C" >> | 2: Setting LC_COLLATE failed, using "C" >> | 3: Setting LC_TIME failed, using "C" >> | 4: Setting LC_MESSAGES failed, using "C" >> | 5: Setting LC_MONETARY failed, using "C" >> | > > options(STERM='iESS', str.dendrogram.last="'", editor='emacsclient', >> show.error.locations=TRUE) >> | > sessionInfo() >> | R version 3.2.2 (2015-08-14) >> | Platform: x86_64-apple-darwin14.5.0 (64-bit) >> | Running under: OS X 10.11 (El Capitan) >> | >> | locale: >> | [1] C >> | >> | attached base packages: >> | [1] stats graphics grDevices utils datasets methods base >> | > version >> |_ >> | platform x86_64-apple-darwin14.5.0 >> | arch x86_64 >> | os darwin14.5.0 >> | system x86_64, darwin14.5.0 >> | status >> | major 3 >> | minor 2.2 >> | year 2015 >> | month 08 >> | day14 >> | svn rev69053 >> | language R >> | version.string R version 3.2.2 (2015-08-14) >> | nickname Fire Safety >> | > >> ` >> >> But I have the following in my .emacs file which should set the locales >> (as far as I know) >> >> , >> | (setq utf-translate-cjk-mode nil) ; disable CJK coding/encoding >> (Chinese/Japanese/Korean characters) >> | (set-language-environment 'utf-8) >> | ;; (set-keyboard-coding-system 'utf-8-mac) ; For old Carbon emacs on OS X >> only >> | (setq locale-coding-system 'utf-8) >> | (set-default-coding-systems 'utf-8) >> | (set-terminal-coding-system 'utf-8) >> | (unless (eq system-type 'windows-nt) >> | (set-selection-coding-system 'utf-8)) >> | (prefer-coding-system 'utf-8) >> ` >> >> which apparently does not work. >> >> Do I have to resort to setting the locales as described at >> http://stackoverflow.com/questions/30264526/why-does-my-ess-r-session-fall-back-to-c-locale >> >> or am I missing something? >> >> Thanks, >> >> Rainer > > > Rainer, > > Download exec-path-from-shell.el from: > > https://github.com/purcell/exec-path-from-shell > > and place it where you may have other Emacs related add ins. > > Then, in your ~/.emacs file, add: > > (load "/PATH.TO/exec-path-from-shell") > (exec-path-from-shell-initialize) > > Replacing PATH.TO with the actual path to the exec-path-from-shell.el file. Thanks - I was using exec-path-from-shell already, but it was supposed to only copy the PATH and MANPATH as you can see here. But all environmental variables were copier=d under emacs 24. My problem is under 25, where exec-path-from-shell bev=haves as it should (or emacs does) as it only copies the PATH and MANPATH. I now added , | (exec-path-from-shell-copy-env "LC_ALL") | (exec-path-from-shell-copy-env "LANG") ` and it works nicely. There seems to be a bug in either emacs 24 or in exec-path-from-shell. > > You should remove the other lines pertaining to locales that you have above. > > That should help Emacs/ESS started from the GUI/dock pick up the > environment that you would normally have in a terminal session of R. > > Also, in case you are not aware, there is a dedicated ESS list here: > > https://stat.ethz.ch/mailman/listinfo/ess-help Yes I know, but I s=decided to ask here, as it is a mac specific problem. The last time I tried it on the ESS list but did not get a response. Thanks a lot, and keep this change in mu=ind when upgrading to emacs 25, Rainer > > > Regards, > > Marc Schwartz > > -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Stellenbosch University South Africa Tel : +33 - (0)9 53 10 27 44 Cell: +33 - (0)6 85 62 59 98 Fax : +33 - (0)9 58 10 27 44 Fax (D):+49 - (0)3 21 21 25 22 44 email: rai...@krugs.de Skype: RMkrug PGP: 0x0F52F982 signature.asc Description: PGP signature ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Rscript?
Roger Koenker <rkoen...@illinois.edu> writes:
> I don’t use Rscript, but thought I would try to see if I could improve my
> workflow this morning and have
> encountered a somewhat baffling roadblock:
>
> I try to run:
>
> yzzy: Rscript --verbose -e "cat('hi')"
> running
> '/Library/Frameworks/R.framework/Versions/bin/R --slave --no-restore -e
> cat('hi')'
>
> Rscript execution error: No such file or directory
>
> so then I wondered:
>
> yzzy: which Rscript
> /usr/bin/Rscript
> yzzy: ls -l /usr/bin/Rscript
> lrwxr-xr-x 1 root wheel 53 Oct 20 11:13 /usr/bin/Rscript ->
> /Library/Frameworks/R.framework/Resources/bin/Rscript
>
> which looked ok, since I had reinstalled R this morning:
>
> yzzy: R --version
> R version 3.2.2 (2015-08-14) -- "Fire Safety"
> Copyright (C) 2015 The R Foundation for Statistical Computing
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
>
> but eventually I noticed (see above) that Rscript seems to be pointing to
> Library/Frameworks/R.framework/Versions/bin/R
> which indeed doesn’t exist. So something is amiss. Naively it would seem
> that Rscript should point to …/Resources/…
> not to …/Versions/…
In my homebrew installation of R it does:
,
| 07:11:38 ~$ Rscript --verbose -e "cat('Hello World')"
| running
| '/usr/local/Cellar/r/3.2.2_1/R.framework/Versions/3.2/Resources/bin/R
--slave --no-restore -e cat('Hello World')'
|
| Hello World07:11:44 ~$
`
Cheers,
Rainer
> but I’m sure that there is a simpler explanation that probably involves some
> weirdness in my
> installation setup.
