Question: stuck in biocLite("GEOquery")
0
gravatar for Jack Luo
8.8 years ago by
Jack Luo410
Jack Luo410 wrote:
Hi, I am trying to use install GEOquery package in R and type: source("http://bioconductor.org/biocLite.R") biocLite("GEOquery") The sliding bar stops at some point, then I stopped the task and repeat it, then it stops in another place ..., but still not 100%. I keep doing this for many times and it is still not successful yet. For some other packages, I've encountered similar problem before, but at most 3 times I repeated, the download should be 100% finished. Does anyone have similar problem? Thanks, -Jack [[alternative HTML version deleted]]
geoquery • 617 views
ADD COMMENTlink modified 8.8 years ago by Dan Tenenbaum8.2k • written 8.8 years ago by Jack Luo410
Answer: stuck in biocLite("GEOquery")
0
gravatar for Dan Tenenbaum
8.8 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k wrote:
On Fri, Mar 4, 2011 at 10:44 AM, Jack Luo <jluo.rhelp at="" gmail.com=""> wrote: > Hi, > > I am trying to use install GEOquery package in R and type: > > source("http://bioconductor.org/biocLite.R") > biocLite("GEOquery") > > The sliding bar stops at some point, then I stopped the task and repeat it, > then it stops in another place ..., but still not 100%. I keep doing this > for many times and it is still not successful yet. For some other packages, > I've encountered similar problem before, but at most 3 times I repeated, the > download should be 100% finished. > > Does anyone have similar problem? I'm guessing you're on Windows (but you should post the output of sessionInfo() so that we can know this, plus other information helpful to diagnose the problem). I was just able to install GEOquery using biocLite() on windows and it didn't take long. Of course, I am here at FHCRC; you may be encountering network latency issues. Several files may be downloaded when you install GEOquery. If you could let us know which ones seem to be getting stuck, that would also help. Thanks Dan > > Thanks, > > -Jack > > ? ? ? ?[[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 8.8 years ago by Dan Tenenbaum8.2k
Hi Dan, Thanks for your reply. You are right that I am using windows and my OS is win7. Do you think the version of R might be a problem? I use 2.12.2 and the first sentence showing after I type biocLite("GEOquery") is: Using R version 2.12.2, biocinstall version 2.7.4. In addition, I am not clear how to figure out which file(s) get stuck, it just shows a sliding window with something like: xxx/bioc/bin/windows/contrib/2.12/GEO_query2.17.4.zip I looked at the folder with downloaded packages and can not find GEOquery, so I presume it will only show in that folder when all the downloads are complete. The output from sessionInfo() is: R version 2.12.2 (2011-02-25) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.12.2 Thanks a bunch, -Jack On Fri, Mar 4, 2011 at 1:50 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > On Fri, Mar 4, 2011 at 10:44 AM, Jack Luo <jluo.rhelp@gmail.com> wrote: > > Hi, > > > > I am trying to use install GEOquery package in R and type: > > > > source("http://bioconductor.org/biocLite.R") > > biocLite("GEOquery") > > > > The sliding bar stops at some point, then I stopped the task and repeat > it, > > then it stops in another place ..., but still not 100%. I keep doing this > > for many times and it is still not successful yet. For some other > packages, > > I've encountered similar problem before, but at most 3 times I repeated, > the > > download should be 100% finished. > > > > Does anyone have similar problem? > > I'm guessing you're on Windows (but you should post the output of > sessionInfo() so that we can know this, plus other information helpful > to diagnose the problem). > > I was just able to install GEOquery using biocLite() on windows and it > didn't take long. > Of course, I am here at FHCRC; you may be encountering network latency > issues. > > Several files may be downloaded when you install GEOquery. If you > could let us know which ones seem to be getting stuck, that would also > help. > > Thanks > Dan > > > > > > Thanks, > > > > -Jack > > > > [[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 > > > [[alternative HTML version deleted]]
ADD REPLYlink written 8.8 years ago by Jack Luo410
On Fri, Mar 4, 2011 at 11:46 AM, Jack Luo <jluo.rhelp at="" gmail.com=""> wrote: > Hi Dan, > > Thanks for your reply. You are right that I am using windows and my OS is > win7. > Do you think the version of R might be a problem? I use 2.12.2 and the first > sentence showing after I type biocLite("GEOquery") is: > Using R version 2.12.2, biocinstall version 2.7.4. > > In addition, I am not clear how to figure out which file(s) get stuck, it > just shows a sliding window with something like: > xxx/bioc/bin/windows/contrib/2.12/GEO_query2.17.4.zip > > I looked at the folder with downloaded packages and can not find GEOquery, > so I presume it will only show in that folder when all the downloads are > complete. > > The output from sessionInfo() is: > > R version 2.12.2 (2011-02-25) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1252? LC_CTYPE=English_United > States.1252 > [3] LC_MONETARY=English_United States.1252 > LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats???? graphics? grDevices utils???? datasets? methods?? base > > loaded via a namespace (and not attached): > [1] tools_2.12.2 > > Thanks a bunch, > > -Jack Hi Jack, It sounds like a network issue, a timeout perhaps. I'm not sure what else it could be. The