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Question: MacOS Package installation problems
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gravatar for Michael Salbaum
6.1 years ago by
Michael Salbaum80 wrote:
Hi everyone, Newbie question: I'm having trouble with package installation on a Mac (OS 10.6.8) > source("http://bioconductor.org/biocLite.R") > biocLite("DESeq") BioC_mirror: http://bioconductor.org Using R version 2.15, BiocInstaller version 1.4.4. Warning: unable to access index for repository http://brainarray.mbni. med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15 Installing package(s) 'DESeq' Warning: unable to access index for repository http://cran.sixsigmaonline.org/bin/macosx/leopard/contrib/2.15 Error: Line starting '
ADD COMMENTlink modified 6.1 years ago by Chinedu Orekie10 • written 6.1 years ago by Michael Salbaum80
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gravatar for Dan Tenenbaum
6.1 years ago by
Dan Tenenbaum ♦♦ 8.2k
United States
Dan Tenenbaum ♦♦ 8.2k wrote:
On Wed, May 30, 2012 at 9:14 AM, Michael Salbaum <michael.salbaum at="" pbrc.edu=""> wrote: > Hi everyone, > > Newbie question: > > I'm having trouble with package installation on a Mac (OS 10.6.8) > >> ?source("http://bioconductor.org/biocLite.R") >> ? ? biocLite("DESeq") > BioC_mirror: http://bioconductor.org > Using R version 2.15, BiocInstaller version 1.4.4. > Warning: unable to access index for repository http://brainarray.mbn i.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15 > Installing package(s) 'DESeq' > Warning: unable to access index for repository http://cran.sixsigmaonline.org/bin/macosx/leopard/contrib/2.15 > Error: Line starting ' > Dialing into http://cran.sixsigmaonline.org/bin/ only lists a linux directory, but no macosx > > Advice ?is greatly appreciated - thanks! I would suggest using bioconductor.org as your repository. Try: chooseBioCmirror() And choose the "Seattle" option. Dan > > J. Michael Salbaum, Ph.D. > Associate Professor > Pennington Biomedical Research Center > Louisiana State University System > 6400 Perkins Road > Baton Rouge, LA 70808 > > (225) 763-2782 > > > ? ? ? ?[[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
ADD COMMENTlink written 6.1 years ago by Dan Tenenbaum ♦♦ 8.2k
On Wed, May 30, 2012 at 12:19 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: > On Wed, May 30, 2012 at 9:14 AM, Michael Salbaum > <michael.salbaum at="" pbrc.edu=""> wrote: >> Hi everyone, >> >> Newbie question: >> >> I'm having trouble with package installation on a Mac (OS 10.6.8) >> >>> ?source("http://bioconductor.org/biocLite.R") >>> ? ? biocLite("DESeq") >> BioC_mirror: http://bioconductor.org >> Using R version 2.15, BiocInstaller version 1.4.4. >> Warning: unable to access index for repository http://brainarray.mb ni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15 >> Installing package(s) 'DESeq' >> Warning: unable to access index for repository http://cran.sixsigmaonline.org/bin/macosx/leopard/contrib/2.15 >> Error: Line starting '> >> Dialing into http://cran.sixsigmaonline.org/bin/ only lists a linux directory, but no macosx >> >> Advice ?is greatly appreciated - thanks! > > I would suggest using bioconductor.org as your repository. > Try: > chooseBioCmirror() > And choose the "Seattle" option. Dan, did you mean CRAN mirror? chooseCRANmirror() It looks like the CRAN mirror was the issue. Sean > Dan > > >> >> J. Michael Salbaum, Ph.D. >> Associate Professor >> Pennington Biomedical Research Center >> Louisiana State University System >> 6400 Perkins Road >> Baton Rouge, LA 70808 >> >> (225) 763-2782 >> >> >> ? ? ? ?[[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 > > _______________________________________________ > 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
ADD REPLYlink written 6.1 years ago by Sean Davis21k
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gravatar for Dan Tenenbaum
6.1 years ago by
Dan Tenenbaum ♦♦ 8.2k
United States
Dan Tenenbaum ♦♦ 8.2k wrote:
On Wed, May 30, 2012 at 9:33 AM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > On Wed, May 30, 2012 at 12:19 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: >> On Wed, May 30, 2012 at 9:14 AM, Michael Salbaum >> <michael.salbaum at="" pbrc.edu=""> wrote: >>> Hi everyone, >>> >>> Newbie question: >>> >>> I'm having trouble with package installation on a Mac (OS 10.6.8) >>> >>>> ?source("http://bioconductor.org/biocLite.R") >>>> ? ? biocLite("DESeq") >>> BioC_mirror: http://bioconductor.org >>> Using R version 2.15, BiocInstaller version 1.4.4. >>> Warning: unable to access index for repository http://brainarray.m bni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15 >>> Installing package(s) 'DESeq' >>> Warning: unable to access index for repository http://cran.sixsigmaonline.org/bin/macosx/leopard/contrib/2.15 >>> Error: Line starting '>> >>> Dialing into http://cran.sixsigmaonline.org/bin/ only lists a linux directory, but no macosx >>> >>> Advice ?is greatly appreciated - thanks! >> >> I would suggest using bioconductor.org as your repository. >> Try: >> chooseBioCmirror() >> And choose the "Seattle" option. > > Dan, did you mean CRAN mirror? > > chooseCRANmirror() > > It looks like the CRAN mirror was the issue. You are correct, my mistake. Dan > > Sean > >> Dan >> >> >>> >>> J. Michael Salbaum, Ph.D. >>> Associate Professor >>> Pennington Biomedical Research Center >>> Louisiana State University System >>> 6400 Perkins Road >>> Baton Rouge, LA 70808 >>> >>> (225) 763-2782 >>> >>> >>> ? ? ? ?[[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 >> >> _______________________________________________ >> 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
