package ‘DAVIDQuery’ is not available (for R version 2.14.0)
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k. brand ▴ 420
@k-brand-1874
Last seen 9.9 years ago
Esteemed BioC UseRs and Devs, I'm trying (and failing) to install the BioC package "DAVIDQuery". There must be a simple way to solve this issue, but my googling failed to solve this issue. Within (ESS/Emacs) R --vanilla i tried: > install.packages("DAVIDQuery", dependencies=TRUE) Installing package(s) into ?/home/kbrand/R/x86_64-pc-linux-gnu- library/2.13? (as ?lib? is unspecified) --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done Warning message: In getDependencies(pkgs, dependencies, available, lib) : package ?DAVIDQuery? is not available (for R version 2.14.0) > This makes me wonder if i need to specify a different library (path). If so, which one? > .libPaths() [1] "/home/kbrand/R/x86_64-pc-linux-gnu-library/2.13" [2] "/usr/local/lib/R/site-library" [3] "/usr/lib/R/site-library" [4] "/usr/lib/R/library" (This is a bigger area of ignorance for me - why has R set up four separate libraries by default? Where some require use of sudo to install/update packages, whilst others do not? And what are the implications when it comes time to upgrade to the next version of R? I have obtained some advice on this before - https://stat.ethz.ch/pipermail/ess-help/2011-September/007120.html - but have failed to implement this given my focus on just using R, neglecting its proper maintenance, and all round inexperience with linux). I'd really appreciate responses on getting "DAVIDQuery" running on my currently installed R 2.14.0 (as well as any tips on 'good practice' when it comes to R library management on linux (ubuntu)). Sincerely, Karl > sessionInfo() R version 2.14.0 (2011-10-31) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_DK.UTF-8" LC_COLLATE=en_AU.UTF-8 [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tcltk_2.14.0 tools_2.14.0 > -- Karl Brand <k.brand at="" erasmusmc.nl=""> Department of Genetics Erasmus MC Dr Molewaterplein 50 3015 GE Rotterdam P +31 (0)10 704 3455 | F +31 (0)10 704 4743 | M +31 (0)642 777 268
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@dan-tenenbaum-4957
Last seen 9.8 years ago
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Hi Karl, On Nov 23, 2011 8:38 AM, "Karl Brand" <k.brand@erasmusmc.nl> wrote: > > > Esteemed BioC UseRs and Devs, > > I'm trying (and failing) to install the BioC package "DAVIDQuery". There must be a simple way to solve this issue, but my googling failed to solve this issue. > > Within (ESS/Emacs) R --vanilla i tried: > > > install.packages("DAVIDQuery", dependencies=TRUE) > Installing package(s) into ‘/home/kbrand/R/x86_64-pc-linux-gnu-library/2.13’ > (as ‘lib’ is unspecified) > --- Please select a CRAN mirror for use in this session --- > Loading Tcl/Tk interface ... done > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > package ‘DAVIDQuery’ is not available (for R version 2.14.0) > > DAVIDQuery is not a CRAN package. As with all Bioconductor packages, you should install it as follows: source("http://bioconductor.org/biocLite.R") biocLite("DAVIDQuery") Dan > > This makes me wonder if i need to specify a different library (path). If so, which one? > > > .libPaths() > [1] "/home/kbrand/R/x86_64-pc-linux-gnu-library/2.13" > [2] "/usr/local/lib/R/site-library" > [3] "/usr/lib/R/site-library" > [4] "/usr/lib/R/library" > > (This is a bigger area of ignorance for me - why has R set up four separate libraries by default? Where some require use of sudo to install/update packages, whilst others do not? And what are the implications when it comes time to upgrade to the next version of R? I have obtained some advice on this before - https://stat.ethz.ch/pipermail/ess-help/2011-September/007120.html - but have failed to implement this given my focus on just using R, neglecting its proper maintenance, and all round inexperience with linux). > > I'd really appreciate responses on getting "DAVIDQuery" running on my currently installed R 2.14.0 (as well as any tips on 'good practice' when it comes to R library management on linux (ubuntu)). > > Sincerely, > > Karl > > > sessionInfo() > R version 2.14.0 (2011-10-31) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_DK.UTF-8" LC_COLLATE=en_AU.UTF-8 > [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tcltk_2.14.0 tools_2.14.0 > > > > -- > Karl Brand <k.brand@erasmusmc.nl> > Department of Genetics > Erasmus MC > Dr Molewaterplein 50 > 3015 GE Rotterdam > P +31 (0)10 704 3455 | F +31 (0)10 704 4743 | M +31 (0)642 777 268 > > _______________________________________________ > 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]]
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@martin-morgan-1513
Last seen 7 days ago
United States
