R hanging up on install of BioConductor
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@anjan-purkayastha-4273
Last seen 10.2 years ago
Hi, Am working on Mac OS X 10.5.8. Just installed R 2.11.1. Tried to install the base packages of Bioconductor with : source("http://bioconductor.org/biocLite.R") biocLite() R hangs while downloading the various modules. Have tried it multiple times (after multiple reinstalls of R) - no success. Anybody else having this problem? Thanks, Anjan -- =================================== anjan purkayastha, phd. research associate fas center for systems biology, harvard university 52 oxford street cambridge ma 02138 phone-703.740.6939 =================================== [[alternative HTML version deleted]]
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@vincent-j-carey-jr-4
Last seen 9 weeks ago
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There is no evidence of a problem at the bioc server end, so you need to consider your network connectivity. Try to work within R, using install.packages, to acquire something small like install.packages("ash") R "hanging" might indicate that you don't have sufficient connectivity to complete the transaction; it is not a bioconductor issue. Various issues regarding the roles of proxies are reviewed in the documentation retrieved with ?download.file in R On Tue, Oct 5, 2010 at 12:14 PM, ANJAN PURKAYASTHA <anjan.purkayastha at="" gmail.com=""> wrote: > Hi, > Am working on ?Mac OS X 10.5.8. Just installed R 2.11.1. > Tried to install the base packages of Bioconductor with : > > source("http://bioconductor.org/biocLite.R") > biocLite() > > > R hangs while downloading the various modules. ? Have tried it multiple > times (after multiple reinstalls of R) - no success. ?Anybody else having > this problem? > Thanks, > Anjan > > > > > -- > =================================== > anjan purkayastha, phd. > research associate > fas center for systems biology, > harvard university > 52 oxford street > cambridge ma 02138 > phone-703.740.6939 > =================================== > > ? ? ? ?[[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 >
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For what it's worth, the Fred Hutch mirror does seem to be agonizingly slow for me at the moment. I switched to the Bethesda mirror with chooseBioCMirror and setRepositories and it is installing at normal speed. Could be worth a try. Hollis Wright, PhD Oregon Clinical and Translational Research Institute ________________________________________ From: bioconductor-bounces@stat.math.ethz.ch [bioconductor- bounces@stat.math.ethz.ch] On Behalf Of Vincent Carey [stvjc@channing.harvard.edu] Sent: Tuesday, October 05, 2010 11:01 AM To: ANJAN PURKAYASTHA Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] R hanging up on install of BioConductor There is no evidence of a problem at the bioc server end, so you need to consider your network connectivity. Try to work within R, using install.packages, to acquire something small like install.packages("ash") R "hanging" might indicate that you don't have sufficient connectivity to complete the transaction; it is not a bioconductor issue. Various issues regarding the roles of proxies are reviewed in the documentation retrieved with ?download.file in R On Tue, Oct 5, 2010 at 12:14 PM, ANJAN PURKAYASTHA <anjan.purkayastha at="" gmail.com=""> wrote: > Hi, > Am working on Mac OS X 10.5.8. Just installed R 2.11.1. > Tried to install the base packages of Bioconductor with : > > source("http://bioconductor.org/biocLite.R") > biocLite() > > > R hangs while downloading the various modules. Have tried it multiple > times (after multiple reinstalls of R) - no success. Anybody else having > this problem? > Thanks, > Anjan > > > > > -- > =================================== > anjan purkayastha, phd. > research associate > fas center for systems biology, > harvard university > 52 oxford street > cambridge ma 02138 > phone-703.740.6939 > =================================== > > [[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 > _______________________________________________ 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
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On Tue, Oct 5, 2010 at 11:36 AM, Hollis Wright <wrighth@ohsu.edu> wrote: > For what it's worth, the Fred Hutch mirror does seem to be agonizingly slow > for me at the moment. I switched to the Bethesda mirror with > chooseBioCMirror and setRepositories and it is installing at > normal speed. Could be worth a try. > You might try the Fred Hutch mirror again, it seems there were some rude processes running which have now been terminated and load looks good again. Dan [[alternative HTML version deleted]]