repository seems to be working ok. You might try chooseBioCmirror() and see if there is a mirror closer to you, then try installing GEOquery again. Let us know if that works. Dan > > > > On Fri, Mar 4, 2011 at 1:50 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: >> >> On Fri, Mar 4, 2011 at 10:44 AM, Jack Luo <jluo.rhelp at="" gmail.com=""> wrote: >> > Hi, >> > >> > I am trying to use install GEOquery package in R and type: >> > >> > source("http://bioconductor.org/biocLite.R") >> > biocLite("GEOquery") >> > >> > The sliding bar stops at some point, then I stopped the task and repeat >> > it, >> > then it stops in another place ..., but still not 100%. I keep doing >> > this >> > for many times and it is still not successful yet. For some other >> > packages, >> > I've encountered similar problem before, but at most 3 times I repeated, >> > the >> > download should be 100% finished. >> > >> > Does anyone have similar problem? >> >> I'm guessing you're on Windows (but you should post the output of >> sessionInfo() so that we can know this, plus other information helpful >> to diagnose the problem). >> >> I was just able to install GEOquery using biocLite() on windows and it >> didn't take long. >> Of course, I am here at FHCRC; you may be encountering network latency >> issues. >> >> Several files may be downloaded when you install GEOquery. If you >> could let us know which ones seem to be getting stuck, that would also >> help. >> >> Thanks >> Dan >> >> >> > >> > Thanks, >> > >> > -Jack >> > >> > ? ? ? ?[[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 REPLYlink written 8.8 years ago by Dan Tenenbaum8.2k
Answer: stuck in biocLite("GEOquery")
0
gravatar for Dan Tenenbaum
8.8 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k wrote:
On Mon, Mar 7, 2011 at 1:19 PM, Jack Luo <jluo.rhelp at="" gmail.com=""> wrote: > Dan, > > Thanks, it works. I guess it's just the network issue as you mentioned. > > -Jack Thanks, glad to hear it. Are you saying that you can now install GEOquery using the default mirror at bioconductor.org, or that it works after you changed mirrors? Dan > > On Fri, Mar 4, 2011 at 3:36 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: >> >> On Fri, Mar 4, 2011 at 11:46 AM, Jack Luo <jluo.rhelp at="" gmail.com=""> wrote: >> > Hi Dan, >> > >> > Thanks for your reply. You are right that I am using windows and my OS >> > is >> > win7. >> > Do you think the version of R might be a problem? I use 2.12.2 and the >> > first >> > sentence showing after I type biocLite("GEOquery") is: >> > Using R version 2.12.2, biocinstall version 2.7.4. >> > >> > In addition, I am not clear how to figure out which file(s) get stuck, >> > it >> > just shows a sliding window with something like: >> > xxx/bioc/bin/windows/contrib/2.12/GEO_query2.17.4.zip >> > >> > I looked at the folder with downloaded packages and can not find >> > GEOquery, >> > so I presume it will only show in that folder when all the downloads are >> > complete. >> > >> > The output from sessionInfo() is: >> > >> > R version 2.12.2 (2011-02-25) >> > Platform: i386-pc-mingw32/i386 (32-bit) >> > >> > locale: >> > [1] LC_COLLATE=English_United States.1252? LC_CTYPE=English_United >> > States.1252 >> > [3] LC_MONETARY=English_United States.1252 >> > LC_NUMERIC=C >> > [5] LC_TIME=English_United States.1252 >> > >> > attached base packages: >> > [1] stats???? graphics? grDevices utils???? datasets? methods?? base >> > >> > loaded via a namespace (and not attached): >> > [1] tools_2.12.2 >> > >> > Thanks a bunch, >> > >> > -Jack >> >> >> Hi Jack, >> >> It sounds like a network issue, a timeout perhaps. I'm not sure what >> else it could be. The repository seems to be working ok. >> >> You might try chooseBioCmirror() and see if there is a mirror closer >> to you, then try installing GEOquery again. >> >> Let us know if that works. >> Dan >> >> >> > >> > >> > >> > On Fri, Mar 4, 2011 at 1:50 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> >> > wrote: >> >> >> >> On Fri, Mar 4, 2011 at 10:44 AM, Jack Luo <jluo.rhelp at="" gmail.com=""> wrote: >> >> > Hi, >> >> > >> >> > I am trying to use install GEOquery package in R and type: >> >> > >> >> > source("http://bioconductor.org/biocLite.R") >> >> > biocLite("GEOquery") >> >> > >> >> > The sliding bar stops at some point, then I stopped the task and >> >> > repeat >> >> > it, >> >> > then it stops in another place ..., but still not 100%. I keep doing >> >> > this >> >> > for many times and it is still not successful yet. For some other >> >> > packages, >> >> > I've encountered similar problem before, but at most 3 times I >> >> > repeated, >> >> > the >> >> > download should be 100% finished. >> >> > >> >> > Does anyone have similar problem? >> >> >> >> I'm guessing you're on Windows (but you should post the output of >> >> sessionInfo() so that we can know this, plus other information helpful >> >> to diagnose the problem). >> >> >> >> I was just able to install GEOquery using biocLite() on windows and it >> >> didn't take long. >> >> Of course, I am here at FHCRC; you may be encountering network latency >> >> issues. >> >> >> >> Several files may be downloaded when you install GEOquery. If you >> >> could let us know which ones seem to be getting stuck, that would also >> >> help. >> >> >> >> Thanks >> >> Dan >> >> >> >> >> >> > >> >> > Thanks, >> >> > >> >> > -Jack >> >> > >> >> > ? ? ? ?[[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 8.8 years ago by Dan Tenenbaum8.2k
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