Installing Bioconductor with 'sudo' privilege
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Sharon Anbu ▴ 480
@sharon-anbu-1524
Last seen 10.2 years ago
Hi, I am allowed to install programs thro' sudo on my LINUX server. I have installed R 2.9.0 and trying to install bioconductor. As expected, when I tried to install bioconductor inside R, it says 'lib = "/usr/lib64/R/library"' is not writable. This means, I have to download the source of each package and install using R CMD INSTALL. Is there any other elegant way of installing bioconductor with 'sudo' privilege? Many thanks in advance. Kind regards, Sharon [[alternative HTML version deleted]]
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@sean-davis-490
Last seen 3 months ago
United States
On Tue, Sep 1, 2009 at 10:29 AM, Sharon <sharonanandhi@gmail.com> wrote: > Hi, > > I am allowed to install programs thro' sudo on my LINUX server. I have > installed R 2.9.0 and trying to install bioconductor. As expected, when I > tried to install bioconductor inside R, it says 'lib = > "/usr/lib64/R/library"' is not writable. This means, I have to download the > source of each package and install using R CMD INSTALL. Is there any other > elegant way of installing bioconductor with 'sudo' privilege? > > Run R as "sudo" and then do the normal bioconductor install procedure. Alternatively, you can chmod or chown that directory recursively to be writable by you as a normal user. Finally, if the directory is not writable, you can install into your own home directory--R will give you that option. The latter is the default behavior. Sean [[alternative HTML version deleted]]
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@steve-lianoglou-2771
Last seen 21 months ago
United States
Hi Sharon, On Sep 1, 2009, at 10:29 AM, Sharon wrote: > Hi, > > I am allowed to install programs thro' sudo on my LINUX server. I have > installed R 2.9.0 and trying to install bioconductor. As expected, > when I > tried to install bioconductor inside R, it says 'lib = > "/usr/lib64/R/library"' is not writable. This means, I have to > download the > source of each package and install using R CMD INSTALL. Is there any > other > elegant way of installing bioconductor with 'sudo' privilege? Can you just sudo-launch R? That should give you the appropriate privs to then install packages "in the normal way," no? eg: $ sudo R ## do password song and dance ## ... welcome to R ... R> source('http://bioconductor.org/biocLite.R') R> biocLite(c('some', 'packages')) ... -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
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@wolfgang-huber-3550
Last seen 12 weeks ago
EMBL European Molecular Biology Laborat…
Hi Sharon don't use root privileges to install R and its package, but rather, create a dedicated user account and group for that, and make yourself member of that group. There is no advantage in using the root account for installing R, and some potential security and system safety risks. Best wishes Wolfgang Sharon ha scritto: > Hi, > > I am allowed to install programs thro' sudo on my LINUX server. I have > installed R 2.9.0 and trying to install bioconductor. As expected, when I > tried to install bioconductor inside R, it says 'lib = > "/usr/lib64/R/library"' is not writable. This means, I have to download the > source of each package and install using R CMD INSTALL. Is there any other > elegant way of installing bioconductor with 'sudo' privilege? > > Many thanks in advance. > > Kind regards, > Sharon > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Best wishes Wolfgang ------------------------------------------------------- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
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On Tue, Sep 1, 2009 at 10:59 AM, Wolfgang Huber <whuber@embl.de> wrote: > > Hi Sharon > > don't use root privileges to install R and its package, but rather, create > a dedicated user account and group for that, and make yourself member of > that group. > > There is no advantage in using the root account for installing R, and some > potential security and system safety risks. > > Hi, again, Sharon. Just to be clear, what Wolfgang describes here is "best practice" and better than what I and others describe using "sudo" to start R. Sean > Sharon ha scritto: > >> Hi, >> >> I am allowed to install programs thro' sudo on my LINUX server. I have >> installed R 2.9.0 and trying to install bioconductor. As expected, when I >> tried to install bioconductor inside R, it says 'lib = >> "/usr/lib64/R/library"' is not writable. This means, I have to download >> the >> source of each package and install using R CMD