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Also, if you are running R using the R.app GUI, I believe it just looks like it's doing nothing when all the install process is going on. It's actually been a long time since I used the GUI (I just run through terminal, or emacs), so I'm not sure if this is your problem, but I remember it doing that back when I was first using "it" (the GUI) and getting into R. -steve On Tue, Oct 5, 2010 at 2:36 PM, Hollis Wright <wrighth at="" ohsu.edu=""> wrote: > For what it's worth, the Fred Hutch mirror does seem to be agonizingly slow for me at the moment. I switched to the Bethesda mirror with chooseBioCMirror and setRepositories and it is installing at > normal speed. Could be worth a try. > > Hollis Wright, PhD > Oregon Clinical and Translational Research Institute > ________________________________________ > From: bioconductor-bounces at stat.math.ethz.ch [bioconductor- bounces at stat.math.ethz.ch] On Behalf Of Vincent Carey [stvjc at channing.harvard.edu] > Sent: Tuesday, October 05, 2010 11:01 AM > To: ANJAN PURKAYASTHA > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] R hanging up on install of BioConductor > > There is no evidence of a problem at the bioc server end, so you need > to consider your > network connectivity. ?Try to work within R, using install.packages, > to acquire something small > like > > install.packages("ash") > > R "hanging" might indicate that you don't have sufficient connectivity > to complete the transaction; > it is not a bioconductor issue. ?Various issues regarding the roles of > proxies are reviewed in the > documentation retrieved with ?download.file in R > > On Tue, Oct 5, 2010 at 12:14 PM, ANJAN PURKAYASTHA > <anjan.purkayastha at="" gmail.com=""> wrote: >> Hi, >> Am working on ?Mac OS X 10.5.8. Just installed R 2.11.1. >> Tried to install the base packages of Bioconductor with : >> >> source("http://bioconductor.org/biocLite.R") >> biocLite() >> >> >> R hangs while downloading the various modules. ? Have tried it multiple >> times (after multiple reinstalls of R) - no success. ?Anybody else having >> this problem? >> Thanks, >> Anjan >> >> >> >> >> -- >> =================================== >> anjan purkayastha, phd. >> research associate >> fas center for systems biology, >> harvard university >> 52 oxford street >> cambridge ma 02138 >> phone-703.740.6939 >> =================================== >> >> ? ? ? ?[[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 >> > > _______________________________________________ > 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 > > _______________________________________________ > 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 > -- 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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Sorry for not finishing that thought, but in short: try running R through the terminal to see if it reports installation progress better. -steve On Tue, Oct 5, 2010 at 3:14 PM, Steve Lianoglou <mailinglist.honeypot at="" gmail.com=""> wrote: > Also, if you are running R using the R.app GUI, I believe it just > looks like it's doing nothing when all the install process is going > on. > > It's actually been a long time since I used the GUI (I just run > through terminal, or emacs), so I'm not sure if this is your problem, > but I remember it doing that back when I was first using "it" (the > GUI) and getting into R. > > -steve > > On Tue, Oct 5, 2010 at 2:36 PM, Hollis Wright <wrighth at="" ohsu.edu=""> wrote: >> For what it's worth, the Fred Hutch mirror does seem to be agonizingly slow for me at the moment. I switched to the Bethesda mirror with chooseBioCMirror and setRepositories and it is installing at >> normal speed. Could be worth a try. >> >> Hollis Wright, PhD >> Oregon Clinical and Translational Research Institute >> ________________________________________ >> From: bioconductor-bounces at stat.math.ethz.ch [bioconductor- bounces at stat.math.ethz.ch] On Behalf Of Vincent Carey [stvjc at channing.harvard.edu] >> Sent: Tuesday, October 05, 2010 11:01 AM >> To: ANJAN PURKAYASTHA >> Cc: bioconductor at stat.math.ethz.ch >> Subject: Re: [BioC] R hanging up on install of BioConductor >> >> There is no evidence of a problem at the bioc server end, so you need >> to consider your >> network connectivity. ?Try to work within R, using install.packages, >> to acquire something small >> like >> >> install.packages("ash") >> >> R "hanging" might indicate that you don't have sufficient connectivity >> to complete the transaction; >> it is not a bioconductor issue. ?Various issues regarding the roles of >> proxies are reviewed in the >> documentation retrieved with ?download.file in R >> >> On Tue, Oct 5, 2010 at 12:14 PM, ANJAN PURKAYASTHA >> <anjan.purkayastha at="" gmail.com=""> wrote: >>> Hi, >>> Am working on ?Mac OS X 10.5.8. Just installed R 2.11.1. >>> Tried to install the base packages of Bioconductor with : >>> >>> source("http://bioconductor.org/biocLite.R") >>> biocLite() >>> >>> >>> R hangs while downloading the various modules. ? Have tried it multiple >>> times (after multiple reinstalls of R) - no success. ?Anybody else having >>> this problem? >>> Thanks, >>> Anjan >>> >>> >>> >>> >>> -- >>> =================================== >>> anjan purkayastha, phd. >>> research associate >>> fas center for systems biology, >>> harvard university >>> 52 oxford street >>> cambridge ma 02138 >>> phone-703.740.6939 >>> =================================== >>> >>> ? ? ? ?