Question

Installing an older release of Bioconductor

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Veni Kurup ▴ 30

@veni-kurup-3536

Last seen 9.6 years ago

Hi, I am trying to install Bioconductor 2.3. I found this link which has the release I need: http://www.bioconductor.org/download/oldrelease/BioC2.3/ Is there an easy way to install all of these packages from BioC2.3? Or do I need to download each windows binary and install one by one? Thank you for your help. Veni [[alternative HTML version deleted]]

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ADD COMMENT • link updated 6.1 years ago by howarth.mailing.lists ▴ 10 • written 14.8 years ago by Veni Kurup ▴ 30

score 1 · Answer 1 · 2018-03-16

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howarth.mailing.lists ▴ 10

@howarthmailinglists-13534

Last seen 4.6 years ago

One doesn't have to downgrade R which is an imperfect solution as it would only install the last supported version of Bioconductor rather than a specific version. Assuming you have been installing the Bioconductor packages in /usr/local/lib/R/site-library. you can just use the following commands from within R to install the 3.5 release rather than the current 3.6 one.

install.packages("BiocInstaller",repos="http://bioconductor.org/packages/3.5/bioc",lib="/usr/local/lib/R/site-library")

library("BiocInstaller")

biocLite()

ADD COMMENT • link 6.1 years ago howarth.mailing.lists ▴ 10

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This may *technically* work, however the bioconductor ecosystem (v3.4, v3.5, etc) is only tested to work against a very specific version of R. Installing bioc packages using anything but `biocLite()` can land you into a mess. It doesn't mean that you can't try, but you'll be on your own if/when things go awry.

ADD REPLY • link 6.1 years ago Steve Lianoglou ★ 13k

score 0 · Answer 2 · 2009-06-24

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Steve Lianoglou ★ 13k

@steve-lianoglou-2771

Last seen 13 months ago

United States

Hi, On Jun 24, 2009, at 2:43 PM, Veni Kurup wrote: > Hi, > > I am trying to install Bioconductor 2.3. I found this link which has > the > release I need: http://www.bioconductor.org/download/oldrelease/BioC2.3/ > > Is there an easy way to install all of these packages from BioC2.3? > Or do I > need to download each windows binary and install one by one? Since each version of bioconductor is meant to be used with a specific version of R, if you want to use packages from BioC 2.3, I think your best bet would be to install R 2.8.x and do the normal: source('http://bioconductor.org/biocLite.R') biocLite(... whatever ...) You should find that you're pulling packages from Bioc 2.3. I'm pretty sure that mixing BioC packages from different BioC versions into the same R distro isn't advised ... perhaps the gurus will chime in with better advice, but that's my 2 cents. Hope that helps, -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

ADD COMMENT • link 14.8 years ago Steve Lianoglou ★ 13k

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Thank you very much. That worked. - Veni On Wed, Jun 24, 2009 at 2:50 PM, Steve Lianoglou < mailinglist.honeypot@gmail.com> wrote: > Hi, > > > On Jun 24, 2009, at 2:43 PM, Veni Kurup wrote: > > Hi, >> >> I am trying to install Bioconductor 2.3. I found this link which has the >> release I need: http://www.bioconductor.org/download/oldrelease/BioC2.3/ >> >> Is there an easy way to install all of these packages from BioC2.3? Or do >> I >> need to download each windows binary and install one by one? >> > > > Since each version of bioconductor is meant to be used with a specific > version of R, if you want to use packages from BioC 2.3, I think your best > bet would be to install R 2.8.x and do the normal: > > source('http://bioconductor.org/biocLite.R') > biocLite(... whatever ...) > > You should find that you're pulling packages from Bioc 2.3. > > I'm pretty sure that mixing BioC packages from different BioC versions into > the same R distro isn't advised ... perhaps the gurus will chime in with > better advice, but that's my 2 cents. > > Hope that helps, > -steve > > -- > Steve Lianoglou > Graduate Student: Physiology, Biophysics and Systems Biology > Weill Medical College of Cornell University > > Contact Info: http://cbio.mskcc.org/~lianos/contact<http: cbio.mskc="" c.org="" %7elianos="" contact=""> > > > > [[alternative HTML version deleted]]

ADD REPLY • link 14.8 years ago Veni Kurup ▴ 30