>
> url:www.econ.uiuc.edu/~rogerRoger Koenker
> emailrkoen...@uiuc.eduDepartment of Economics
> vox: 217-333-4558University of Illinois
> fax: 217-244-6678Urbana, IL 61801
>
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology,
UCT), Dipl. Phys. (Germany)
Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa
Tel : +33 - (0)9 53 10 27 44
Cell: +33 - (0)6 85 62 59 98
Fax : +33 - (0)9 58 10 27 44
Fax (D):+49 - (0)3 21 21 25 22 44
email: rai...@krugs.de
Skype: RMkrug
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Re: [R-SIG-Mac] sort() under terminal
Adrian Dușa <dusa.adr...@unibuc.ro> writes:
> Dear All,
>
> I tried to search some information about this on Google, but didn't find
> anything yet.
> There seems to be a difference between sorting in the Terminal app and
> sorting in the Rgui:
>
> In the Terminal:
Just a guess: Check the sessionInfo(). Mine is:
,
| > sessionInfo()
| R version 3.2.2 (2015-08-14)
| Platform: x86_64-apple-darwin14.5.0 (64-bit)
| Running under: OS X 10.11 (El Capitan)
|
| locale:
| [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
|
| attached base packages:
| [1] stats graphics grDevices utils datasets methods base
| >
`
I guess it is the locale settings which are different?
Cheers,
Rainer
>
>> sort(c("W", "e", "E"))
> [1] "E" "W" "e"
>> R.version
>_
> platform x86_64-apple-darwin13.4.0
> arch x86_64
> os darwin13.4.0
> system x86_64, darwin13.4.0
> status
> major 3
> minor 2.2
> year 2015
> month 08
> day14
> svn rev69053
> language R
> version.string R version 3.2.2 (2015-08-14)
> nickname Fire Safety
>
>
>
> In the Rgui:
>
>> sort(c("W", "e", "E"))
> [1] "e" "E" "W"
>> R.version
>_
> platform x86_64-apple-darwin13.4.0
> arch x86_64
> os darwin13.4.0
> system x86_64, darwin13.4.0
> status
> major 3
> minor 2.2
> year 2015
> month 08
> day14
> svn rev69053
> language R
> version.string R version 3.2.2 (2015-08-14)
> nickname Fire Safety
>
>
> Could anyone point me to some information, please?
> Best wishes,
> Adrian
--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology,
UCT), Dipl. Phys. (Germany)
Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa
Tel : +33 - (0)9 53 10 27 44
Cell: +33 - (0)6 85 62 59 98
Fax : +33 - (0)9 58 10 27 44
Fax (D):+49 - (0)3 21 21 25 22 44
email: rai...@krugs.de
Skype: RMkrug
PGP: 0x0F52F982
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Re: [R-SIG-Mac] Experiences with El Capitan
Simon Urbanek <simon.urba...@r-project.org> writes: > On Oct 5, 2015, at 3:34 AM, Rainer M Krug <rai...@krugs.de> wrote: > >> peter dalgaard <pda...@gmail.com> writes: >> >>> >> >> Agreed. >> >> I just would like to dd that in the case of using homebrew, which >> installs everything under /usr/local/... which did not cause any >> problems at all. I moved the contents of /usr/local to an other location >> before upgrade because the upgrade to Yosemite took because of a large >> /usr/local several hours instead of about half an hour, moved it back >> afterwards and everything worked fins without problems. >> >> One question concerning mixed usage of homebrew and the Official R >> installers: >> >> do the Official R installers fail if an R binary already exist, or do >> they raise a warning? >> >> To make this easier, would it be possible, to install the binaries under >> /usr/local/bin/R.X.Y.Z and then just create links in /usr/local/bin ? >> Tghis would make the whole process more transparent and easier to switch >> between different versions and means of installation. >> > > R installer never installs any R binaries outside of the > framework/app. The only thing we provide on 10.10 is a softlink for R > and Rscript in /usr/local/bin into the framework (removing anything > else in that name if it exists). In earlier OS X versions this applies > to /usr/bin instead. OK - thanks for the clarification. Maybe I am overly careful, but I would very much prefer that the user is asked how to proceed if something would be overwritten. Due to e.g. homebrew /usr/local/bin becomes used quite a bit, so an approach which does not overwrite existing files / links in /usr/local/bin would be, in my opinion, a plus. Homebrew does for example installs the files, but does issue an error if the links in e.g. /usr/local/bin would overwrite existing files / links. Cheers, Rainer > > Cheers, > Simon > > >> Thanks for the clarifications, >> >> Rainer >> >>> >>> -pd >>> >>>> On 04 Oct 2015, at 18:53 , Prof Brian Ripley <rip...@stats.ox.ac.uk> wrote: >>>> >>>> The machine which provides the 'r-devel-osx-x86_64-clang' checks on >>>> the CRAN check farm has been upgraded from Yosemite to El Capitan >>>> and a complete round of checks has been run. >>>> >>>> >>>> 1) There is a lot of misinformation around about 'System Integrity >>>> Protection' aka 'rootless'. >>>> >>>> Upgrading to El Capitan moves files which are not allowed under /usr >>>> to /Library/SystemMigration/usr, so you will be able to see what was >>>> lost. This includes /usr/bin/R, /usr/bin/Rscript (but the installer >>>> installs these under /usr/local/bin on El Capitan as from R 3.2.2), >>>> /usr/X11R6, /usr/texbin . Contrary to reports from betas, the link >>>> /usr/X11 is preserved. >>>> >>>> If an installer tries to create a disallowed file such as >>>> /usr/bin/R, this is silently ignored (at least in the cases we >>>> tested). So you can install e.g. R 3.1.3 but the executables will >>>> not appear in the default Terminal path (more details in the current >>>> manual). >>>> >>>> >>>> 2) After updating you need to re-install the Command Line Tools and >>>> R (to get the links in /usr/local). I did not need to re-install >>>> Java nor XQuartz. >>>> >>>> >>>> 3) All the 'Mavericks' binary packages tested worked. The source >>>> packages of rJava and rgl (only) cannot be installed and the >>>> maintainers have patched versions available. >>>> >>>> >>>> There is updated information in the latest 'R Installation and >>>> Administration' manual in R-patched and R-devel (in the sources, or >>>> the online versions at https://cran.r-project.org/manuals.html will >>>> update in a day or two). >>>> >>>> -- >>>> Brian D. Ripley, rip...@stats.ox.ac.uk >>>> Emeritus Professor of Applied Statistics, University of Oxford >>>> 1 South Parks Road, Oxford OX1 3TG, UK >>>> >>>> ___ >>>> R-SIG-Mac mailing list >>>> R-SIG-Mac@r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> >> -- >> Rainer M. Krug >> email: Rainerkrugsde >> PGP: 0x0F52F982 >> ___ >> R-SIG-Mac mailing list >> R-SIG-Mac@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Rainer M. Krug email: Rainerkrugsde PGP: 0x0F52F982 signature.asc Description: PGP signature ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Bug related to locale changes.