ADD COMMENTlink written 6.1 years ago by Dan Tenenbaum ♦♦ 8.2k
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gravatar for Michael Salbaum
6.1 years ago by
Michael Salbaum80 wrote:
Got it to work. A bit tedious, loading single packages by hand, but nevertheless. Thanks for the help, Cheers, michael -----Original Message----- From: Dan Tenenbaum [mailto:dtenenba@fhcrc.org] Sent: Wed 5/30/2012 11:35 AM To: Sean Davis Cc: Michael Salbaum; bioconductor@r-project.org Subject: Re: [BioC] MacOS Package installation problems On Wed, May 30, 2012 at 9:33 AM, Sean Davis <sdavis2@mail.nih.gov> wrote: > On Wed, May 30, 2012 at 12:19 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: >> On Wed, May 30, 2012 at 9:14 AM, Michael Salbaum >> <michael.salbaum@pbrc.edu> wrote: >>> Hi everyone, >>> >>> Newbie question: >>> >>> I'm having trouble with package installation on a Mac (OS 10.6.8) >>> >>>>  source("http://bioconductor.org/biocLite.R") >>>>     biocLite("DESeq") >>> BioC_mirror: http://bioconductor.org >>> Using R version 2.15, BiocInstaller version 1.4.4. >>> Warning: unable to access index for repository http://brainarray.m bni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15 >>> Installing package(s) 'DESeq' >>> Warning: unable to access index for repository http://cran.sixsigmaonline.org/bin/macosx/leopard/contrib/2.15 >>> Error: Line starting '>> >>> Dialing into http://cran.sixsigmaonline.org/bin/ only lists a linux directory, but no macosx >>> >>> Advice  is greatly appreciated - thanks! >> >> I would suggest using bioconductor.org as your repository. >> Try: >> chooseBioCmirror() >> And choose the "Seattle" option. > > Dan, did you mean CRAN mirror? > > chooseCRANmirror() > > It looks like the CRAN mirror was the issue. You are correct, my mistake. Dan > > Sean > >> Dan >> >> >>> >>> J. Michael Salbaum, Ph.D. >>> Associate Professor >>> Pennington Biomedical Research Center >>> Louisiana State University System >>> 6400 Perkins Road >>> Baton Rouge, LA 70808 >>> >>> (225) 763-2782 >>> >>> >>>        [[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 >> >> _______________________________________________ >> 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]]
ADD COMMENTlink written 6.1 years ago by Michael Salbaum80
Hi Michael, On Wed, May 30, 2012 at 11:16 AM, Michael Salbaum <michael.salbaum at="" pbrc.edu=""> wrote: > Got it to work. > A bit tedious, loading single packages by hand, but nevertheless. What do you mean by this? You should not have to *install* single packages by hand. The following should install DESeq and all its dependencies in one step (assuming you set your CRAN mirror to a working mirror as discussed earlier): source("http://bioconductor.org/biocLite.R") biocLite("DESeq") Then, to *load* DESeq, the following should load it and all its dependencies: library(DESeq) What was the tedious part? Dan > Thanks for the help, > > Cheers, michael > > > > > > -----Original Message----- > From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] > Sent: Wed 5/30/2012 11:35 AM > To: Sean Davis > Cc: Michael Salbaum; bioconductor at r-project.org > Subject: Re: [BioC] MacOS Package installation problems > > On Wed, May 30, 2012 at 9:33 AM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >> On Wed, May 30, 2012 at 12:19 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >> wrote: >>> On Wed, May 30, 2012 at 9:14 AM, Michael Salbaum >>> <michael.salbaum at="" pbrc.edu=""> wrote: >>>> Hi everyone, >>>> >>>> Newbie question: >>>> >>>> I'm having trouble with package installation on a Mac (OS 10.6.8) >>>> >>>>> ?source("http://bioconductor.org/biocLite.R") >>>>> ? ? biocLite("DESeq") >>>> BioC_mirror: http://bioconductor.org >>>> Using R version 2.15, BiocInstaller version 1.4.4. >>>> Warning: unable to access index for repository >>>> http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/cont rib/2.15 >>>> Installing package(s) 'DESeq' >>>> Warning: unable to access index for repository >>>> http://cran.sixsigmaonline.org/bin/macosx/leopard/contrib/2.15 >>>> Error: Line starting '>>> >>>> Dialing into http://cran.sixsigmaonline.org/bin/ only lists a linux >>>> directory, but no macosx >>>> >>>> Advice ?is greatly appreciated - thanks! >>> >>> I would suggest using bioconductor.org as your repository. >>> Try: >>> chooseBioCmirror() >>> And choose the "Seattle" option. >> >> Dan, did you mean CRAN mirror? >> >> chooseCRANmirror() >> >> It looks like the CRAN mirror was the issue. > > You are correct, my mistake. > Dan > > > >> >> Sean >> >>> Dan >>> >>> >>>> >>>> J. Michael Salbaum, Ph.D. >>>> Associate Professor >>>> Pennington Biomedical Research Center >>>> Louisiana State University System >>>> 6400 Perkins Road >>>> Baton Rouge, LA 70808 >>>> >>>> (225) 763-2782 >>>> >>>> >>>> ? ? ? ?[[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 >>> >>> _______________________________________________ >>> 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 >