[[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 >>> >> >> _______________________________________________ >> 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 >> >> _______________________________________________ >> 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 >> > > > > -- > 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 > -- 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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Thanks all. It does seem to have been a connectivity issue after all. The base package was installed after an hour's wait. Yes, Steve I was using the R GUI; interestingly R was showing as "not responding" on the activitiy monitor as well. Anjan On Tue, Oct 5, 2010 at 3:15 PM, Steve Lianoglou < mailinglist.honeypot@gmail.com> wrote: > Sorry for not finishing that thought, but in short: try running R > through the terminal to see if it reports installation progress > better. > > -steve > > On Tue, Oct 5, 2010 at 3:14 PM, Steve Lianoglou > <mailinglist.honeypot@gmail.com> wrote: > > Also, if you are running R using the R.app GUI, I believe it just > > looks like it's doing nothing when all the install process is going > > on. > > > > It's actually been a long time since I used the GUI (I just run > > through terminal, or emacs), so I'm not sure if this is your problem, > > but I remember it doing that back when I was first using "it" (the > > GUI) and getting into R. > > > > -steve > > > > On Tue, Oct 5, 2010 at 2:36 PM, Hollis Wright <wrighth@ohsu.edu> wrote: > >> For what it's worth, the Fred Hutch mirror does seem to be agonizingly > slow for me at the moment. I switched to the Bethesda mirror with > chooseBioCMirror and setRepositories and it is installing at > >> normal speed. Could be worth a try. > >> > >> Hollis Wright, PhD > >> Oregon Clinical and Translational Research Institute > >> ________________________________________ > >> From: bioconductor-bounces@stat.math.ethz.ch [ > bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Vincent Carey [ > stvjc@channing.harvard.edu] > >> Sent: Tuesday, October 05, 2010 11:01 AM > >> To: ANJAN PURKAYASTHA > >> Cc: bioconductor@stat.math.ethz.ch > >> Subject: Re: [BioC] R hanging up on install of BioConductor > >> > >> There is no evidence of a problem at the bioc server end, so you need > >> to consider your > >> network connectivity. Try to work within R, using install.packages, > >> to acquire something small > >> like > >> > >> install.packages("ash") > >> > >> R "hanging" might indicate that you don't have sufficient connectivity > >> to complete the transaction; > >> it is not a bioconductor issue. Various issues regarding the roles of > >> proxies are reviewed in the > >> documentation retrieved with ?download.file in R > >> > >> On Tue, Oct 5, 2010 at 12:14 PM, ANJAN PURKAYASTHA > >> <anjan.purkayastha@gmail.com> wrote: > >>> Hi, > >>> Am working on Mac OS X 10.5.8. Just installed R 2.11.1. > >>> Tried to install the base packages of Bioconductor with : > >>> > >>> source("http://bioconductor.org/biocLite.R") > >>> biocLite() > >>> > >>> > >>> R hangs while downloading the various modules. Have tried it multiple > >>> times (after multiple reinstalls of R) - no success. Anybody else > having > >>> this problem? > >>> Thanks, > >>> Anjan > >>> > >>> > >>> > >>> > >>> -- > >>> =================================== > >>> anjan purkayastha, phd. > >>> research associate > >>> fas center for systems biology, > >>> harvard university > >>> 52 oxford street > >>> cambridge ma 02138 > >>> phone-703.740.6939 > >>> =================================== > >>> > >>> [[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 > >>> > >> > >> _______________________________________________ > >> 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 > >> > >> _______________________________________________ > >> 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 > >> > > > > > > > > -- > > 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<http: cbio.ms="" kcc.org="" %7elianos="" contact=""> > > > > > > -- > 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<http: cbio.mskc="" c.org="" %7elianos="" contact=""> > -- =================================== anjan purkayastha, phd. research associate fas center for systems biology, harvard university 52 oxford street cambridge ma 02138 phone-703.740.6939 =================================== [[alternative HTML version deleted]]
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