Simon Urbanek simon.urba...@r-project.org writes: Interesting - it seems to fail only the first time after the locale is set: Sys.setlocale(locale=en_CA) [1] en_CA/en_CA/en_CA/C/en_CA/en_US.UTF-8 320 300 [1] NA 320 300 [1] TRUE 320 300 [1] TRUE There is probably an associated error. I'll have a look later today unless someone beats me to it. Some more datapoints to this: , | Sys.getlocale() | [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 | Sys.setlocale(locale=en_US) | [1] en_US/en_US/en_US/C/en_US/en_US.UTF-8 | 320 300 | [1] NA | Sys.setlocale(locale=en_US) | [1] en_US/en_US/en_US/C/en_US/en_US.UTF-8 | 320 300 | [1] TRUE | Sys.getlocale() | [1] en_US/en_US/en_US/C/en_US/en_US.UTF-8 | 320 300 | [1] TRUE | Sys.setlocale(locale=en_CA) | [1] en_CA/en_CA/en_CA/C/en_CA/en_US.UTF-8 | 320 300 | [1] NA | 320 300 | [1] TRUE | Sys.getlocale() | [1] en_CA/en_CA/en_CA/C/en_CA/en_US.UTF-8 | Sys.setlocale(locale=en_US) | [1] en_US/en_US/en_US/C/en_US/en_US.UTF-8 | 320 300 | [1] TRUE | Sys.setlocale(locale=en_CA) | [1] en_CA/en_CA/en_CA/C/en_CA/en_US.UTF-8 | 320 300 | [1] TRUE ` Even when I set the locale to the same it is, I observe this error. Rainer Thanks, Simon On Jun 8, 2015, at 7:40 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: I posted this to R-devel yesterday; from responses received, it appears to be OSX-specific (maybe Mavericks-specific). In an R session started from the terminal with R --vanilla, I see this: Sys.setlocale(locale=en_CA) [1] en_CA/en_CA/en_CA/C/en_CA/en_CA.UTF-8 320 300 [1] NA 320 300 [1] TRUE The first string comparison after the locale change produces NA, while later ones are fine. The locale string en_CA doesn't appear to matter, as long as it is different from my previous locale. Do others see this? Can we fix it before the 3.2.1 release? Duncan Murdoch ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Rainer M. Krug email: Raineratkrugsdotde PGP: 0x0F52F982 signature.asc Description: PGP signature ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Bug related to locale changes.
Berend Hasselman b...@xs4all.nl writes: On 08-06-2015, at 13:40, Duncan Murdoch murdoch.dun...@gmail.com wrote: I posted this to R-devel yesterday; from responses received, it appears to be OSX-specific (maybe Mavericks-specific). In an R session started from the terminal with R --vanilla, I see this: Sys.setlocale(locale=en_CA) [1] en_CA/en_CA/en_CA/C/en_CA/en_CA.UTF-8 320 300 [1] NA 320 300 [1] TRUE The first string comparison after the locale change produces NA, while later ones are fine. I see the similar things on R version 3.2.0 Patched (2015-05-11 r68355) Sys.setlocale(locale=en_CA) [1] en_CA/en_CA/en_CA/C/en_CA/en_GB 320 300 [1] NA 320 300 [1] TRUE Confirmed on Yosemite: , | Sys.setlocale(locale=en_CA) | [1] en_CA/en_CA/en_CA/C/en_CA/en_US.UTF-8 | 320 300 | [1] NA | 320 300 | [1] TRUE | version |_ | platform x86_64-apple-darwin14.3.0 | arch x86_64 | os darwin14.3.0 | system x86_64, darwin14.3.0 | status | major 3 | minor 2.0 | year 2015 | month 04 | day16 | svn rev68180 | language R | version.string R version 3.2.0 (2015-04-16) | nickname Full of Ingredients ` Berend -- Rainer M. Krug email: Raineratkrugsdotde PGP: 0x0F52F982 signature.asc Description: PGP signature ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] R on Mac: framework or homebrew?