ADD REPLYlink written 6.1 years ago by Dan Tenenbaum ♦♦ 8.2k
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gravatar for Michael Salbaum
6.1 years ago by
Michael Salbaum80 wrote:
Hi Dan, I tried setting BioC as well as CRAN mirror as suggested. Using source("http://bioconductor.org/biocLite.R") biocLite("DESeq") still directed to the resources listed below, with access problems, and single packages listed as missing. So, I set the BioC mirror to Seattle, the CRAN mirror to TX1 (assuming that it's close to Louisiana), and used the R package installer to fetch the 'missing' packages one by one (things like: xtable, genefilter, geneplotter and a few more). I apologize for my clumsiness in the ways of R, but I'm originally a wetbench person... Cheers, michael -----Original Message----- From: Dan Tenenbaum [mailto:dtenenba@fhcrc.org] Sent: Wed 5/30/2012 1:21 PM To: Michael Salbaum Cc: Sean Davis; bioconductor@r-project.org Subject: Re: [BioC] MacOS Package installation problems Hi Michael, On Wed, May 30, 2012 at 11:16 AM, Michael Salbaum <michael.salbaum@pbrc.edu> wrote: > Got it to work. > A bit tedious, loading single packages by hand, but nevertheless. What do you mean by this? You should not have to *install* single packages by hand. The following should install DESeq and all its dependencies in one step (assuming you set your CRAN mirror to a working mirror as discussed earlier): source("http://bioconductor.org/biocLite.R") biocLite("DESeq") Then, to *load* DESeq, the following should load it and all its dependencies: library(DESeq) What was the tedious part? Dan > Thanks for the help, > > Cheers, michael > > > > > > -----Original Message----- > From: Dan Tenenbaum [mailto:dtenenba@fhcrc.org] > Sent: Wed 5/30/2012 11:35 AM > To: Sean Davis > Cc: Michael Salbaum; bioconductor@r-project.org > Subject: Re: [BioC] MacOS Package installation problems > > On Wed, May 30, 2012 at 9:33 AM, Sean Davis <sdavis2@mail.nih.gov> wrote: >> On Wed, May 30, 2012 at 12:19 PM, Dan Tenenbaum <dtenenba@fhcrc.org> >> wrote: >>> On Wed, May 30, 2012 at 9:14 AM, Michael Salbaum >>> <michael.salbaum@pbrc.edu> wrote: >>>> Hi everyone, >>>> >>>> Newbie question: >>>> >>>> I'm having trouble with package installation on a Mac (OS 10.6.8) >>>> >>>>>  source("http://bioconductor.org/biocLite.R") >>>>>     biocLite("DESeq") >>>> BioC_mirror: http://bioconductor.org >>>> Using R version 2.15, BiocInstaller version 1.4.4. >>>> Warning: unable to access index for repository >>>> http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/cont rib/2.15 >>>> Installing package(s) 'DESeq' >>>> Warning: unable to access index for repository >>>> http://cran.sixsigmaonline.org/bin/macosx/leopard/contrib/2.15 >>>> Error: Line starting '>>> >>>> Dialing into http://cran.sixsigmaonline.org/bin/ only lists a linux >>>> directory, but no macosx >>>> >>>> Advice  is greatly appreciated - thanks! >>> >>> I would suggest using bioconductor.org as your repository. >>> Try: >>> chooseBioCmirror() >>> And choose the "Seattle" option. >> >> Dan, did you mean CRAN mirror? >> >> chooseCRANmirror() >> >> It looks like the CRAN mirror was the issue. > > You are correct, my mistake. > Dan > > > >> >> Sean >> >>> Dan >>> >>> >>>> >>>> J. Michael Salbaum, Ph.D. >>>> Associate Professor >>>> Pennington Biomedical Research Center >>>> Louisiana State University System >>>> 6400 Perkins Road >>>> Baton Rouge, LA 70808 >>>> >>>> (225) 763-2782 >>>> >>>> >>>>        [[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 >>> >>> _______________________________________________ >>> 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]]
ADD COMMENTlink written 6.1 years ago by Michael Salbaum80
Hi Michael, On Wed, May 30, 2012 at 11:49 AM, Michael Salbaum <michael.salbaum at="" pbrc.edu=""> wrote: > Hi Dan, > > I tried setting BioC as well as CRAN mirror as suggested. > It looks like there is a problem with the CRAN mirrors. I tried installing DESeq on my own Mac and got the same problem as you. I got it even if I tried the master mirror in Switzerland (http://stat.ethz.ch/CRAN). I will report this to the CRAN people and let you know what I hear from them. In the meantime, you might try biocLite("DESeq", type="source") If you have the right development tools installed, that should work. The "tedious" solution you came up with will also work until this is resolved. Dan > Using > > > > source("http://bioconductor.org/biocLite.R") > biocLite("DESeq") > > still directed to the resources listed below, with access problems, and > single packages listed as missing. > > So, I set the BioC mirror to Seattle, the CRAN mirror to TX1 (assuming that > it's close to Louisiana), > and used the R package installer to fetch the 'missing' packages one by one > (things like: xtable, genefilter, geneplotter and a few more). > > I apologize for my clumsiness in the ways of R, but I'm originally a > wetbench person... > > > Cheers, michael > > > > > -----Original Message----- > From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] > Sent: Wed 5/30/2012 1:21 PM > To: Michael