INSTALL. Is there any other >> elegant way of installing bioconductor with 'sudo' privilege? >> >> Many thanks in advance. >> >> Kind regards, >> Sharon >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > -- > > Best wishes > Wolfgang > > ------------------------------------------------------- > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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Hi, Thank you very much for all your suggestions. I have created an user account and installed R & biocondutor locally for that user. Thanks again, Sharon On Tue, Sep 1, 2009 at 4:22 PM, Sean Davis <seandavi@gmail.com> wrote: > > > On Tue, Sep 1, 2009 at 10:59 AM, Wolfgang Huber <whuber@embl.de> wrote: > >> >> Hi Sharon >> >> don't use root privileges to install R and its package, but rather, create >> a dedicated user account and group for that, and make yourself member of >> that group. >> >> There is no advantage in using the root account for installing R, and some >> potential security and system safety risks. >> >> > Hi, again, Sharon. Just to be clear, what Wolfgang describes here is "best > practice" and better than what I and others describe using "sudo" to start > R. > > Sean > > >> Sharon ha scritto: >> >>> Hi, >>> >>> I am allowed to install programs thro' sudo on my LINUX server. I have >>> installed R 2.9.0 and trying to install bioconductor. As expected, when >>> I >>> tried to install bioconductor inside R, it says 'lib = >>> "/usr/lib64/R/library"' is not writable. This means, I have to download >>> the >>> source of each package and install using R CMD INSTALL. Is there any >>> other >>> elegant way of installing bioconductor with 'sudo' privilege? >>> >>> Many thanks in advance. >>> >>> Kind regards, >>> Sharon >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> -- >> >> Best wishes >> Wolfgang >> >> ------------------------------------------------------- >> Wolfgang Huber >> EMBL >> http://www.embl.de/research/units/genome_biology/huber >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]
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@joern-toedling-3465
Last seen 10.2 years ago
Hello, the elegant way is to set the environment variable $R_LIBS to a directory where you do have write-access to. See the bottom lines of http://onertipaday.blogspot.com/2008/04/r-installing-on-unixlinux-no- root.html for details. Regards, Joern On Tue, 1 Sep 2009 15:29:43 +0100, Sharon wrote > Hi, > > I am allowed to install programs thro' sudo on my LINUX server. I > have installed R 2.9.0 and trying to install bioconductor. As > expected, when I tried to install bioconductor inside R, it says > 'lib = "/usr/lib64/R/library"' is not writable. This means, I have > to download the source of each package and install using R CMD > INSTALL. Is there any other elegant way of installing bioconductor > with 'sudo' privilege? > > Many thanks in advance. > > Kind regards, > Sharon > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor --- Joern Toedling Institut Curie -- U900 26 rue d'Ulm, 75005 Paris, FRANCE Tel. +33 (0)156246926
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amit mandal ▴ 140
@amit-mandal-3151
Last seen 10.2 years ago
hello sharon, I'm on Ubuntu 9 and to install any package in R (including Bioconductor) - ~$ sudo R Then when you give the command for BioC installation - source("http://bioconductor.org/biocLite.R") biocLite(lib="/usr/lib64/R/library") This time the error won't be thrown that the "dir" is not writable. Starting R with *sudo* but not giving the lib location downstream will install the packages but in the users home dir. and not on "/usr/lib..." This worked for me. Should do in your case also. regards, amit mandal Graduate student Genomics & Molecular Medicine lab IGIB, Delhi On Tue, Sep 1, 2009 at 7:59 PM, Sharon <sharonanandhi@gmail.com> wrote: > Hi, > > I am allowed to install programs thro' sudo on my LINUX server. I have > installed R 2.9.0 and trying to install bioconductor. As expected, when I > tried to install bioconductor inside R, it says 'lib = > "/usr/lib64/R/library"' is not writable. This means, I have to download the > source of each package and install using R CMD INSTALL. Is there any other > elegant way of installing bioconductor with 'sudo' privilege? > > Many thanks in advance. > > Kind regards, > Sharon > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- --------------------------------------------------------------- The robbed that smiles, steals something from the thief. - Shakespeare --------------------------------------------------------------- [[alternative HTML version deleted]]
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