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unable to re-install after interupted installation

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Adaikalavan Ramasamy ★ 1.8k

@adaikalavan-ramasamy-675

Last seen 9.6 years ago

While installing all BioConductor packages, my laptop crashed (forgot to plug it in the power socket). Ever since that, I have not been unable to re-install all the packages. ---------------------------------------------------------------------- --- > source("http://www.bioconductor.org/getBioC.R") > getBioC(libName="all") Running getBioC version 1.2.69.... If you encounter problems, first make sure that you are running the latest version of getBioC() which can be found at: www.bioconductor.org/getBioC.R Please direct any concerns or questions to bioconductor@stat.math.ethz.ch. You are downloading all of the Bioconductor packages and any dependencies. Depending on your system this will be about 160 packages and be roughly 1GB in size. Are you sure that you want to do this? [y/n] y Note: You did not specify a download type. Using a default value of: Source This will be fine for almost all users [1] "Attempting to download GO from http://www.bioconductor.org/data/metaData/" Error in download.file(fileURL, destFile, mode = "wb", quiet = TRUE, method = method) : cannot open URL `http://www.bioconductor.org/data/metaData//./GO_1.6.8.tar.gz' In addition: Warning message: cannot open: HTTP status was `404 Not Found' ---------------------------------------------------------------------- --- Indeed the URL does not exist but where did getBioC get the link from ? Does anyone know how to fix this please. Or is this a file lock issue ( I checked for 00LOCK directory in $R_HOME/lib/R/library/ ) I am using R-2.0.1 and on a Redhat 8.0 (kernel 2.4.18) and gcc 3.2. Thank you very much in advance. Regards, -- Adaikalavan Ramasamy ramasamy@cancer.org.uk Centre for Statistics in Medicine http://www.ihs.ox.ac.uk/csm/ Cancer Research UK Tel : 07906 308 566 Old Road Campus, Headington, Oxford Fax : 01865 226 962

GO GO • 731 views

ADD COMMENT • link updated 19.1 years ago by Seth Falcon ★ 7.4k • written 19.1 years ago by Adaikalavan Ramasamy ★ 1.8k

score 0 · Answer 1 · 2005-03-11

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Seth Falcon ★ 7.4k

@seth-falcon-992

Last seen 9.6 years ago

Hi there, I've just tried what you tried on one of our Linux systems using R-patched. >> source("http://www.bioconductor.org/getBioC.R") >> getBioC(libName="all") It is still installing, but GO at version 1.7.0 installed fine (not the version change which explains the missing URL). Adaikalavan Ramasamy <ramasamy@cancer.org.uk> writes: > While installing all BioConductor packages, my laptop crashed > (forgot to plug it in the power socket). Ever since that, I have not > been unable to re-install all the packages. I have a hunch that the problem is that your first install attempt occured before a site update and so you have some packages installed that are stale. Here are two suggestions to try to fix this: 1. Clean out your library directory of all Bioconductor packages. Since it looks from your mail that you installed to the default package library, you need to be careful not to remove everything, just things that came from Bioconductor. 2. Try installing to a non-default package library. You can do this as follows: 1. Before starting R, set the R_LIBS environment variable: mkdir bioc-pkg-lib export R_LIBS=bioc-pkg-lib R 2. Run getBioC as you did before. You will be given an option to install into bioc-pkg-lib. Let us know if this helps or if the problem persists. Thanks, + seth

ADD COMMENT • link 19.1 years ago Seth Falcon ★ 7.4k

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Dear Seth, Many thanks for your informative suggestion. I think I solved the problem by following Jeff Gentry's suggestion as follows all <- CRAN.packages(CRAN=getOption("BIOC")) install.packages( all, CRAN=getOption("BIOC") ) I am not sure why it worked at all but am just glad it did. I still cannot fully appreciate the need to source the installation script from the web when it could be called directly from R. I thought about your suggestion about wiping out only BioConductor packages but was too lazy to identify them one by one. It would have been a lot easier if R packages were installed in $R_HOME/lib/R/library and BioConductor packages in $R_HOME/lib/BioC/library . If another significant user group like BioConductor comes along, it would make it easier to expand the current R directory structure. Anyway I am sure the BioConductor core have their reasons. Thank you again. Regards, Adai On Fri, 2005-03-11 at 07:49 -0800, Seth Falcon wrote: > Hi there, > > I've just tried what you tried on one of our Linux systems using > R-patched. > > >> source("http://www.bioconductor.org/getBioC.R") > >> getBioC(libName="all") > > It is still installing, but GO at version 1.7.0 installed fine (not > the version change which explains the missing URL). > > Adaikalavan Ramasamy <ramasamy@cancer.org.uk> writes: > > While installing all BioConductor packages, my laptop crashed > > (forgot to plug it in the power socket). Ever since that, I have not > > been unable to re-install all the packages. > > I have a hunch that the problem is that your first install attempt > occured before a site update and so you have some packages installed > that are stale. Here are two suggestions to try to fix this: > > 1. Clean out your library directory of all Bioconductor packages. > Since it looks from your mail that you installed to the default > package library, you need to be careful not to remove everything, > just things that came from Bioconductor. > > 2. Try installing to a non-default package library. You can do this > as follows: > > 1. Before starting R, set the R_LIBS environment variable: > > mkdir bioc-pkg-lib > export R_LIBS=bioc-pkg-lib > R > > 2. Run getBioC as you did before. You will be given an option to > install into bioc-pkg-lib. > > Let us know if this helps or if the problem persists. > > Thanks, > > + seth >

ADD REPLY • link 19.1 years ago Adaikalavan Ramasamy ★ 1.8k