Salbaum > Cc: Sean Davis; bioconductor at r-project.org > Subject: Re: [BioC] MacOS Package installation problems > > Hi Michael, > > On Wed, May 30, 2012 at 11:16 AM, Michael Salbaum > <michael.salbaum at="" pbrc.edu=""> wrote: >> Got it to work. >> A bit tedious, loading single packages by hand, but nevertheless. > > What do you mean by this? You should not have to *install* single > packages by hand. > The following should install DESeq and all its dependencies in one > step (assuming you set your CRAN mirror to a working mirror as > discussed earlier): > > source("http://bioconductor.org/biocLite.R") > biocLite("DESeq") > > Then, to *load* DESeq, the following should load it and all its > dependencies: > > library(DESeq) > > What was the tedious part? > Dan > > > >> Thanks for the help, >> >> Cheers, michael >> >> >> >> >> >> -----Original Message----- >> From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] >> Sent: Wed 5/30/2012 11:35 AM >> To: Sean Davis >> Cc: Michael Salbaum; bioconductor at r-project.org >> Subject: Re: [BioC] MacOS Package installation problems >> >> On Wed, May 30, 2012 at 9:33 AM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >>> On Wed, May 30, 2012 at 12:19 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >>> wrote: >>>> On Wed, May 30, 2012 at 9:14 AM, Michael Salbaum >>>> <michael.salbaum at="" pbrc.edu=""> wrote: >>>>> Hi everyone, >>>>> >>>>> Newbie question: >>>>> >>>>> I'm having trouble with package installation on a Mac (OS 10.6.8) >>>>> >>>>>> ?source("http://bioconductor.org/biocLite.R") >>>>>> ? ? biocLite("DESeq") >>>>> BioC_mirror: http://bioconductor.org >>>>> Using R version 2.15, BiocInstaller version 1.4.4. >>>>> Warning: unable to access index for repository >>>>> >>>>> http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/con trib/2.15 >>>>> Installing package(s) 'DESeq' >>>>> Warning: unable to access index for repository >>>>> http://cran.sixsigmaonline.org/bin/macosx/leopard/contrib/2.15 >>>>> Error: Line starting '>>>> >>>>> Dialing into http://cran.sixsigmaonline.org/bin/ only lists a linux >>>>> directory, but no macosx >>>>> >>>>> Advice ?is greatly appreciated - thanks! >>>> >>>> I would suggest using bioconductor.org as your repository. >>>> Try: >>>> chooseBioCmirror() >>>> And choose the "Seattle" option. >>> >>> Dan, did you mean CRAN mirror? >>> >>> chooseCRANmirror() >>> >>> It looks like the CRAN mirror was the issue. >> >> You are correct, my mistake. >> Dan >> >> >> >>> >>> Sean >>> >>>> Dan >>>> >>>> >>>>> >>>>> J. Michael Salbaum, Ph.D. >>>>> Associate Professor >>>>> Pennington Biomedical Research Center >>>>> Louisiana State University System >>>>> 6400 Perkins Road >>>>> Baton Rouge, LA 70808 >>>>> >>>>> (225) 763-2782 >>>>> >>>>> >>>>> ? ? ? ?[[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 >>>> >>>> _______________________________________________ >>>> 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 >> >
ADD REPLYlink written 6.1 years ago by Dan Tenenbaum ♦♦ 8.2k
0
gravatar for Michael Salbaum
6.1 years ago by
Michael Salbaum80 wrote:
Thanks for the help, I thought it was just me... michael -----Original Message----- From: Dan Tenenbaum [mailto:dtenenba@fhcrc.org] Sent: Wed 5/30/2012 1:57 PM To: Michael Salbaum Cc: Sean Davis; bioconductor@r-project.org Subject: Re: [BioC] MacOS Package installation problems Hi Michael, On Wed, May 30, 2012 at 11:49 AM, Michael Salbaum <michael.salbaum@pbrc.edu> wrote: > Hi Dan, > > I tried setting BioC as well as CRAN mirror as suggested. > It looks like there is a problem with the CRAN mirrors. I tried installing DESeq on my own Mac and got the same problem as you. I got it even if I tried the master mirror in Switzerland (http://stat.ethz.ch/CRAN). I will report this to the CRAN people and let you know what I hear from them. In the meantime, you might try biocLite("DESeq", type="source") If you have the right development tools installed, that should work. The "tedious" solution you came up with will also work until this is resolved. Dan > Using > > > > source("http://bioconductor.org/biocLite.R") > biocLite("DESeq") > > still directed to the resources listed below, with access problems, and > single packages listed as missing. > > So, I set the BioC mirror to Seattle, the CRAN mirror to TX1 (assuming that > it's close to Louisiana), > and used the R package installer to fetch the 'missing' packages one by one > (things like: xtable, genefilter, geneplotter and a few more). > > I apologize for my clumsiness in the ways of R, but I'm originally a > wetbench person... > > > Cheers, michael > > > > > -----Original Message----- > From: Dan Tenenbaum [mailto:dtenenba@fhcrc.org] > Sent: Wed 5/30/2012 1:21 PM > To: Michael Salbaum > Cc: Sean Davis; bioconductor@r-project.org > Subject: Re: [BioC] MacOS Package installation problems > > Hi Michael, > > On Wed, May 30, 2012 at 11:16 AM, Michael Salbaum > <michael.salbaum@pbrc.edu> wrote: >> Got it to work. >> A bit tedious, loading single packages by hand, but nevertheless. > > What do you mean by this? You should not have to *install* single > packages by hand. > The following should install DESeq and all its dependencies in one > step (assuming you set your CRAN mirror to a working