Zhang Xinlian coral90zh...@gmail.com writes: I used brew install R to install R and I use the most recent version of Rstudio. And when I use the export in Rstudio, it tells me the following. Warning messages: 1: In cairo_pdf(file = /Users/xinlianzhang/Desktop/Rplot.pdf, width = 5.22917, : unable to load shared object '/usr/local/Cellar/r/3.2.0_1/R.framework/Resources/library/grDevices/libs//cairo.so': dlopen(/usr/local/Cellar/r/3.2.0_1/R.framework/Resources/library/grDevices/libs//cairo.so, 6): Library not loaded: /usr/local/lib/libjpeg.8.dylib Referenced from: /usr/local/Cellar/r/3.2.0_1/R.framework/Resources/library/grDevices/libs//cairo.so Reason: Incompatible library version: cairo.so requires version 13.0.0 or later, but libjpeg.8.dylib provides version 12.0.0 2: In cairo_pdf(file = /Users/xinlianzhang/Desktop/Rplot.pdf, width = 5.22917, : failed to load cairo DLL Did you upgrade cpp in homebrew after the installation from R? Errors like seem to happen when compiler versions / libraries don't match. If yes, reinstall libjpeg and the cairo programs, and, maybe, even R. Otherwise I would suggest to try the same in an R session from the terminal and see if you have the error there - because I don't know how well RStutio works together with homebrew installed R - doesn't RStudio come with it's own R installation? Cheers, Rainer 在 2013年9月12日星期四 UTC-4上午10:20:07，Rainer M Krug写道： Hi I am using R at the moment installed from the official installation as a framework, buit I also installed it from homebrew. As I am not using the Mac GUI (I am using mainly emacs, a little bit RStudio), so from there there was no difference. So which approach has which advantages? I can think of advantages when using homebrew (updates and upgrades of R) and also the framework approach (Ease of maintenance). I personaly lean towards the homebrew installation (linux background), but are there any disadvantages to using the official framework installation? Any comments? Cheers, Rainer -- Rainer M. Krug email: RMKrugatgmaildotcom -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Stellenbosch University South Africa Tel : +33 - (0)9 53 10 27 44 Cell: +33 - (0)6 85 62 59 98 Fax : +33 - (0)9 58 10 27 44 Fax (D):+49 - (0)3 21 21 25 22 44 email: rai...@krugs.de Skype: RMkrug PGP: 0x0F52F982 signature.asc Description: PGP signature ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Non-root OS X installation?
boB Rudis b...@rudis.net writes: Hey Branden, This http://unix.stackexchange.com/questions/149451/install-r-in-my-own-directory has some basic steps, but the gist is to compile it from scratch (good compile options in the homebrew recipe for R https://github.com/Homebrew/homebrew-science/blob/master/r.rb ). I can only recommend using homebrew for installation of R (and everything else you need). Works perfectly for me. Just be careful not to mix up the official R packages and their dependencies (especially fortran and tcltk) with the homebrew ones - I started with the official ones and moved gradually to a full homebrew setup - and it is much easier to maintain for me. I did not have as many probles on the swithch to Yosemite as the uers of the official R version. In a nutshell: go for homebrew and you might even not have to change anything and it will install under /usr/local/ as a normal user - homebrew does not need root access for most programs. Cheers, Rainer I'd highly suggest getting an admin-assisted install of official/base R. It'll only be a couple of times a year for updates but worth it for the stability factor. You can then have all package installs be relative to your local dir. But you'll still need the OS X dev tools installed for non-binary packages that need compilation, so you should also probably get that admin-assisted installed as well. -Bob On Mon, May 4, 2015 at 9:12 AM, Branden R. Williams jee...@brw.net wrote: Greetings. I am getting a new mac procured through my company, and I am pretty sure I’m not going to have local administrator access to it. Is there a clean way to install R locally for one user, including all the packages that might be required, so that I don’t need admin access? thx. Regards, Branden R. Williams, DBA, CISSP, CISM b...@brandenwilliams.com Phone: +1 (214) 727-8227 http://www.brandenwilliams.com/ Cal: http://meetme.so/drbrando ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Rainer M. Krug email: Raineratkrugsdotde PGP: 0x0F52F982 signature.asc Description: PGP signature ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] gstat package on Mavericks
Kevin Wolz wo...@illinois.edu writes: Trying to get the gstat package installed on R 3.1.0 running on mac OSX Mavericks, for which a binary has not yet been built. A previous R-SIG-Mac thread provided a good solution for rgeos and rgdal, but this doesn't work for gstat. Any suggestions? I just tried it, and it installed flawless. BUT: I have installed R, fortran, gdal, ... using homebrew. In my experience, this simplifies the process of compiling, as always the same compiler is used and everything is installed from source. I made it a habit of installing *all* packages from source and did not have any problems so far. Hope this helps, Rainer I'm trying to install from source, but R isn't liking the fact that gstat is from source but the dependencies are in CRAN. Also, I think that one or more of the dependencies don't have Mavericks binaries yet either! Thanks, Kevin -- Kevin Wolz PhD Student, DeLucia Lab University of Illinois at Urbana-Champaign [[alternative HTML version deleted]] -- Rainer M. Krug email: Raineratkrugsdotde PGP: 0x0F52F982 pgp9M4mju0Ffr.pgp Description: PGP signature ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Best installation approach of R on Mavericks for Emacs/Homebrew users?
