Warning when running biocLite with $R

Warning when running biocLite with $R_LIBS been set

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Peng Yu ▴ 940

@peng-yu-3586

Last seen 9.6 years ago

Hi, Have $R_LIBS set. And I got the following warning, when install the package with biocLite. Will there be any consequence of the warning? How to get rid of the warning? Regards, Peng > source("http://bioconductor.org/biocLite.R") > biocLite("hgu95av2probe") Running biocinstall version 2.4.11 with R version 2.9.1 Your version of R requires version 2.4 of Bioconductor. Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : argument 'lib' is missing: using '/path/to/a/directory/that/I/have/access/to'

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ADD COMMENT • link updated 14.7 years ago by Sean Davis 21k • written 14.7 years ago by Peng Yu ▴ 940

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Sean Davis 21k

@sean-davis-490

Last seen 3 months ago

United States

On Sat, Aug 8, 2009 at 11:52 AM, Peng Yu <pengyu.ut@gmail.com> wrote: > Hi, > > Have $R_LIBS set. And I got the following warning, when install the > package with biocLite. Will there be any consequence of the warning? > How to get rid of the warning? > Hi, Peng. The warning explains that the packages will be installed into the "/path/to/a/directory/that/I/have/access/to". Is that what you wanted based on R_LIBS? You can specify libs to get rid of the warning. Sean > > Regards, > Peng > > > source("http://bioconductor.org/biocLite.R") > > biocLite("hgu95av2probe") > Running biocinstall version 2.4.11 with R version 2.9.1 > Your version of R requires version 2.4 of Bioconductor. > Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > argument 'lib' is missing: using > '/path/to/a/directory/that/I/have/access/to' > > _______________________________________________ > 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]]

ADD COMMENT • link 14.7 years ago Sean Davis 21k

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On Sat, Aug 8, 2009 at 11:05 AM, Sean Davis<seandavi at="" gmail.com=""> wrote: > > > On Sat, Aug 8, 2009 at 11:52 AM, Peng Yu <pengyu.ut at="" gmail.com=""> wrote: >> >> Hi, >> >> Have $R_LIBS set. And I got the following warning, when install the >> package with biocLite. Will there be any consequence of the warning? >> How to get rid of the warning? > > Hi, Peng. > > The warning explains that the packages will be installed into the > "/path/to/a/directory/that/I/have/access/to".? Is that what you wanted based > on R_LIBS?? You can specify libs to get rid of the warning. Hi Sean, Yes, that path is what R_LIBS is set to. So this warning does not really matter, right? BTW, how to specify libs in biocLite? Can I specify a environment variable (in my command shell, say bash) so that biocLite would take it as 'libs' and does not generate a warning? Regards, Peng

ADD REPLY • link 14.7 years ago Peng Yu ▴ 940

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On Sat, Aug 8, 2009 at 12:18 PM, Peng Yu <pengyu.ut@gmail.com> wrote: > On Sat, Aug 8, 2009 at 11:05 AM, Sean Davis<seandavi@gmail.com> wrote: > > > > > > On Sat, Aug 8, 2009 at 11:52 AM, Peng Yu <pengyu.ut@gmail.com> wrote: > >> > >> Hi, > >> > >> Have $R_LIBS set. And I got the following warning, when install the > >> package with biocLite. Will there be any consequence of the warning? > >> How to get rid of the warning? > > > > Hi, Peng. > > > > The warning explains that the packages will be installed into the > > "/path/to/a/directory/that/I/have/access/to". Is that what you wanted > based > > on R_LIBS? You can specify libs to get rid of the warning. > > Hi Sean, > > Yes, that path is what R_LIBS is set to. So this warning does not > really matter, right? > > BTW, how to specify libs in biocLite? Can I specify a environment > variable (in my command shell, say bash) so that biocLite would take > it as 'libs' and does not generate a warning? > Warnings are not inherently bad, so there isn't really a problem with getting one as long as you understand what it means. That said, you can pass lib=... to biocLite() and I think it will be passed along to install.packages(). Sean [[alternative HTML version deleted]]

ADD REPLY • link 14.7 years ago Sean Davis 21k

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