mirror as > discussed earlier): > > source("http://bioconductor.org/biocLite.R") > biocLite("DESeq") > > Then, to *load* DESeq, the following should load it and all its > dependencies: > > library(DESeq) > > What was the tedious part? > Dan > > > >> Thanks for the help, >> >> Cheers, michael >> >> >> >> >> >> -----Original Message----- >> From: Dan Tenenbaum [mailto:dtenenba@fhcrc.org] >> Sent: Wed 5/30/2012 11:35 AM >> To: Sean Davis >> Cc: Michael Salbaum; bioconductor@r-project.org >> Subject: Re: [BioC] MacOS Package installation problems >> >> On Wed, May 30, 2012 at 9:33 AM, Sean Davis <sdavis2@mail.nih.gov> wrote: >>> On Wed, May 30, 2012 at 12:19 PM, Dan Tenenbaum <dtenenba@fhcrc.org> >>> wrote: >>>> On Wed, May 30, 2012 at 9:14 AM, Michael Salbaum >>>> <michael.salbaum@pbrc.edu> wrote: >>>>> Hi everyone, >>>>> >>>>> Newbie question: >>>>> >>>>> I'm having trouble with package installation on a Mac (OS 10.6.8) >>>>> >>>>>>  source("http://bioconductor.org/biocLite.R") >>>>>>     biocLite("DESeq") >>>>> BioC_mirror: http://bioconductor.org >>>>> Using R version 2.15, BiocInstaller version 1.4.4. >>>>> Warning: unable to access index for repository >>>>> >>>>> http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/con trib/2.15 >>>>> Installing package(s) 'DESeq' >>>>> Warning: unable to access index for repository >>>>> http://cran.sixsigmaonline.org/bin/macosx/leopard/contrib/2.15 >>>>> Error: Line starting '>>>> >>>>> Dialing into http://cran.sixsigmaonline.org/bin/ only lists a linux >>>>> directory, but no macosx >>>>> >>>>> Advice  is greatly appreciated - thanks! >>>> >>>> I would suggest using bioconductor.org as your repository. >>>> Try: >>>> chooseBioCmirror() >>>> And choose the "Seattle" option. >>> >>> Dan, did you mean CRAN mirror? >>> >>> chooseCRANmirror() >>> >>> It looks like the CRAN mirror was the issue. >> >> You are correct, my mistake. >> Dan >> >> >> >>> >>> Sean >>> >>>> Dan >>>> >>>> >>>>> >>>>> J. Michael Salbaum, Ph.D. >>>>> Associate Professor >>>>> Pennington Biomedical Research Center >>>>> Louisiana State University System >>>>> 6400 Perkins Road >>>>> Baton Rouge, LA 70808 >>>>> >>>>> (225) 763-2782 >>>>> >>>>> >>>>>        [[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 >>>> >>>> _______________________________________________ >>>> 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]]
ADD COMMENTlink written 6.1 years ago by Michael Salbaum80
On Wed, May 30, 2012 at 12:02 PM, Michael Salbaum <michael.salbaum at="" pbrc.edu=""> wrote: > Thanks for the help, I thought it was just me... > > > > michael > > > -----Original Message----- > From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] > Sent: Wed 5/30/2012 1:57 PM > To: Michael Salbaum > Cc: Sean Davis; bioconductor at r-project.org > Subject: Re: [BioC] MacOS Package installation problems > > Hi Michael, > > > On Wed, May 30, 2012 at 11:49 AM, Michael Salbaum > <michael.salbaum at="" pbrc.edu=""> wrote: >> Hi Dan, >> >> I tried setting BioC as well as CRAN mirror as suggested. > >> > > It looks like there is a problem with the CRAN mirrors. > I tried installing DESeq on my own Mac and got the same problem as > you. I got it even if I tried the master mirror in Switzerland > (http://stat.ethz.ch/CRAN). > > I will report this to the CRAN people and let you know what I hear from > them. Actually, it turns out the problem was on our end. The BiocInstaller package should not include CRANextra in its list of repositories if you are not on Windows. That repository is meant for Windows only and going to the Mac portion of the URL will cause an error. This is fixed in BiocInstaller 1.4.5 (release) and 1.5.9 (devel). It will not propagate to you until late tomorow (Thursday) morning Seattle time, so in the meantime you could try something like this: library(BiocInstaller) repos <- biocinstallRepos() repos <- repos[!names(repos) %in% "CRANextra"] install.packages("DEseq", repos=repos) I apologize for the inconvenience. Dan > > In the meantime, you might try > biocLite("DESeq", type="source") > If you have the right development tools installed, that should work. > The "tedious" solution you came up with will also work until this is > resolved. > > Dan > > > >> Using >> >> >> >> source("http://bioconductor.org/biocLite.R") >> biocLite("DESeq") >> >> still directed to the resources listed below, with access problems, and >> single packages listed as missing. >> >> So, I set the BioC mirror to Seattle, the CRAN mirror to TX1 (assuming >> that >> it's close to Louisiana), >> and used the R package installer to fetch the 'missing' packages one by >> one >> (things like: xtable, genefilter, geneplotter and a few more). >> >> I apologize for my clumsiness in the ways of R, but I'm originally a >> wetbench person... >> >> >> Cheers, michael >> >> >> >> >> -----Original Message----- >> From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] >> Sent: Wed 5/30/2012 1:21 PM >> To: Michael Salbaum >> Cc: Sean Davis; bioconductor at r-project.org >> Subject: Re: [BioC] MacOS Package installation problems >> >> Hi Michael, >> >> On Wed, May 30, 2012 at 11:16 AM, Michael Salbaum >> <michael.salbaum at="" pbrc.edu=""> wrote: >>> Got it to work. >>> A bit tedious, loading single packages