Re: [R-SIG-Mac] R for macOS Big Sur
> Le 11 janv. 2021 à 16:26, Kasper Daniel Hansen > a écrit : > > Jean: _guessing_ this may be about parallel processing in BLAS? Does your > timing include linear algebra? Yes it is mostly linear algebra, but the slowdown is the same in parallel processing and in single processor mode (4 times slower in both). > On Mon, Jan 11, 2021 at 2:38 PM Jean Thioulouse > wrote: > Hi > > Both versions seem to run fine indeed, but on my Mac mini M1, the arm version > (homebrew R) is much slower than the intel version (CRAN R), which is quite > disappointing. > > The speed ratio I get is about 4 times slower for the arm version compared to > the intel version, both in single processor and parallel computing mode. > > Any idea about why I get these results ? > > Thanks, > Jean > > —- > Jean THIOULOUSE - orcid.org/-0001-7664-0598 > http://lbbe.univ-lyon1.fr/-Thioulouse-Jean-.html > https://www.springer.com/fr/book/9781493988488 > > > > Le 11 janv. 2021 à 10:53, Denis-Alexander Engemann > > a écrit : > > > > I have been using both Rosetta emulation and the homebrew builds and > > everything looks very good so far. > > > > Here are two Twitter threads on M1 benchmarks. > > > > https://twitter.com/fxcoudert/status/1342598509418176514?s=20 > > > > https://twitter.com/dngman/status/1342580260815200257?s=20 > > > > Best, > > Denis > > > > On Mon, Jan 11, 2021 at 10:11 AM Dr Eberhard W Lisse wrote: > >> > >> I use the homebrew R for the Intel and then install.packages(), > >> update.package() from scripts and Rstudio’s Tools->. > >> > >> I don’t have an M1 (yet) but would be interested in seeing how that works > >> on the M1. Probably this will pull the sources and hence I would be > >> grateful to read about that. > >> > >> > >> greetings, el > >> > >> — > >> Sent from Dr Lisse’s iPhone > >> On 11 Jan 2021, 10:05 +0200, Patrick Schratz , > >> wrote: > >>> There is a [native arm64 big sur > >>> binary](https://github.com/Homebrew/homebrew-core/blob/8a6807be6abb44634e7d6d153348b6bba2a5ddc6/Formula/r.rb#L16) > >>> in homebrew since some days. > >>> > >>> On 10 Jan 2021, at 22:39, Gregory Coats via R-SIG-Mac wrote: > >>> > >>>> I purchased a new 13 inch Apple MacBook Pro with the M1 System on a > >>>> Chip. I understand that R is not yet available compiled for the M1 SoC > >>>> hardware, and so I am using Apple’s Rosetta 2. > >>>> However, this MacBook Pro requires Apple macOS Big Sur. From what I > >>>> see at https://mac.r-project.org/ R has not been compiled for macOS > >>>> Big Sur. Is there an executable of R for macOS Big Sur available to > >>>> download? > >>>> Greg Coats > >>>> > >>>> > >>>> [[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 > >> > >>[[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 > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > > -- > Best, > Kasper ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] problem with tkrplot package
I had this problem too. You can find messages in r-sig-mac about it. You must recompile the tkrplot package instead of using the binary from CRAN. Jean —- Jean THIOULOUSE - orcid.org/-0001-7664-0598 http://lbbe.univ-lyon1.fr/-Thioulouse-Jean-.html > Le 20 janv. 2016 à 14:01, ANA BELÉN NIETO LIBRERO a écrit : > > Hello, > I am trying to use the tkrplot in the last version of R in mac but the > program abort the session when I execute > library(tkrplot). > > My own package use this packages and I can't in this moment to use them due > to this problem. > What could be the problem of this library? > Thank you. > Ana B. Nieto > > [[alternative HTML version deleted]] > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac smime.p7s Description: S/MIME cryptographic 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] loading tkrplot causes a segfault
Hi
Loading the CRAN binary version of the tkrplot package version 0.0-23 causes a
segfault of R version 3.2.2 on OS X 10.11.1 too.
Installing form sources solves the problem.
Still no idea ?
Jean
[MacPro:~] jthioulo% R
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)
R est un logiciel libre livré sans AUCUNE GARANTIE.