Grant Rettke g...@wisdomandwonder.com writes: Hi, I'm working on setting up a new to me OSX machine with R. My preference is via Homebrew, with which I'll be using Emacs and ESS. Looking out for trouble, I tried to do a little legwork first of all to see what is the status quo for installing R on Mavericks. There are more than a few options and I am wanting to get your feedback on what worked for you, and if you happened to follow any of these directions. Here is what I found: I am using R emacs (the version provided by [1]) installed via homebrew, ESS and org-mode installed From git, and it works without problems for me. I somehow prefer to install all packages fro source, which works nicely, and one needs s-code anyway when using homebrew. https://onote2.github.io/2013/12/04/install-r-on-mac-os-x-109-mavericks/ The simplest. Looks great. Be aware, that gfortran is not available anymore: , | $ brew search gfortran | GNU Fortran is now provided as part of GCC, and can be installed with: | brew install gcc ` I don't know which one I followed, but so far all look more or less correct. I would suggest to follow the first one, and look at error messages, and then follow these. Be aware that if you install R and gfortran from the official R repos (or Simons), the gfortran *will* interfere with homebrew's R (unless my memory is misleading me completely). I had to completely remove it before installing R from homebrew. Also: when swithching, you have to re-compile *all your installed packages* due to different compiler versions. This (and the from Prof Ripley later mentioned limited availability of packages for R in binary) is the reason why I am using the homebrew installation of R and compiling all packages from source - no problems so far. Cheers and keep us posted about your success / problems, Rainer http://davidsimpson.me/2013/02/26/installing-r-on-os-x/ Also simple. http://zmjones.com/mac-setup/#R Also quite simple. http://www.moncefbelyamani.com/how-to-install-xcode-homebrew-git-rvm-ruby-on-mac/#step-1 https://github.com/Homebrew/homebrew-science/issues/427 Sometimes things go wrong? http://cran.r-project.org/bin/macosx/ If all else fails, or perhaps are any of you Emacs users using this instead of Homebrew? It looks pretty straightforward at this point; just wanted to talk to some other folks and see what worked for them. Kind regards, Grant Rettke | AAAS, ACM, ASA, FSF, IEEE, SIAM, Sigma Xi g...@wisdomandwonder.com | http://www.wisdomandwonder.com/ Wisdom begins in wonder. --Socrates ((» (x) (x x)) (» (x) (x x))) Life has become immeasurably better since I have been forced to stop taking it seriously. --Thompson [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac Footnotes: [1] https://github.com/railwaycat/emacs-mac-port -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Stellenbosch University South Africa Tel : +33 - (0)9 53 10 27 44 Cell: +33 - (0)6 85 62 59 98 Fax : +33 - (0)9 58 10 27 44 Fax (D):+49 - (0)3 21 21 25 22 44 email: rai...@krugs.de Skype: RMkrug PGP: 0x0F52F982 pgp9r7oVG0EYE.pgp Description: PGP signature ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Best installation approach of R on Mavericks for Emacs/Homebrew users?
peter dalgaard pda...@gmail.com writes: On 22 May 2014, at 00:32 , Vincent Goulet vincent.gou...@me.com wrote: Ok, I'm biased here, but for me (and my students!) the simple procedure is: 1. Install the R binary from CRAN; 2. Install my Emacs distribution for OS X that comes bundled with ESS: http://vgoulet.act.ulaval.ca/en/emacs/mac 2a. (variant) Install Aquamacs, which also comes with ESS and AUCTeX. There are differning opinions about Aquamacs (Macified version of emacs and bundled with some packages) or emacs - I decided (after using Linux for several years) to use emacs, due to 1) compatibility with other OS (different config files for emacs and Aquamacs) 2) Same keyboard shortcuts between OS 3) newer versions of emacs then used in Aquamacs But I am sure Aquamacs makes some things easier then using emacs, but I think emacs fits better tigether with the idea of using homebrew, while Aquamacs fits better to the approach of using native Mac installers. Cheers, Rainer 3. Enjoy. Envoyé de mon iPad Le 2014-05-21 à 15:37, Grant Rettke g...@wisdomandwonder.com a écrit : Hi, I'm working on setting up a new to me OSX machine with R. My preference is via Homebrew, with which I'll be using Emacs and ESS. Looking out for trouble, I tried to do a little legwork first of all to see what is the status quo for installing R on Mavericks. There are more than a few options and I am wanting to get your feedback on what worked for you, and if you happened to follow any of these directions. Here is what I found: https://onote2.github.io/2013/12/04/install-r-on-mac-os-x-109-mavericks/ The simplest. Looks great. http://davidsimpson.me/2013/02/26/installing-r-on-os-x/ Also simple. http://zmjones.com/mac-setup/#R Also quite simple. http://www.moncefbelyamani.com/how-to-install-xcode-homebrew-git-rvm-ruby-on-mac/#step-1 https://github.com/Homebrew/homebrew-science/issues/427 Sometimes things go wrong? http://cran.r-project.org/bin/macosx/ If all else fails, or perhaps are any of you Emacs users using this instead of Homebrew? It looks pretty straightforward at this point; just wanted to talk to some other folks and see what worked for them. Kind regards, Grant Rettke | AAAS, ACM, ASA, FSF, IEEE, SIAM, Sigma Xi g...@wisdomandwonder.com | http://www.wisdomandwonder.com/ “Wisdom begins in wonder.” --Socrates ((λ (x) (x x)) (λ (x) (x x))) “Life has become immeasurably better since I have been forced to stop taking it seriously.” --Thompson [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Stellenbosch University South Africa Tel : +33 - (0)9 53 10 27 44 Cell: +33 - (0)6 85 62 59 98 Fax : +33 - (0)9 58 10 27 44 Fax (D):+49 - (0)3 21 21 25 22 44 email: rai...@krugs.de Skype: RMkrug PGP: 0x0F52F982 pgp2Xoe6azrDj.pgp Description: PGP signature ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] rgdal on mac os 10.9
