R hanging up on install of BioConductor
1
0
Entering edit mode
@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]]
• 2.3k views
ADD COMMENT •
0
Entering edit mode
@vincent-j-carey-jr-4
Last seen 9 weeks ago
United States
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 >
ADD COMMENT •
0
Entering edit mode
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
ADD REPLY •
0
Entering edit mode
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]]
ADD REPLY •
0
Entering edit mode
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
ADD REPLY •
0
Entering edit mode
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
ADD REPLY •
0
Entering edit mode
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]]
ADD REPLY •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 571 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6