Vous pouvez le redistribuer sous certaines conditions.
Tapez 'license()' ou 'licence()' pour plus de détails.
R est un projet collaboratif avec de nombreux contributeurs.
Tapez 'contributors()' pour plus d'information et
'citation()' pour la façon de le citer dans les publications.
Tapez 'demo()' pour des démonstrations, 'help()' pour l'aide
en ligne ou 'help.start()' pour obtenir l'aide au format HTML.
Tapez 'q()' pour quitter R.
[Sauvegarde de la session précédente restaurée]
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.1 (El Capitan)
locale:
[1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
> install.packages("tkrplot")
essai de l'URL
'http://cran.univ-lyon1.fr/bin/macosx/mavericks/contrib/3.2/tkrplot_0.0-23.tgz'
Content type 'application/x-gzip' length 24752 bytes (24 KB)
==
downloaded 24 KB
Les packages binaires téléchargés sont dans
/var/folders/qg/wgr2ssj52259lkbxq2z_dwwcgn/T//RtmpWSrqzX/downloaded_packages
> library(tkrplot)
Le chargement a nécessité le package : tcltk
*** caught segfault ***
address 0x998, cause 'memory not mapped'
Traceback:
1: structure(.External(.C_dotTclObjv, objv), class = "tclObj")
2: .Tcl.objv(.Tcl.args.objv(...))
3: tcl("load", file, "Rplot")
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(tcl("load", file, "Rplot"), error = function(e) warning("loading
Rplot failed", call. = FALSE))
8: fun(libname, pkgname)
9: doTryCatch(return(expr), name, parentenv, handler)
10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
11: tryCatchList(expr, classes, parentenv, handlers)
12: tryCatch(fun(libname, pkgname), error = identity)
13: runHook(".onLoad", env, package.lib, package)
14: loadNamespace(package, c(which.lib.loc, lib.loc))
15: doTryCatch(return(expr), name, parentenv, handler)
16: tryCatchOne(expr, names, parentenv, handlers[[1L]])
17: tryCatchList(expr, classes, parentenv, handlers)
18: 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))})
19: try({ns <- loadNamespace(package, c(which.lib.loc, lib.loc))env <-
attachNamespace(ns, pos = pos, deps)})
20: library(tkrplot)
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: 4
[MacPro:~] jthioulo% R
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)
R est un logiciel libre livré sans AUCUNE GARANTIE.
Vous pouvez le redistribuer sous certaines conditions.
Tapez 'license()' ou 'licence()' pour plus de détails.
R est un projet collaboratif avec de nombreux contributeurs.
Tapez 'contributors()' pour plus d'information et
'citation()' pour la façon de le citer dans les publications.
Tapez 'demo()' pour des démonstrations, 'help()' pour l'aide
en ligne ou 'help.start()' pour obtenir l'aide au format HTML.
Tapez 'q()' pour quitter R.
[Sauvegarde de la session précédente restaurée]
> install.packages("tkrplot", type="source")
essai de l'URL 'http://cran.univ-lyon1.fr/src/contrib/tkrplot_0.0-23.tar.gz'
Content type 'application/x-gzip' length 39037 bytes (38 KB)
==
downloaded 38 KB
* installing *source* package ‘tkrplot’ ...
** package ‘tkrplot’ correctement décompressé et som
Re: [R-SIG-Mac] sort() under terminal
The difference is not between the Terminal and Rgui. Check your locale: in the
Terminal, I get
> sort(c("W", "e", "E"))
[1] "e" "E" "W"
> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)
locale:
[1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] adegraphics_1.0-4 RColorBrewer_1.1-2 sp_1.1-1 KernSmooth_2.23-14
[5] grid_3.2.1 ade4_1.7-2 lattice_0.20-31
Jean
> Le 12 oct. 2015 à 16:59, Adrian Dușa a écrit :
>
> 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:
>
>> 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
>
>
> --
> Adrian Dusa
> University of Bucharest
> Romanian Social Data Archive
> Soseaua Panduri nr.90
> 050663 Bucharest sector 5
> Romania
>
> [[alternative HTML version deleted]]
>
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
—-
Jean THIOULOUSE
http://lbbe.univ-lyon1.fr/-Thioulouse-Jean-.html
___
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Re: [R-SIG-Mac] loading tkrplot causes a segfault
Re-install X11 XQuartz (I think that this is in the FAQ).