If I remember correctly, the installation from source was quite easy: apart from the usual compilers, you need gdal installed, which installs easily via homebrew [1]. After this, installation of rgdal from source worked without any additional configurations? Rainer Ian Fellows ian.fell...@stat.ucla.edu writes: Hi All, Does anyone know if there are plans to have rgdal compile correctly on the CRAN Mavericks machine? I’ve really been enjoying the binaries that have been available as building from source is a non-trival hassle. http://www.r-project.org/nosvn/R.check/r-release-osx-x86_64-mavericks/rgdal-00check.html Best, Ian ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac Footnotes: [1] http://brew.sh/ -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Stellenbosch University South Africa Tel : +33 - (0)9 53 10 27 44 Cell: +33 - (0)6 85 62 59 98 Fax : +33 - (0)9 58 10 27 44 Fax (D):+49 - (0)3 21 21 25 22 44 email: rai...@krugs.de Skype: RMkrug PGP: 0x0F52F982 pgpomf5kIyGzB.pgp Description: PGP signature ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] rgdal on mac os 10.9
Prof Brian Ripley rip...@stats.ox.ac.uk writes: On 30/04/2014 13:56, Rainer M Krug wrote: If I remember correctly, the installation from source was quite easy: apart from the usual compilers, you need gdal installed, which installs easily via homebrew [1]. After this, installation of rgdal from source worked without any additional configurations? No, not really. 1) for a portable package you will need static GDAL. 2) GDAL can make use of a wide range of external software to read raster files: without quite a lot of the optional ones it is not much use for rgdal and other R packages. Simon needs to build that for Mavericks, and statically too. Sorry - I was talking of installing it in R via type=source not on CRAN. For CRAN it is definitely a different issue. Rainer However, Fellows has ignored all the advice to use the Snow Leopard package of R 3.1.0 if he wants rgdal. That is in the current manual (http://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-R-under-OS-X) and was posted to this list recently (https://stat.ethz.ch/pipermail/r-sig-mac/2014-April/010835.html). That is by far the easiest solution. Rainer Ian Fellows ian.fell...@stat.ucla.edu writes: Hi All, Does anyone know if there are plans to have rgdal compile correctly on the CRAN Mavericks machine? I’ve really been enjoying the binaries that have been available as building from source is a non-trival hassle. http://www.r-project.org/nosvn/R.check/r-release-osx-x86_64-mavericks/rgdal-00check.html Best, Ian ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac Footnotes: [1] http://brew.sh/ ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Stellenbosch University South Africa Tel : +33 - (0)9 53 10 27 44 Cell: +33 - (0)6 85 62 59 98 Fax : +33 - (0)9 58 10 27 44 Fax (D):+49 - (0)3 21 21 25 22 44 email: rai...@krugs.de Skype: RMkrug PGP: 0x0F52F982 pgpGPkXtggpzH.pgp Description: PGP signature ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] R stops abruptly applying textures in rgl
Agustin Diez Castilloagustin.d...@uv.es writes: Duncan, Find the script [1] , SessionInfo [2] and the Mac error [3] in case it helps. Executing R from the terminal R doesn't freeze and I got the same message that in Ubuntu 13.04 [4] # With rgl installed in ~/Library/R/ library(rgl) # Set directory setwd(~/) #Working rgl.bg(sphere=TRUE, texture=system.file(textures/bump_dust.png, package=rgl),back=filled) #Copying the same texture to the working directory system(cp ~/Library/R/3.0/library/rgl/textures/bump_dust.png bump_dust.png) # expanded version also works expanded-paste(getwd(),/bump_dust.png,sep=) # Testing rgl.bg(sphere=TRUE, texture=expanded,back=filled) #Hanging R.app rgl.bg(sphere=TRUE, texture=~/bump_dust.png,back=filled) Confirmed as described - works in terminal, crashes R gui Additionally: works in RStudio with the following error: , | rgl.bg(sphere=TRUE, texture=~/bump_dust.png,back=filled) | Warning message: | In rgl.material(color = color, back = back, ...) : | RGL: Pixmap load: unable to open file '~/bump_dust.png' for reading ` , | version |_ | platform x86_64-apple-darwin10.8.0 | arch x86_64 | os darwin10.8.0 | system x86_64, darwin10.8.0 | status Patched | major 3 | minor 0.3 | year 2014 | month 03 | day06 | svn rev65134 | language R | version.string R version 3.0.3 Patched (2014-03-06 r65134) | nickname Warm Puppy | library(rgl) | sessionInfo() | R version 3.0.3 Patched (2014-03-06 r65134) | Platform: x86_64-apple-darwin10.8.0 (64-bit) | | locale: | [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 | | attached base packages: | [1] stats graphics grDevices utils datasets methods base | | other attached packages: | [1] rgl_0.93.996 | ` Cheers, Rainer --- [2] R version 3.0.3 (2014-03-06) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rgl_0.93.996 -- [3] http://pastebin.com/tQ8FRFzc [4] Warning message: In rgl.material(color = color, back = back, ...) : RGL: Pixmap load: unable to open file '~/bump_dust.png' for reading Agustín On 14-03-19 10:22 AM, Agustin Angel Diez Castillo wrote: Hi, When applying textures to an rgl object I can do it without problem if the applied texture if the texture file is called in an expand form [1]. However if the same file is called with tilde [2], R will stop abruptly. I've tested it in three different machines, all running 9.2. The same in Unbuntu 13.04 drops a warning message [3] but R continues running. Agustin [1] /Users/myuser/myfile.png [2] ~/myfile.png [3] In rgl.material(...) : RGL: Pixmap load: unable to open file '~/gvSIG-desktop/gvSIG-desktop-2066/theme/splash.png' for reading I am unable to reproduce this. Could you please post a complete script that reproducibly causes the crash for you, and post information about rgl, R, and MacOS versions? Duncan Murdoch -- ** Dr. Agustín Diez Castillo Departament de Prehistòria i Arqueologia Phone: +34 963 86 42 42 Avda. Blasco Ibañez, 28 Fax: +34 963 86 42 34 València 46010 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Rainer M. Krug email: Raineratkrugsdotde PGP: 0x0F52F982 pgpShTkkH0ojL.pgp Description: PGP signature ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Suggested New Mac for Heavy R Use
