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 <ivan.calan...@u-bourgogne.fr> 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 <ivan.calan...@u-bourgogne.fr> 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 <ivan.calan...@u-bourgogne.fr >>>> <mailto:ivan.calan...@u-bourgogne.fr>> 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 <mailto: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 uninstalled). It happens on more than one so that's >>>>>> why I thought it might be something generic I am doing. Here is a copy >>>>>> of the command line results: >>>>>> >>>>>> Rosss-MacBook-Pro:~ rosstinsley$ R CMD INSTALL >>>>>> /private/var/folders/ld/3f2dl80154z47_864skpt2_80000gn/T/Rtmp0ittcT/downloaded_packages/Hmisc_3.10-1.tar.gz >>>>>> * installing to library >>>>>> ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library’ >>>>>> * installing *source* package ‘Hmisc’ ... >>>>>> ** package ‘Hmisc’ successfully unpacked and MD5 sums checked >>>>>> ** libs >>>>>> *** arch - i386 >>>>>> sh: make: command not found >>>>>> ERROR: compilation failed for package ‘Hmisc’ >>>>>> * removing >>>>>> ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Hmisc’ >>>>>> Rosss-MacBook-Pro:~ rosstinsley$ R CMD INSTALL >>>>>> /private/var/folders/ld/3f2dl80154z47_864skpt2_80000gn/T/Rtmp0ittcT/downloaded_packages/acepack_1.3-3.2.tar.gz >>>>>> * installing to library >>>>>> ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library’ >>>>>> * installing *source* package ‘acepack’ ... >>>>>> ** package ‘acepack’ successfully unpacked and MD5 sums checked >>>>>> ** libs >>>>>> *** arch - i386 >>>>>> sh: make: command not found >>>>>> ERROR: compilation failed for package ‘acepack’ >>>>>> * removing >>>>>> ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/acepack’ >>>>>> Rosss-MacBook-Pro:~ rosstinsley$ R CMD INSTALL >>>>>> /private/var/folders/ld/3f2dl80154z47_864skpt2_80000gn/T/Rtmp0ittcT/downloaded_packages/arm_1.6-01.02.tar.gz >>>>>> * installing to library >>>>>> ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library’ >>>>>> ERROR: dependency ‘lme4’ is not available for package ‘arm’ >>>>>> * removing >>>>>> ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/arm’ >>>>>> Rosss-MacBook-Pro:~ rosstinsley$ R CMD INSTALL >>>>>> /private/var/folders/ld/3f2dl80154z47_864skpt2_80000gn/T/Rtmp0ittcT/downloaded_packages/chron_2.3-43.tar.gz >>>>>> * installing to library >>>>>> ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library’ >>>>>> * installing *source* package ‘chron’ ... >>>>>> ** package ‘chron’ successfully unpacked and MD5 sums checked >>>>>> ** libs >>>>>> *** arch - i386 >>>>>> sh: make: command not found >>>>>> ERROR: compilation failed for package ‘chron’ >>>>>> * removing >>>>>> ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library/chron’ >>>>>> >>>>>> >>>>>> >>>>>> Berend's response: >>>>>> >>>>>> 1. This belongs on the R-SIG-Mac mailing list >>>>>> >>>>>> 2. Why don't you use the R.app GUI to install the binary versions of the >>>>>> required packages? Much easier. >>>>>> >>>>>> 3. The message: "sh: make: command not found" means that you don't have >>>>>> make installed. >>>>>> Most likely you don't have other required tools installed. >>>>>> If you use the R.app GUI you don't really need tall those tools. >>>>>> >>>>>> Advice: use R.app to install and if needed get the Xcode tools but only >>>>>> if you intend to compile your own packages. >>>>>> >>>>>> Berend >>>>>> >>>>>> >>>>>> >>>>>> [[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 >> >> -- >> Federico C. F. Calboli >> Neuroepidemiology and Ageing Research >> Imperial College, St. Mary's Campus >> Norfolk Place, London W2 1PG >> >> Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 >> >> f.calboli [.a.t] imperial.ac.uk >> f.calboli [.a.t] gmail.com >> >> > > _______________________________________________ > 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