Jean
> Le 11 juil. 2015 à 00:54, Dan Tenenbaum a écrit :
>
> Hi,
>
> loading the tkrplot package (version 0.0-23) causes a segfault. This only
> seems to happen on Mavericks, not Snow Leopard, Linux, or Windows.
>
>> library(tkrplot)
> Loading required package: tcltk
>
> *** caught segfault ***
> address 0x998, cause 'memory not mapped'
>
> Traceback:
> 1: structure(.External(.C_dotTclObjv, objv), class = "tclObj")
> 2: .Tcl.objv(.Tcl.args.objv(...))
> 3: tcl("load", file, "Rplot")
> 4: doTryCatch(return(expr), name, parentenv, handler)
> 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
> 6: tryCatchList(expr, classes, parentenv, handlers)
> 7: tryCatch(tcl("load", file, "Rplot"), error = function(e) warning("loading
> Rplot failed", call. = FALSE))
> 8: fun(libname, pkgname)
> 9: doTryCatch(return(expr), name, parentenv, handler)
> 10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
> 11: tryCatchList(expr, classes, parentenv, handlers)
> 12: tryCatch(fun(libname, pkgname), error = identity)
> 13: runHook(".onLoad", env, package.lib, package)
> 14: loadNamespace(package, c(which.lib.loc, lib.loc))
> 15: doTryCatch(return(expr), name, parentenv, handler)
> 16: tryCatchOne(expr, names, parentenv, handlers[[1L]])
> 17: tryCatchList(expr, classes, parentenv, handlers)
> 18: 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))})
> 19: try({ns <- loadNamespace(package, c(which.lib.loc, lib.loc))env
> <- attachNamespace(ns, pos = pos, deps)})
> 20: library(tkrplot)
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
>
>
>
> My sessionInfo() is:
>
>> sessionInfo()
> R version 3.2.1 (2015-06-18)
> Platform: x86_64-apple-darwin13.4.0 (64-bit)
> Running under: OS X 10.9.5 (Mavericks)
>
> 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
>
>
> Any ideas?
>
> Thanks,
> Dan
>
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
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Re: [R-SIG-Mac] R packages on Mac
The "install dependencies" checkbox sets the "dependencies" argument to TRUE in
the install.packages command, so it is indeed recursive (which is the only
coherent behaviour, I think).
Jean
--
Jean THIOULOUSE - CNRS - Université Lyon 1
http://www.thioulouse.fr/ref/
Le 23 janv. 2013 à 12:27, Ivan Calandra
a écrit :
> It happened to me that when I clicked on the "install dependencies" checkbox,
> it basically installed every possible package. I remember it happened with
> doBy, where it installed tens of packages. The problem is likely because it
> installs the dependencies of the dependencies of the dependencies and so on.
> It might be fixed by now. But this has never happened with install.packages()
> so I don't try to use the package installer anymore.
>
> Ivan
>
> --
> Ivan CALANDRA
> Université de Bourgogne
> UMR CNRS/uB 6282 Biogéosciences
> 6 Boulevard Gabriel
> 21000 Dijon, FRANCE
> +33(0)3.80.39.63.06
> ivan.calan...@u-bourgogne.fr
> http://biogeosciences.u-bourgogne.fr/calandra
>
> Le 23/01/13 12:18, Federico Calboli a écrit :
>> On 23 Jan 2013, at 11:07, Ivan Calandra wrote:
>>
>>> Hi again,
>>>
>>> It probably won't be of any help for now, but you might need it in the
>>> future: I used to install packages from the package installer. Then I
>>> realized that it often messed up with dependencies.
>> I notice there is a nice 'install dependencies' checkbox on the GUI package
>> installer. It has always worked for me.
>>
>> BW
>>
>> F
>>
>>
>>
>>
>>> That's why the best way to install packages and their dependencies on Mac
>>> is to run install.packages("package") in the console.