Nick franken_beans2...@yahoo.com writes: Good afternoon, I am looking at buying my first Mac and thought i'd ask for advice for what I should get. I have it down to the two models below (but am open to realistic suggestions). I will primarily be using R for machine learning packages, and the data sets are very large. If any other specs are needed let me know. Thanks in advance. - 13 inch is quite small - I would go for the 15-inch - 128GB SSD is to small - at least in my experience. I have 256 GB and this works, but only 35 GB free - so I have a second USB3 HDD for additional data - 8GB RAM is fine I have the MacBookPro 10,1 Retina, 8GB memory and the 256 GB SSD drive - with Intel Core i7 I really like this machine The cores do make a difference. Cheers, Rainer 13-inch MacBook Air ($1,349) 1.7GHz Dual-Core Intel Core i7, Turbo Boost up to 3.3GHz 8GB 1600MHz LPDDR3 SDRAM 128GB Flash Storage 13-inch MacBook Pro with Retina ($1,399.00) 2.4GHz Dual-core Intel Core i5, Turbo Boost up to 2.9GHz 8GB 1600MHz DDR3L SDRAM 128GB PCIe-based Flash Storage [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Rainer M. Krug email: RMKrugatgmaildotcom pgp34YZ_8jgMe.pgp Description: PGP signature ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] R and Xcode 5
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Simon I have problem acessing the site via a web browser (neither safari nor firefox), altough I can ping it. Is there an alternative site where I can download the binaries? Thanks, Rainer On 01/07/14, 03:11 , Simon Urbanek wrote: - -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Stellenbosch University South Africa Tel : +33 - (0)9 53 10 27 44 Cell: +33 - (0)6 85 62 59 98 Fax : +33 - (0)9 58 10 27 44 Fax (D):+49 - (0)3 21 21 25 22 44 email: rai...@krugs.de Skype: RMkrug -BEGIN PGP SIGNATURE- Version: GnuPG/MacGPG2 v2.0.22 (Darwin) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iQEcBAEBAgAGBQJSy729AAoJENvXNx4PUvmC+cUH/1mnc8duBJoD5MswG77quJJZ KNXSNmxZdDrrq0Kb/xsH8EtR+wefBtArF8FqlroDIM488SXEmdEmmGlr6z8CGYkt mQWHBAqXGpnZAVQQVnUMB4NAdIFOllOMvc0427JaIBKFZAFnhGOmZOxi9MnmIcBB DY4+/8AOxpzglTI1ibVkkYExYSwG/OmgZCA6yP18YOYDLQ+3QSlLohPcgWJJXAtO 5FDBJMFvhgE9YU3WOY7oixTXyQOeo+7ZCdBv8ge2MBJBal43Z2wZaCZoG4K2rMAX 4IvWkChUyy16xlTUYfZwc/qH2u1zEmLEXeo3n22WIk3T7YR/U1mqGyvl00/OyGY= =ByX2 -END PGP SIGNATURE- ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] R crashes on preferences screen
/.Rapp.history] sessionInfo() R Under development (unstable) (2012-12-30 r61489) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base -R.app from Simon- R Under development (unstable) (2012-12-30 r61489) -- Unsuffered Consequences Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-apple-darwin9.8.0/x86_64 (64-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. [R.app GUI 1.53 (6418) x86_64-apple-darwin9.8.0] [Workspace restored from /Users/rob/Projects/.RData] [History restored from /Users/rob/Projects/.Rapp.history] sessionInfo() R Under development (unstable) (2012-12-30 r61489) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base -- Brian D. Ripley, rip...@stats.ox.ac.uk mailto:rip...@stats.ox.ac.ukrip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 On Oct 2, 2013, at 6:09 AM, Brandon Hurr bhiv...@gmail.com wrote: I cannot reproduce on my mac mini (2011). OS X 10.8.5. R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base On Wed, Oct 2, 2013 at 2:03 PM, John Magnotti john.magno...@gmail.com wrote: Going to the preferences screen in R.app (Command + , or R-preferences) and selecting any of the icons causes R to crash with a segfault. If I click any the tabs at the top of the preferences window R doesn't crash, but if I go back to the show all tab and choose an option it causes an immediate failure. I'm running OS X 10.8.5, sessionInfo pasted below Thoughts? John sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Rainer M. Krug email: RMKrugatgmaildotcom ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] R crashes on preferences screen
John Magnotti john.magno...@gmail.com writes: Going to the preferences screen in R.app (Command + , or R-preferences) and selecting any of the icons causes R to crash with a segfault. If I click any the tabs at the top of the preferences window R doesn't crash, but if I go back to the show all tab and choose an option it causes an immediate failure. I'm running OS X 10.8.5, sessionInfo pasted below I can confirm this, but only when selecting the icons in the Show All section. Selecting the top ones, it works. Cheers, Rainer , | sessionInfo() | R version 3.0.1 (2013-05-16) | Platform: x86_64-apple-darwin10.8.0 (64-bit) | | locale: | [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 | | attached base packages: | [1] stats graphics grDevices utils datasets methods base | version |_ | platform x86_64-apple-darwin10.8.0 | arch x86_64 | os darwin10.8.0 | system x86_64, darwin10.8.0 | status | major 3 | minor 0.1 | year 2013 | month 05 | day16 | svn rev62743 | language R | version.string R version 3.0.1 (2013-05-16) | nickname Good Sport ` Thoughts? John sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base #secure method=pgpmime mode=sign -- Rainer M. Krug email: RMKrugatgmaildotcom ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] New to OS X - from where to install R?