by hand, but nevertheless. >> >> What do you mean by this? You should not have to *install* single >> packages by hand. >> The following should install DESeq and all its dependencies in one >> step (assuming you set your CRAN mirror to a working mirror as >> discussed earlier): >> >> source("http://bioconductor.org/biocLite.R") >> biocLite("DESeq") >> >> Then, to *load* DESeq, the following should load it and all its >> dependencies: >> >> library(DESeq) >> >> What was the tedious part? >> Dan >> >> >> >>> Thanks for the help, >>> >>> Cheers, michael >>> >>> >>> >>> >>> >>> -----Original Message----- >>> From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] >>> Sent: Wed 5/30/2012 11:35 AM >>> To: Sean Davis >>> Cc: Michael Salbaum; bioconductor at r-project.org >>> Subject: Re: [BioC] MacOS Package installation problems >>> >>> On Wed, May 30, 2012 at 9:33 AM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >>>> On Wed, May 30, 2012 at 12:19 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >>>> wrote: >>>>> On Wed, May 30, 2012 at 9:14 AM, Michael Salbaum >>>>> <michael.salbaum at="" pbrc.edu=""> wrote: >>>>>> Hi everyone, >>>>>> >>>>>> Newbie question: >>>>>> >>>>>> I'm having trouble with package installation on a Mac (OS 10.6.8) >>>>>> >>>>>>> ?source("http://bioconductor.org/biocLite.R") >>>>>>> ? ? biocLite("DESeq") >>>>>> BioC_mirror: http://bioconductor.org >>>>>> Using R version 2.15, BiocInstaller version 1.4.4. >>>>>> Warning: unable to access index for repository >>>>>> >>>>>> >>>>>> http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/co ntrib/2.15 >>>>>> Installing package(s) 'DESeq' >>>>>> Warning: unable to access index for repository >>>>>> http://cran.sixsigmaonline.org/bin/macosx/leopard/contrib/2.15 >>>>>> Error: Line starting '>>>>> >>>>>> Dialing into http://cran.sixsigmaonline.org/bin/ only lists a linux >>>>>> directory, but no macosx >>>>>> >>>>>> Advice ?is greatly appreciated - thanks! >>>>> >>>>> I would suggest using bioconductor.org as your repository. >>>>> Try: >>>>> chooseBioCmirror() >>>>> And choose the "Seattle" option. >>>> >>>> Dan, did you mean CRAN mirror? >>>> >>>> chooseCRANmirror() >>>> >>>> It looks like the CRAN mirror was the issue. >>> >>> You are correct, my mistake. >>> Dan >>> >>> >>> >>>> >>>> Sean >>>> >>>>> Dan >>>>> >>>>> >>>>>> >>>>>> J. Michael Salbaum, Ph.D. >>>>>> Associate Professor >>>>>> Pennington Biomedical Research Center >>>>>> Louisiana State University System >>>>>> 6400 Perkins Road >>>>>> Baton Rouge, LA 70808 >>>>>> >>>>>> (225) 763-2782 >>>>>> >>>>>> >>>>>> ? ? ? ?[[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 >>>>> >>>>> _______________________________________________ >>>>> 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 >>> >> >
ADD REPLYlink written 6.1 years ago by Dan Tenenbaum ♦♦ 8.2k
On Wed, May 30, 2012 at 12:28 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: > On Wed, May 30, 2012 at 12:02 PM, Michael Salbaum > <michael.salbaum at="" pbrc.edu=""> wrote: >> Thanks for the help, I thought it was just me... >> >> >> >> michael >> >> >> -----Original Message----- >> From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] >> Sent: Wed 5/30/2012 1:57 PM >> To: Michael Salbaum >> Cc: Sean Davis; bioconductor at r-project.org >> Subject: Re: [BioC] MacOS Package installation problems >> >> Hi Michael, >> >> >> On Wed, May 30, 2012 at 11:49 AM, Michael Salbaum >> <michael.salbaum at="" pbrc.edu=""> wrote: >>> Hi Dan, >>> >>> I tried setting BioC as well as CRAN mirror as suggested. >> >>> >> >> It looks like there is a problem with the CRAN mirrors. >> I tried installing DESeq on my own Mac and got the same problem as >> you. I got it even if I tried the master mirror in Switzerland >> (http://stat.ethz.ch/CRAN). >> >> I will report this to the CRAN people and let you know what I hear from >> them. > > Actually, it turns out the problem was on our end. The BiocInstaller > package should not include CRANextra in its list of repositories if > you are not on Windows. That repository is meant for Windows only and > going to the Mac portion of the URL will cause an error. > > This is fixed in BiocInstaller 1.4.5 (release) and 1.5.9 (devel). It > will not propagate to you until late tomorow (Thursday) morning > Seattle time, so in the meantime you could try something like this: > > library(BiocInstaller) > repos <- biocinstallRepos() > repos <- repos[!names(repos) %in% "CRANextra"] > install.packages("DEseq", repos=repos) > There was a typo, that last line should be: install.packages("DESeq", repos=repos) Thanks, Dan > I apologize for the inconvenience. > > Dan > > >> >> In the meantime, you might try >> biocLite("DESeq", type="source") >> If you have the right development tools installed, that should work. >> The "tedious" solution you came up with will also work until this is >> resolved. >> >> Dan >> >> >> >>> Using >>> >>> >>> >>> source("http://bioconductor.org/biocLite.R") >>> biocLite("DESeq") >>> >>> still directed to the resources listed below, with access problems, and >>> single packages listed as missing. >>> >>> So, I set the BioC mirror to Seattle, the CRAN mirror to TX1 (assuming >>> that >>> it's close to Louisiana), >>> and used the R package