>>>
>>> I hope you'll be able to fix your problem soon
>>> Ivan
>>>
>>> --
>>> Ivan CALANDRA
>>> Université de Bourgogne
>>> UMR CNRS/uB 6282 Biogéosciences
>>> 6 Boulevard Gabriel
>>> 21000 Dijon, FRANCE
>>> +33(0)3.80.39.63.06
>>> ivan.calan...@u-bourgogne.fr
>>> http://biogeosciences.u-bourgogne.fr/calandra
>>>
>>> Le 23/01/13 11:59, Ross Tinsley a écrit :
Hi Ivan
In R I was going to the Packages and Data menu then clicking on Packages
Installer option. From there I selected CRAN sources and used that to
search for the below libraries (I also ticked the option to install
dependencies). Some such as Amelia did install but others one didn't. Prof
Brian has given some suggestions so I will follow up on those first, as I
think my overall install is not correct just yet.
Will get back to you all on how I get on.
Thanks
Ross
*
Dr Ross Tinsley*
Head of Research | Editor IHTSJ
International Hospitality and Tourism Research Centre
*HTMi* | Hotel and Tourism Management Institute | Switzerland
On 23 Jan 2013, at 11:43, Ivan Calandra >>> > wrote:
> Hi!
>
> Not sure it will help you, but in the R.app, have you run
> install.packages("name of package") first? What is the error when you
> type library(name of package)?
>
> HTH,
> Ivan
>
> --
> Ivan CALANDRA
> Université de Bourgogne
> UMR CNRS/uB 6282 Biogéosciences
> 6 Boulevard Gabriel
> 21000 Dijon, FRANCE
> +33(0)3.80.39.63.06
> ivan.calan...@u-bourgogne.fr
> http://biogeosciences.u-bourgogne.fr/calandra
>
> Le 23/01/13 11:27, Ross Tinsley a écrit :
>> Originally posted this on the standard mailing list and it was suggested
>> that I post here on SIG Mac list. Have also included Beren's response
>> who emphasised using the R.app GUI, however I am doing this as my first
>> step. The below error message turns up there as well. Am stuck on the
>> 'make' command and how to make that work.
>>
>> Here are the commands in R I am trying to run.
>>
>> library(Amelia)
>> library(Hmisc)
>> library(polycor)
>> library(psych)
>> library(qgraph)
>> library(lavaan)
>> library(semTools)
>> library(paran)
>> library(nFactors)
>> library(GPArotation)
>> library(sem)
>> library(polycor)
>> library(rrcov)
>>
>> Thanks for any help.
>>
>>
>> Hello all
>>
>> I am a researcher in the field of tourism and have just recently
>> installed R64 and RStudio onto my Mac (running latest OS). I am ran into
>> some problems installing additional packages. I have looked through the
>> General FAQs and Mac FAQS but haven't been able to find a solution.
>>
>> I have downloaded the various packages I need from CRAN sources and
>> while some have successfully installed others have not. I have been
>> following the instructions on the Mac FAQ to unzip and install the
>> downloaded packages using the command line but the results seem to
>> indicate an error (they are installed but then don't work properly and
>> so are subsequently unin
Re: [R-SIG-Mac] error compiling package - ld: library not found for -lSystemStubs
Le 27 mars 2012 à 22:02, "Simon Urbanek" a écrit : > > On Mar 27, 2012, at 3:44 PM, THIOULOUSE JEAN wrote: > >> >> Le 27 mars 2012 à 16:49, Simon Urbanek a écrit : >>> >>> On Mar 27, 2012, at 10:40 AM, THIOULOUSE JEAN wrote: >>> >>>> Hi, >>>> >>>> Sorry to bother you about what is probably a bad configuration of my >>>> system. I have the following error when checking a package on my Mac (Mac >>>> Pro mid-2010 with Mac OS X Lion 10.7.3 (11D50), running R-2.14.2 from >>>> CRAN). I have Xcode 4.3.2 and the GNU Fortran compiler from >>>> http://r.research.att.com/. The package is prepRISA and it compiles >>>> without problem on R-Forge. >>>> >>>> Here is the install.out file of R CMD check prepRISA: >>>> >>>> * installing *source* package ‘prepRISA’ ... >>>> ** libs >>>> *** arch - i386 >>>> gcc -arch i386 -std=gnu99 >>>> -I/Library/Frameworks/R.framework/Resources/include >>>> -I/Library/Frameworks/R.framework/Resources/include/i386 >>>> -I/usr/local/mysql/include -I/usr/local/include-fPIC -g -O2 -c >>>> repClass.c -o repClass.o >>>> gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names >>>> -undefined dynamic_lookup -single_module -multiply_defined suppress >>>> -L/usr/local/lib -o prepRISA.so repClass.o -L/usr/local/mysql/lib >>>> -lmysqlclient -lSystemStubs -F/Library/Frameworks/R.framework/.. >>>> -framework R -Wl,-framework -Wl,CoreFoundation >>>> ld: library not found for -lSystemStubs >>>> collect2: ld returned 1 exit status >>>> make: *** [prepRISA.so] Error 1 >>>> ERROR: compilation failed for package ‘prepRISA’ >>>> * removing >>>> ‘/Volumes/Macintosh-HD/Users/jthioulo/Desktop/prepRISA.Rcheck/prepRISA’ >>>> >>>> I tried to search about this SystemStubs library, but could only find that >>>> it is deprecated in MacOS X 10.7. >>>> >>>> Here is my sessionInfo: >>>>> sessionInfo() >>>> R version 2.14.2 (2012-02-29) >>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>>> >>>> locale: >>>> [1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8 >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets tcltk methods >>>> [8] base >>>> >>>> other attached packages: >>>> [1] ade4TkGUI_0.2-5 ade4_1.4-17 >>>>> >>>> >>>> What can I do to get rid of this problem ? >>>> >>> >>> The problem seems local to your R or settings - did you perhaps override >>> any PKG_* with bogus flags? This is what you get with released R: >>> >>> ** libs >>> *** arch - i386 >>> gcc -arch i386 -std=gnu99 >>> -I/Library/Frameworks/R.framework/Resources/include >>> -I/Library/Frameworks/R.framework/Resources/include/i386 >>> -I/usr/local/include-fPIC -Wall -pedantic -g -O2 -c repClass.c -o >>> repClass.o >>> gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names >>> -undefined dynamic_lookup -single_module -multiply_defined suppress >>> -L/usr/local/lib -o prepRISA.so repClass.o >>> -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework >>> -Wl,CoreFoundation >>> installing to >>> /Library/Frameworks/R.framework/Versions/2.14/Resources/library/prepRISA/libs/i386 >>> >>> note that you have superfluous "-L/usr/local/mysql/lib -lmysqlclient >>> -lSystemStubs" in your linking step which is *not* part of R ... >>> >>> Cheers, >>> Simon >> >> Thank you, this probably comes from a previous install of a mysql server >> implementation. Is there a way to know how these flags get added to the R >> CMD gcc command line ? I deleted all the R and mysql instances I found on my >> Mac and re-installed R from CRAN, but the problem remains. >> > > It has nothing to do with those -- it is your user setting. It could be in > your environment (try set | grep PKG) or any startup files (.Rprofile, > .Renviron or any of the site-configuration files of .R/Makevars and friends > ..). > > Cheers, > Simon Yes indeed, it was in my .cshrc file. Thanks a lot, and sorry for the trouble ! Jean ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] error compiling package - ld: library not found for -lSystemStubs
Le 27 mars 2012 à 16:49, Simon Urbanek a écrit : > > On Mar 27, 2012, at 10:40 AM, THIOULOUSE JEAN wrote: > >> Hi, >> >> Sorry to bother you about what is probably a bad configuration of my system. >> I have the following error when checking a package on my Mac (Mac Pro >> mid-2010 with Mac OS X Lion 10.7.3 (11D50), running R-2.14.2 from CRAN). I >> have Xcode 4.3.2 and the GNU Fortran compiler from >> http://r.research.att.com/. The package is prepRISA and it compiles without >> problem on R-Forge. >> >> Here is the install.out file of R CMD check prepRISA: >> >> * installing *source* package ‘prepRISA’ ... >> ** libs >> *** arch - i386 >> gcc -arch i386 -std=gnu99 >> -I/Library/Frameworks/R.framework/Resources/include >> -I/Library/Frameworks/R.framework/Resources/include/i386 >> -I/usr/local/mysql/include -I/usr/local/include-fPIC -g -O2 -c >> repClass.c -o repClass.o >> gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names >> -undefined dynamic_lookup -single_module -multiply_defined suppress >> -L/usr/local/lib -o prepRISA.so repClass.o -L/usr/local/mysql/lib >> -lmysqlclient -lSystemStubs -F/Library/Frameworks/R.framework/.. -framework >> R -Wl,-framework -Wl,CoreFoundation >> ld: library not found for -lSystemStubs >> collect2: ld returned 1 exit status >> make: *** [prepRISA.so] Error 1 >> ERROR: compilation failed for package ‘prepRISA’ >> * removing >> ‘/Volumes/Macintosh-HD/Users/jthioulo/Desktop/prepRISA.Rcheck/prepRISA’ >> >> I tried to search about this SystemStubs library, but could only find that >> it is deprecated in MacOS X 10.7. >> >> Here is my sessionInfo: >>> sessionInfo() >> R version 2.14.2 (2012-02-29) >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >> >> locale: >> [1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets tcltk methods >> [8] base >> >> other attached packages: >> [1] ade4TkGUI_0.2-5 ade4_1.4-17 >>> >> >> What can I do to get rid of this problem ? >> > > The problem seems local to your R or settings - did you perhaps override any > PKG_* with bogus flags? This is what you get with released R: > > ** libs > *** arch - i386 > gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include > -I/Library/Frameworks/R.framework/Resources/include/i386 > -I/usr/local/include-fPIC -Wall -pedantic -g -O2 -c repClass.c -o > repClass.o > gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names > -undefined dynamic_lookup -single_module -multiply_defined suppress > -L/usr/local/lib -o prepRISA.so repClass.o > -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework > -Wl,CoreFoundation > installing to > /Library/Frameworks/R.framework/Versions/2.14/Resources/library/prepRISA/libs/i386 > > note that you have superfluous "-L/usr/local/mysql/lib -lmysqlclient > -lSystemStubs" in your linking step which is *not* part of R ... > > Cheers, > Simon Thank you, this probably comes from a previous install of a mysql server implementation. Is there a way to know how these flags get added to the R CMD gcc command line ? I deleted all the R and mysql instances I found on my Mac and re-installed R from CRAN, but the problem remains. Jean ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] error compiling package - ld: library not found for -lSystemStubs
Hi, Sorry to bother you about what is probably a bad configuration of my system. I have the following error when checking a package on my Mac (Mac Pro mid-2010 with Mac OS X Lion 10.7.3 (11D50), running R-2.14.2 from CRAN). I have Xcode 4.3.2 and the GNU Fortran compiler from http://r.research.att.com/. The package is prepRISA and it compiles without problem on R-Forge. Here is the install.out file of R CMD check prepRISA: * installing *source* package ‘prepRISA’ ... ** libs *** arch - i386 gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/mysql/include -I/usr/local/include-fPIC -g -O2 -c repClass.c -o repClass.o gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o prepRISA.so repClass.o -L/usr/local/mysql/lib -lmysqlclient -lSystemStubs -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: library not found for -lSystemStubs collect2: ld returned 1 exit status make: *** [prepRISA.so] Error 1 ERROR: compilation failed for package ‘prepRISA’ * removing ‘/Volumes/Macintosh-HD/Users/jthioulo/Desktop/prepRISA.Rcheck/prepRISA’ I tried to search about this SystemStubs library, but could only find that it is deprecated in MacOS X 10.7. Here is my sessionInfo: > sessionInfo() R version 2.14.2 (2012-02-29) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets tcltk methods [8] base other attached packages: [1] ade4TkGUI_0.2-5 ade4_1.4-17 > What can I do to get rid of this problem ? Thank you, Jean -- Jean Thioulouse - Labo Biometrie et Biologie Evolutive, UMR CNRS 5558 Universite Lyon 1, Batiment Mendel, 69622 Villeurbanne Cedex - France Tel : (33)(0)472432756 Fax : (33)(0)472431388 Cel : (33)(0)675122302 http://pbil.univ-lyon1.fr/JTHome/Biblio/ ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
