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/marginalmodelplots_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 Ligges
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.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 Ligges
I retried the command but I got the same error.
install.packages("/home/bioadm/install/R_packages/test/marginalmodelpl
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.gzâ
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/marginalmode
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 available
Then 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 Ligges
For 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 Ligges
Thanks 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
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PLEASE do read the posting guide
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and provide commented, minimal, self-contained, reproducible code.
______________________________________________
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
