On 18.04.2012 14:01, mail.bioi...@fr.netgrs.com wrote:
Hi Uwe
I tried
install.packages("marginalmodelplots", dependencies=TRUE,
contriburl="/home/bioadm/install/R_packages/test")
Whoops, this was untested an it turns out you need: contriburl="file:/home/bioadm/install/R_packages/test"reaing the help file tell us it must be an URL rather than a file specification.
Uwe Ligges
But I got always the same error install.packages("marginalmodelplots", dependencies=TRUE, contriburl="/home/bioadm/install/R_packages/test/") Warning: unable to access index for repository /home/bioadm/install/R_packages/test/ Warning message: package âmarginalmodelplotsâ is not available (for R version 2.15.0) below, I paste the content of my PACKAGES file Package: locfit Version: 1.5-7 Depends: R (>= 2.0.1) Imports: akima, lattice Suggests: gam License: GPL (>= 2) MD5sum: 6c90e03f93305789b74c7fc6a56ebdc1 Package: marginalmodelplots Version: 0.4.2 Depends: R (>= 2.0.1), locfit (>= 1.5-4), grid License: GPL (>= 2) MD5sum: 1c4c0325a5f9f0e29d669207a7ad6b68 Regards, Joël -----Message d'origine----- De : Uwe Ligges [mailto:lig...@statistik.tu-dortmund.de] Envoyé : mercredi 18 avril 2012 10:51 À :<FRsr BioInfo Cc : r-help@r-project.org Objet : Re: [R] packages install dependencies On 18.04.2012 10:48, mail.bioi...@fr.netgrs.com wrote:Hi I created a directory which contains just the two packages "marginalmodelplots_0.4.2.tar.gz " and " locfit_1.5-7.tar.gz " called test I launched the command write_PACKAGES as follows write_PACKAGES("/home/bioadm/install/R_packages/test/", type ="source") As you can see I have now in my directory 4 files. [bioadm@srsu148 test]$ ll total 228 -rw-r--r-- 1 bioadm bio 200614 Apr 18 10:33 locfit_1.5-7.tar.gz -rw-r--r-- 1 bioadm bio 18559 Apr 18 10:32 marginalmodelplots_0.4.2.tar.gz -rw-r--r-- 1 bioadm bio 305 Apr 18 10:34 PACKAGES -rw-r--r-- 1 bioadm bio 222 Apr 18 10:34 PACKAGES.gz [bioadm@srsu148 test]$ pwd /home/bioadm/install/R_packages/test So the files PACKAGES are created but if I run the command install.packages as follows in the R editor, I get always the same error. install.packages("/home/bioadm/install/R_packages/test/marginalmodelpl ots_0.4.2.tar.gz", repos=TRUE, dependencies=TRUE,contriburl="/home/bioadm/install/R_packages/test/")install.packages("marginalmodelplots", dependencies=TRUE, contriburl="/home/bioadm/install/R_packages/test") seems to be the documented way you want to try. Uwe LiggesInstalling package(s) into â/soft/R-2.8.1/lib64/R/libraryâ (as âlibâ is unspecified) Warning: unable to access index for repository /home/bioadm/install/R_packages/test/ Warning message: package â/home/bioadm/install/R_packages/test/marginalmodelplots_0.4.2.tar.gzâ is not available (for R version 2.15.0) I don't understand the error because my files PACKAGES are inside the directory that I specified using the option contriburl and this directory is full access for everyone. Is the command not correct ? Joël -----Message d'origine----- De : Uwe Ligges [mailto:lig...@statistik.tu-dortmund.de] Envoyé : mardi 17 avril 2012 15:30 À :<FRsr BioInfo Cc : r-help@r-project.org Objet : Re: [R] packages install dependencies On 17.04.2012 15:21, mail.bioi...@fr.netgrs.com wrote:Hi I checked inside the directory but I have the PACKAGE file as you can see ls /home/bioadm/install/R_packages/test/PACKAGES PACKAGES PACKAGES.gz I created them using this command write_PACKAGES("../test/", type="win.binary" )Errr, given your path specifications, I assume you are not under Windows and given the extensions of the files, I assume you have source packages, hence you need a PACKAGES file for a source repository. Uwe LiggesI retried the command but I got the same error. install.packages("/home/bioadm/install/R_packages/test/marginalmodelp l ots_0.4.2.tar.gz", repos=NULL, dependencies =TRUE, contriburl="/home/bioadm/install/R_packages/test/") Installing package(s) into â/soft/R-2.8.1/lib64/R/libraryâ (as âlibâ is unspecified) Warning: unable to access index for repository /home/bioadm/install/R_packages/test/ Warning message: package â/home/bioadm/install/R_packages/test/marginalmodelplots_0.4.2.tar.gz â is not available (for R version 2.15.0) i checked also the permissions for this directory but it's OK as I created it with full acess for everyone drwxrwxrwx 2 bioadm test 155648 Apr 17 14:49 test Do you have any suggestions ? Joël -----Message d'origine----- De : Uwe Ligges [mailto:lig...@statistik.tu-dortmund.de] Envoyé : mardi 17 avril 2012 14:25 À :<FRsr BioInfo Cc : r-help@r-project.org Objet : Re: [R] packages install dependencies On 17.04.2012 10:57, mail.bioi...@fr.netgrs.com wrote:Hi Uwe Thanks for your answer. I tried to install the packages "marginalmodelplots_0.4.2.tar.gz" from a local repository "/home/bioadm/install/R_packages/120416/" using your suggestion (i.e. install.packages(...., contriburl="/home/joel/RPacks")) I paste below the command install.packages("/home/bioadm/install/R_packages/120416/marginalmod e l plots_0.4.2.tar.gz", repos=NULL, dependencies= TRUE, type="source", contriburl="/home/bioadm/install/R_packages/120416/") Warning: unable to access index for repository /home/bioadm/install/R_packages/120416/ Warning message: In install.packages("/home/bioadm/install/R_packages/120416/marginalmodelplots_0.4.2.tar.gz", : package â/home/bioadm/install/R_packages/120416/marginalmodelplots_0.4.2.tar. g zâ is not availableThen you do not have a repository. Its defintiion is that it contains a PACKAGES file which it obviously does not contain. Nevertheless, you can create a PACKAGE file via function write_PACKAGES() in package tools. Uwe LiggesFor info this package depends of the "locfit" package. What should I do ? Thanks in advance Joël Masciocchi -----Message d'origine----- De : Uwe Ligges [mailto:lig...@statistik.tu-dortmund.de] Envoyé : lundi 16 avril 2012 19:06 À :<FRsr BioInfo Cc : r-help@r-project.org Objet : Re: [R] packages install dependencies On 16.04.2012 15:41, mail.bioi...@fr.netgrs.com wrote:Hello R-Members I have to install several R packages on a Unix server which doesn't have internet connection. I downloaded some packages manually and I installed it from source using the command R CMD INSTALL and it's work but in some cases I can't install the package because of the dependencies. So I download all the R packages into a directory for example /home/joel/RPacks. Is it possible to configure the R commands (i.e. CMD INSTALL command or install.packages() function) in order that R looks for dependencies in my repository.install.packages(...., contriburl="/home/joel/RPacks") Uwe LiggesThanks in advance, Best Regards - Cordialement, Joël ------------------------------------------------------------------- - - -- Joel Masciocchi Bioinformatician Informatics Department Institut de Recherches SERVIER (I.d.R.S) 125, chemin de Ronde 78290 CROISSY-SUR-SEINE - FRANCE [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
