rpy save session and package downloads
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rna seq ▴ 90
@rna-seq-4145
Last seen 8.2 years ago
Hi Sean, Thanks for getting back. There are two questions, the first I will direct towards the rpy list as you suggest. But the second is that as you say these packages are loaded using "library", but once I log off a session, the packages that are loaded are lost once a session is over. I am trying to save these packages because some such as "BSgenome.Hsapiens.UCSC.hg19" are rather large. Pete On Mon, Feb 28, 2011 at 2:41 PM, Sean Davis <sdavis2@mail.nih.gov> wrote: > > > On Mon, Feb 28, 2011 at 3:48 PM, rna seq <rna.seeker@gmail.com> wrote: > >> Dear R, >> >> Using Ubuntu 10.04 OS and R 2.10, I am running R through python using >> "rpy". >> > > Hi, Peter. > > This isn't really on-topic for the bioconductor list. I would encourage > you to use the rpy support mechanisms for further details. > > >> I have noticed thatmy sessions are not saved and I am wondering if there >> is >> a way to do this. > > > You would need to save them. See save(). > > >> Also and more importantly. Is there a way to direct R to >> save downloaded packages in a specific file that will be recognized when >> the >> "saved" session is restored? >> > > I'm not sure what you mean here. Packages are "installed" into R and then > loaded using "library". Simply having a downloaded package in a file will > not allow you to use it in R--it must be installed. > > Sean > > [[alternative HTML version deleted]]
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@herve-pages-1542
Last seen 2 days ago
Seattle, WA, United States
Hi Pete, On 02/28/2011 03:34 PM, rna seq wrote: > Hi Sean, > > Thanks for getting back. There are two questions, the first I will direct > towards the rpy list as you suggest. But the second is that as you say these > packages are loaded using "library", but once I log off a session, the > packages that are loaded are lost once a session is over. I am trying to > save these packages because some such as "BSgenome.Hsapiens.UCSC.hg19" are > rather large. What do you mean by "saving" a package? As Sean already explained, packages are "installed" into R and then loaded in a session using "library". When you quit the session, the loaded packages are not "lost" (did you mean "deleted from the disk"?) and you will of course be able to load them again next time you start a session without having to re-install them. So you don't need to "save" any package before you quit the session. There is no such mechanism because it's not needed. Cheers, H. > > Pete > > On Mon, Feb 28, 2011 at 2:41 PM, Sean Davis<sdavis2 at="" mail.nih.gov=""> wrote: > >> >> >> On Mon, Feb 28, 2011 at 3:48 PM, rna seq<rna.seeker at="" gmail.com=""> wrote: >> >>> Dear R, >>> >>> Using Ubuntu 10.04 OS and R 2.10, I am running R through python using >>> "rpy". >>> >> >> Hi, Peter. >> >> This isn't really on-topic for the bioconductor list. I would encourage >> you to use the rpy support mechanisms for further details. >> >> >>> I have noticed thatmy sessions are not saved and I am wondering if there >>> is >>> a way to do this. >> >> >> You would need to save them. See save(). >> >> >>> Also and more importantly. Is there a way to direct R to >>> save downloaded packages in a specific file that will be recognized when >>> the >>> "saved" session is restored? >>> >> >> I'm not sure what you mean here. Packages are "installed" into R and then >> loaded using "library". Simply having a downloaded package in a file will >> not allow you to use it in R--it must be installed. >> >> Sean >> >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
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and you will of course be able to load them again next time you start a session without having to re-install them I see this now The first part of my question was that my R session is not being saved because I am not 2011/2/28 Hervé Pagès <hpages@fhcrc.org> > Hi Pete, > > > On 02/28/2011 03:34 PM, rna seq wrote: > >> Hi Sean, >> >> Thanks for getting back. There are two questions, the first I will direct >> towards the rpy list as you suggest. But the second is that as you say >> these >> packages are loaded using "library", but once I log off a session, the >> packages that are loaded are lost once a session is over. I am trying to >> save these packages because some such as "BSgenome.Hsapiens.UCSC.hg19" are >> rather large. >> > > What do you mean by "saving" a package? As Sean already explained, > packages are "installed" into R and then loaded in a session > using "library". When you quit the session, the loaded packages > are not "lost" (did you mean "deleted from the disk"?) and you > will of course be able to load them again next time you start a > session without having to re-install them. So you don't need to "save" > any package before you quit the session. There is no such mechanism > because it's not needed. > > Cheers, > > H. > > >> Pete >> >> On Mon, Feb 28, 2011 at 2:41 PM, Sean Davis<sdavis2@mail.nih.gov> wrote: >> >> >>> >>> On Mon, Feb 28, 2011 at 3:48 PM, rna seq<rna.seeker@gmail.com> wrote: >>> >>> Dear R, >>>> >>>> Using Ubuntu 10.04 OS and R 2.10, I am running R through python using >>>> "rpy". >>>> >>>> >>> Hi, Peter. >>> >>> This isn't really on-topic for the bioconductor list. I would encourage >>> you to use the rpy support mechanisms for further details. >>> >>> >>> I have noticed thatmy sessions are not saved and I am wondering if there >>>> is >>>> a way to do this. >>>> >>> >>> >>> You would need to save them. See save(). >>> >>> >>> Also and more importantly. Is there a way to direct R to >>>> save downloaded packages in a specific file that will be recognized when >>>> the >>>> "saved" session is restored? >>>> >>>> >>> I'm not sure what you mean here. Packages are "installed" into R and >>> then >>> loaded using "library". Simply having a downloaded package in a file >>> will >>> not allow you to use it in R--it must be installed. >>> >>> Sean >>> >>> >>> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M2-B876 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpages@fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > 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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@sean-davis-490
Last seen 3 months ago
United States
On Mon, Feb 28, 2011 at 6:34 PM, rna seq <rna.seeker@gmail.com> wrote: > Hi Sean, > > Thanks for getting back. There are two questions, the first I will direct > towards the rpy list as you suggest. But the second is that as you say these > packages are loaded using "library", but once I log off a session, the > packages that are loaded are lost once a session is over. I am trying to > save these packages because some such as "BSgenome.Hsapiens.UCSC.hg19" are > rather large. > > Hi, Pete. They are not lost. They remain installed in R and stored in one of several locations known to R. They can be loaded in a new session using library(); see the help for library() for more details. You might want read the Intro to R manual for more background. Sean > Pete > > On Mon, Feb 28, 2011 at 2:41 PM, Sean Davis <sdavis2@mail.nih.gov> wrote: > >> >> >> On Mon, Feb 28, 2011 at 3:48 PM, rna seq <rna.seeker@gmail.com> wrote: >> >>> Dear R, >>> >>> Using Ubuntu 10.04 OS and R 2.10, I am running R through python using >>> "rpy". >>> >> >> Hi, Peter. >> >> This isn't really on-topic for the bioconductor list. I would encourage >> you to use the rpy support mechanisms for further details. >> >> >>> I have noticed thatmy sessions are not saved and I am wondering if there >>> is >>> a way to do this. >> >> >> You would need to save them. See save(). >> >> >>> Also and more importantly. Is there a way to direct R to >>> save downloaded packages in a specific file that will be recognized when >>> the >>> "saved" session is restored? >>> >> >> I'm not sure what you mean here. Packages are "installed" into R and then >> loaded using "library". Simply having a downloaded package in a file will >> not allow you to use it in R--it must be installed. >> >> Sean >> >> > [[alternative HTML version deleted]]
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@steve-lianoglou-2771
Last seen 21 months ago
United States
Hi, On Mon, Feb 28, 2011 at 6:34 PM, rna seq <rna.seeker at="" gmail.com=""> wrote: > Hi Sean, > > Thanks for getting back. There are two questions, the first I will direct > towards the rpy list as you suggest. But the second is that as you say these > packages are loaded using "library", but once I log off a session, the > packages that are loaded are lost once a session is over. They're not lost -- they're still installed on your system. > I am trying to > save these packages because some such as "BSgenome.Hsapiens.UCSC.hg19" are > rather large. How do you mean? R> > system.time(suppressPackageStartupMessages(library(BSgenome.Hsapi ens.UCSC.hg19))) user system elapsed 3.888 0.068 3.956 It takes so long because it also has to load several other packages. But still, this is a one time cost. Is that what you're talking about, though? Also -- it's usually bad form to cross post between lists (the previous emails were sent to bioc and r-help) -- I removed r-help from the cc field. -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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