installer to fetch the 'missing' packages one by >>> one >>> (things like: xtable, genefilter, geneplotter and a few more). >>> >>> I apologize for my clumsiness in the ways of R, but I'm originally a >>> wetbench person... >>> >>> >>> Cheers, michael >>> >>> >>> >>> >>> -----Original Message----- >>> From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] >>> Sent: Wed 5/30/2012 1:21 PM >>> To: Michael Salbaum >>> Cc: Sean Davis; bioconductor at r-project.org >>> Subject: Re: [BioC] MacOS Package installation problems >>> >>> Hi Michael, >>> >>> On Wed, May 30, 2012 at 11:16 AM, Michael Salbaum >>> <michael.salbaum at="" pbrc.edu=""> wrote: >>>> Got it to work. >>>> A bit tedious, loading single packages by hand, but nevertheless. >>> >>> What do you mean by this? You should not have to *install* single >>> packages by hand. >>> The following should install DESeq and all its dependencies in one >>> step (assuming you set your CRAN mirror to a working mirror as >>> discussed earlier): >>> >>> source("http://bioconductor.org/biocLite.R") >>> biocLite("DESeq") >>> >>> Then, to *load* DESeq, the following should load it and all its >>> dependencies: >>> >>> library(DESeq) >>> >>> What was the tedious part? >>> Dan >>> >>> >>> >>>> Thanks for the help, >>>> >>>> Cheers, michael >>>> >>>> >>>> >>>> >>>> >>>> -----Original Message----- >>>> From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] >>>> Sent: Wed 5/30/2012 11:35 AM >>>> To: Sean Davis >>>> Cc: Michael Salbaum; bioconductor at r-project.org >>>> Subject: Re: [BioC] MacOS Package installation problems >>>> >>>> On Wed, May 30, 2012 at 9:33 AM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >>>>> On Wed, May 30, 2012 at 12:19 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >>>>> wrote: >>>>>> On Wed, May 30, 2012 at 9:14 AM, Michael Salbaum >>>>>> <michael.salbaum at="" pbrc.edu=""> wrote: >>>>>>> Hi everyone, >>>>>>> >>>>>>> Newbie question: >>>>>>> >>>>>>> I'm having trouble with package installation on a Mac (OS 10.6.8) >>>>>>> >>>>>>>> ?source("http://bioconductor.org/biocLite.R") >>>>>>>> ? ? biocLite("DESeq") >>>>>>> BioC_mirror: http://bioconductor.org >>>>>>> Using R version 2.15, BiocInstaller version 1.4.4. >>>>>>> Warning: unable to access index for repository >>>>>>> >>>>>>> >>>>>>> http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/c ontrib/2.15 >>>>>>> Installing package(s) 'DESeq' >>>>>>> Warning: unable to access index for repository >>>>>>> http://cran.sixsigmaonline.org/bin/macosx/leopard/contrib/2.15 >>>>>>> Error: Line starting '>>>>>> >>>>>>> Dialing into http://cran.sixsigmaonline.org/bin/ only lists a linux >>>>>>> directory, but no macosx >>>>>>> >>>>>>> Advice ?is greatly appreciated - thanks! >>>>>> >>>>>> I would suggest using bioconductor.org as your repository. >>>>>> Try: >>>>>> chooseBioCmirror() >>>>>> And choose the "Seattle" option. >>>>> >>>>> Dan, did you mean CRAN mirror? >>>>> >>>>> chooseCRANmirror() >>>>> >>>>> It looks like the CRAN mirror was the issue. >>>> >>>> You are correct, my mistake. >>>> Dan >>>> >>>> >>>> >>>>> >>>>> Sean >>>>> >>>>>> Dan >>>>>> >>>>>> >>>>>>> >>>>>>> J. Michael Salbaum, Ph.D. >>>>>>> Associate Professor >>>>>>> Pennington Biomedical Research Center >>>>>>> Louisiana State University System >>>>>>> 6400 Perkins Road >>>>>>> Baton Rouge, LA 70808 >>>>>>> >>>>>>> (225) 763-2782 >>>>>>> >>>>>>> >>>>>>> ? ? ? ?[[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 >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>> >>> >>
ADD REPLYlink written 6.1 years ago by Dan Tenenbaum ♦♦ 8.2k
Hi everyone, Just a quick note to say that the new version of BiocInstaller is available, so this issue (of biocLite() not working on Mac systems) should not recur. When you use biocLite() it automatically updates you to the latest version of BiocInstaller. Thanks, Dan On Wed, May 30, 2012 at 12:39 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: > On Wed, May 30, 2012 at 12:28 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: >> On Wed, May 30, 2012 at 12:02 PM, Michael Salbaum >> <michael.salbaum at="" pbrc.edu=""> wrote: >>> Thanks for the help, I thought it was just me... >>> >>> >>> >>> michael >>> >>> >>> -----Original Message----- >>> From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] >>> Sent: Wed 5/30/2012 1:57 PM >>> To: Michael Salbaum >>> Cc: Sean Davis; bioconductor at r-project.org >>> Subject: Re: [BioC] MacOS Package installation problems >>> >>> Hi Michael, >>> >>> >>> On Wed, May 30, 2012 at 11:49 AM, Michael Salbaum >>> <michael.salbaum at="" pbrc.edu=""> wrote: >>>> Hi Dan, >>>> >>>> I tried setting BioC as well as CRAN mirror as suggested. >>> >>>> >>> >>> It looks like there is a problem with the CRAN mirrors. >>> I tried installing DESeq on my own Mac and got the same problem as >>> you. I got it even if I tried the master mirror in Switzerland >>> (http://stat.ethz.ch/CRAN). >>> >>> I will report this to the CRAN people and let you know what I hear from >>> them. >> >> Actually, it turns out the problem was on our end. The BiocInstaller >> package should not include CRANextra in its list of repositories if >> you are not on Windows. That repository is meant for Windows only and >> going to the Mac portion