Hi I am completely new to OS X (linux user up to now)- so please excuse my ignorance. What is the best way to install R on OS X? Should I use something like Macports [1]? Or should I install from the official release from the cran site? What are the drawbacks of each? Thanks, Rainer Footnotes: [1] https://www.macports.org/ -- Rainer M. Krug email: RMKrugatgmaildotcom pgpNOj9NL_ACT.pgp Description: PGP signature ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Problems loading Rcmdr on a Mac 10.7.2 and a Mac 10.6.8
peter dalgaard pda...@gmail.com writes: On Sep 20, 2013, at 08:49 , Prof Brian Ripley wrote: I am not so sure about that. It will do no harm running CRAN binary R. But it does mean that there are multiple versions of X11 things about and that will cause problems for other things (including possibly installing packages from source). Or, put differently, we could be shipping libraries that are incompatible with the system libraries (or 3rd party libraries for that matter) if those are not kept up to date. Of course, keeping versions compatible is exactly what package managers are for, on systems that have them. The way things work on commercial platforms tend to lead each applicationq into rolling everything you need into the application itself, which is - in the bigger perspective - wasteful and somewhat risky (as defective components only get replaced upon upgrade of the application). I know Simon distrusts them, but sometimes I do feel that we should work more closely with the people doing managed distributions for OSX, i.e. MacPorts, Homebrew, Fink. (Not sure how they'd cope with missing OS updates, though.) I completely agree here. I can only speak about homebrew, but one additional advantage is that to have multiple versions of R installed (and switching between them) is not a problem at all. If there would be a kind of an official support, I would definitely switch to the homwbrew version. Cheers, Rainer -- Rainer M. Krug email: RMKrugatgmaildotcom ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] R on Mac: framework or homebrew?
Prof Brian Ripley rip...@stats.ox.ac.uk writes: On 12/09/2013 17:15, MacQueen, Don wrote: I've been using R on OS X probably ever since there was an R on OS X, and like you I use it from the command line. In the early days I installed R from sources, but quite a few years ago I switched to using the framework version. I can't think of any disadvantage I've encountered. It is harder to have multiple versions of the framework in use at once. And that is an issue now the R release rate is slower: package developers probably want both the release version and a current R-devel. That is what I was thinking as well - in homebrew, I simply have to use , | brew switch R version ` to switch to another installed version. If I were to not use the framework version, I think I would prefer to install directly from sources, not use a package management system. There might be more initial work installing various prerequisites (things like tcl/tk, png, maybe readline, who knows what all) but it would probably be better in the long run. Some packages, such as a number of spatial packages, require installing other libraries such as rgdal, proj, and others. Currently, these are also available as frameworks, and installing those packages in a framework R is now well-supported. It might be considerably more difficult to install such packages in a non-framework R. I don't know how much would be involved, so I just suggest it as an aspect to consider. Almost nothing. Simon provides binaries for those at http://r.research.att.com/libs/ and if you want later ones they compile simply from the sources. in any case, whether R is a framework or not does not affect installing packages from sources, as you still need to tell the toolchain where to look for the headers and libraries. That is good to know. On my office iMac have almost all of CRAN installed (more than Simon provides as binaries) compiling from source. The exceptions are those 10 or so which are too broken to install on OS X and those depending on Qt, MySQL (I haven't bothered) or BRugs (i386 Windows/Linux only) Thanks a lot for all of your input. I will then, for the moment, stick to the framework (as it works), but keep the homebrew option in mind. Thanks, Rainer -- Rainer M. Krug email: RMKrugatgmaildotcom ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] R on Mac: framework or homebrew?
Hi I am using R at the moment installed from the official installation as a framework, buit I also installed it from homebrew. As I am not using the Mac GUI (I am using mainly emacs, a little bit RStudio), so from there there was no difference. So which approach has which advantages? I can think of advantages when using homebrew (updates and upgrades of R) and also the framework approach (Ease of maintenance). I personaly lean towards the homebrew installation (linux background), but are there any disadvantages to using the official framework installation? Any comments? Cheers, Rainer -- Rainer M. Krug email: RMKrugatgmaildotcom pgpgSGpsOgFW0.pgp Description: PGP signature ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] Installing packages with type=source instead of the default binary?
Hi I am using Snow Leopard and I can compile packages (I have all tools installed) but I am asking myself: Is there an advantage to using type=source instead of the binary install of the packages? For certain packages it makes sense to have fine grained control to link to certain versions of C libraries (e.g. rgdal), but is there a general advantage of compiling locally? Or is that simply a leftover from my Linux days, that I prefer locally compiled packages? Thanks, Rainer -- Rainer M. Krug email: RMKrugatgmaildotcom pgpzEfPnUeH5I.pgp Description: PGP signature ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Installing packages with type=source instead of the default binary?
Prof Brian Ripley rip...@stats.ox.ac.uk writes: On 09/09/2013 10:56, Rainer M Krug wrote: Hi I am using Snow Leopard and I can compile packages (I have all tools installed) but I am asking myself: Is there an advantage to using type=source instead of the binary install of the packages? For certain packages it makes sense to have fine grained control to link to certain versions of C libraries (e.g. rgdal), but is there a general advantage of compiling locally? There is an advantage if you run multiple versions of R and want to share a library directory. The CRAN binary versions are tied to the R.framework installation. But otherwise - for the majority of packages (which have no compiled code), there is almost no advantage in installing from source, but also very little loss (you need no extra tools). True. - The CRAN binaries are built for 3.0.0 I believe, and certainly not re-built for patch versions. For a very few packages it is advantageous to use the latest patch version (I am thinking of some issues with non-Sweave vignettes in recent history, but there have been other issues). - You might well want to use different external C/C++/Fortran software, and you may even need to do so or use a different compiler (there are packages which install with clang but not llvm-gcc and v.v.). Thanks for this detailed response. So if my tool chain for compilation is up and running, there can be an advantage to compile from source. So I will likely stick to that habit. Thanks, Rainer Or is that simply a leftover from my Linux days, that I prefer locally compiled packages? Thanks, Rainer ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac #secure method=pgpmime mode=sign -- Rainer M. Krug email: RMKrugatgmaildotcom ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