of the URL will cause an error. >> >> This is fixed in BiocInstaller 1.4.5 (release) and 1.5.9 (devel). It >> will not propagate to you until late tomorow (Thursday) morning >> Seattle time, so in the meantime you could try something like this: >> >> library(BiocInstaller) >> repos <- biocinstallRepos() >> repos <- repos[!names(repos) %in% "CRANextra"] >> install.packages("DEseq", repos=repos) >> > > There was a typo, that last line should be: > install.packages("DESeq", repos=repos) > > Thanks, > Dan > > > > >> I apologize for the inconvenience. >> >> Dan >> >> >>> >>> In the meantime, you might try >>> biocLite("DESeq", type="source") >>> If you have the right development tools installed, that should work. >>> The "tedious" solution you came up with will also work until this is >>> resolved. >>> >>> Dan >>> >>> >>> >>>> Using >>>> >>>> >>>> >>>> source("http://bioconductor.org/biocLite.R") >>>> biocLite("DESeq") >>>> >>>> still directed to the resources listed below, with access problems, and >>>> single packages listed as missing. >>>> >>>> So, I set the BioC mirror to Seattle, the CRAN mirror to TX1 (assuming >>>> that >>>> it's close to Louisiana), >>>> and used the R package installer to fetch the 'missing' packages one by >>>> one >>>> (things like: xtable, genefilter, geneplotter and a few more). >>>> >>>> I apologize for my clumsiness in the ways of R, but I'm originally a >>>> wetbench person... >>>> >>>> >>>> Cheers, michael >>>> >>>> >>>> >>>> >>>> -----Original Message----- >>>> From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] >>>> Sent: Wed 5/30/2012 1:21 PM >>>> To: Michael Salbaum >>>> Cc: Sean Davis; bioconductor at r-project.org >>>> Subject: Re: [BioC] MacOS Package installation problems >>>> >>>> Hi Michael, >>>> >>>> On Wed, May 30, 2012 at 11:16 AM, Michael Salbaum >>>> <michael.salbaum at="" pbrc.edu=""> wrote: >>>>> Got it to work. >>>>> A bit tedious, loading single packages by hand, but nevertheless. >>>> >>>> What do you mean by this? You should not have to *install* single >>>> packages by hand. >>>> The following should install DESeq and all its dependencies in one >>>> step (assuming you set your CRAN mirror to a working mirror as >>>> discussed earlier): >>>> >>>> source("http://bioconductor.org/biocLite.R") >>>> biocLite("DESeq") >>>> >>>> Then, to *load* DESeq, the following should load it and all its >>>> dependencies: >>>> >>>> library(DESeq) >>>> >>>> What was the tedious part? >>>> Dan >>>> >>>> >>>> >>>>> Thanks for the help, >>>>> >>>>> Cheers, michael >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> -----Original Message----- >>>>> From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] >>>>> Sent: Wed 5/30/2012 11:35 AM >>>>> To: Sean Davis >>>>> Cc: Michael Salbaum; bioconductor at r-project.org >>>>> Subject: Re: [BioC] MacOS Package installation problems >>>>> >>>>> On Wed, May 30, 2012 at 9:33 AM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >>>>>> On Wed, May 30, 2012 at 12:19 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >>>>>> wrote: >>>>>>> On Wed, May 30, 2012 at 9:14 AM, Michael Salbaum >>>>>>> <michael.salbaum at="" pbrc.edu=""> wrote: >>>>>>>> Hi everyone, >>>>>>>> >>>>>>>> Newbie question: >>>>>>>> >>>>>>>> I'm having trouble with package installation on a Mac (OS 10.6.8) >>>>>>>> >>>>>>>>> ?source("http://bioconductor.org/biocLite.R") >>>>>>>>> ? ? biocLite("DESeq") >>>>>>>> BioC_mirror: http://bioconductor.org >>>>>>>> Using R version 2.15, BiocInstaller version 1.4.4. >>>>>>>> Warning: unable to access index for repository >>>>>>>> >>>>>>>> >>>>>>>> http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/ contrib/2.15 >>>>>>>> Installing package(s) 'DESeq' >>>>>>>> Warning: unable to access index for repository >>>>>>>> http://cran.sixsigmaonline.org/bin/macosx/leopard/contrib/2.15 >>>>>>>> Error: Line starting '>>>>>>> >>>>>>>> Dialing into http://cran.sixsigmaonline.org/bin/ only lists a linux >>>>>>>> directory, but no macosx >>>>>>>> >>>>>>>> Advice ?is greatly appreciated - thanks! >>>>>>> >>>>>>> I would suggest using bioconductor.org as your repository. >>>>>>> Try: >>>>>>> chooseBioCmirror() >>>>>>> And choose the "Seattle" option. >>>>>> >>>>>> Dan, did you mean CRAN mirror? >>>>>> >>>>>> chooseCRANmirror() >>>>>> >>>>>> It looks like the CRAN mirror was the issue. >>>>> >>>>> You are correct, my mistake. >>>>> Dan >>>>> >>>>> >>>>> >>>>>> >>>>>> Sean >>>>>> >>>>>>> Dan >>>>>>> >>>>>>> >>>>>>>> >>>>>>>> J. Michael Salbaum, Ph.D. >>>>>>>> Associate Professor >>>>>>>> Pennington Biomedical Research Center >>>>>>>> Louisiana State University System >>>>>>>> 6400 Perkins Road >>>>>>>> Baton Rouge, LA 70808 >>>>>>>> >>>>>>>> (225) 763-2782 >>>>>>>> >>>>>>>> >>>>>>>> ? ? ? ?[[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 >>>>>>> >>>>>>> _______________________________________________ >>>>>>> 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 >>>>> >>>> >>>
ADD REPLYlink written 6.1 years ago by Dan Tenenbaum ♦♦ 8.2k
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Chinedu Orekie10 wrote:
I am having the same problem installing packages (Line starting '
ADD COMMENTlink written 6.1 years ago by Chinedu Orekie10
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