On 11/23/2011 08:34 AM, Karl Brand wrote: > > Esteemed BioC UseRs and Devs, > > I'm trying (and failing) to install the BioC package "DAVIDQuery". There > must be a simple way to solve this issue, but my googling failed to > solve this issue. > > Within (ESS/Emacs) R --vanilla i tried: > > > install.packages("DAVIDQuery", dependencies=TRUE) > Installing package(s) into > ?/home/kbrand/R/x86_64-pc-linux-gnu-library/2.13? > (as ?lib? is unspecified) > --- Please select a CRAN mirror for use in this session --- > Loading Tcl/Tk interface ... done > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > package ?DAVIDQuery? is not available (for R version 2.14.0) DAVIDQuery is a Bioconductor package, but it sounds like you're choosing a 'CRAN' archive. The recommended installation process is source("http://bioconductor.org/biocLite.R") biocLite("DAVIDQuery") > > > > This makes me wonder if i need to specify a different library (path). If > so, which one? > > > .libPaths() > [1] "/home/kbrand/R/x86_64-pc-linux-gnu-library/2.13" > [2] "/usr/local/lib/R/site-library" > [3] "/usr/lib/R/site-library" > [4] "/usr/lib/R/library" That there are four is due to someone / thing other than R; see ?Startup for hints on how these libraries are identified. Martin > > (This is a bigger area of ignorance for me - why has R set up four > separate libraries by default? Where some require use of sudo to > install/update packages, whilst others do not? And what are the > implications when it comes time to upgrade to the next version of R? I > have obtained some advice on this before - > https://stat.ethz.ch/pipermail/ess-help/2011-September/007120.html - but > have failed to implement this given my focus on just using R, neglecting > its proper maintenance, and all round inexperience with linux). > > I'd really appreciate responses on getting "DAVIDQuery" running on my > currently installed R 2.14.0 (as well as any tips on 'good practice' > when it comes to R library management on linux (ubuntu)). > > Sincerely, > > Karl > > > sessionInfo() > R version 2.14.0 (2011-10-31) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_DK.UTF-8" LC_COLLATE=en_AU.UTF-8 > [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tcltk_2.14.0 tools_2.14.0 > > > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
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Hi Karl Are you using Ubuntu? I just looked at my installation and see the same four libs. I wonder if this is due to initially installing R from the official Ubuntu repos and then updating R (to the current version) using the CRAN repos? Just a thought. Best Iain ________________________________ From: Martin Morgan <mtmorgan@fhcrc.org> To: Karl Brand <k.brand@erasmusmc.nl> Cc: bioconductor@r-project.org Sent: Wednesday, 23 November 2011, 17:39 Subject: Re: [BioC] package ‘DAVIDQuery’ is not available (for R version 2.14.0) On 11/23/2011 08:34 AM, Karl Brand wrote: > > Esteemed BioC UseRs and Devs, > > I'm trying (and failing) to install the BioC package "DAVIDQuery". There > must be a simple way to solve this issue, but my googling failed to > solve this issue. > > Within (ESS/Emacs) R --vanilla i tried: > >  > install.packages("DAVIDQuery", dependencies=TRUE) > Installing package(s) into > ‘/home/kbrand/R/x86_64-pc-linux-gnu-library/2.13’ > (as ‘lib’ is unspecified) > --- Please select a CRAN mirror for use in this session --- > Loading Tcl/Tk interface ... done > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > package ‘DAVIDQuery’ is not available (for R version 2.14.0) DAVIDQuery is a Bioconductor package, but it sounds like you're choosing a 'CRAN' archive. The recommended installation process is   source("http://bioconductor.org/biocLite.R")   biocLite("DAVIDQuery") >  > > > This makes me wonder if i need to specify a different library (path). If > so, which one? > >  > .libPaths() > [1] "/home/kbrand/R/x86_64-pc-linux-gnu-library/2.13" > [2] "/usr/local/lib/R/site-library" > [3] "/usr/lib/R/site-library" > [4] "/usr/lib/R/library" That there are four is due to someone / thing other than R; see ?Startup for hints on how these libraries are identified. Martin > > (This is a bigger area of ignorance for me - why has R set up four > separate libraries by default? Where some require use of sudo to > install/update packages, whilst others do not? And what are the > implications when it comes time to upgrade to the next version of R? I > have obtained some advice on this before - > https://stat.ethz.ch/pipermail/ess-help/2011-September/007120.html - but > have failed to implement this given my focus on just using R, neglecting > its proper maintenance, and all round inexperience with linux). > > I'd really appreciate responses on getting "DAVIDQuery" running on my > currently installed R 2.14.0 (as well as any tips on 'good practice' > when it comes to R library management on linux (ubuntu)). > > Sincerely, > > Karl > >  > sessionInfo() > R version 2.14.0 (2011-10-31) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_DK.UTF-8" LC_COLLATE=en_AU.UTF-8 > [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tcltk_2.14.0 tools_2.14.0 >  > > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793 _______________________________________________ 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]]
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Hi Iain, (Martin and James), Yes, Ubuntu. Yes, i've upgraded R versions at least once, and ubuntu version once. Also given @Martin's comments, this could be the outcome of working with R on Ubuntu without paying attention to what goes where during package installation and R upgrading (as applies to here). @James' suggestion to manually download and install packages will solve this issue as well as the appealing avoidance of using sudo. Definitely worth trying out. thanks again for sharing these thoughts, Karl On 2011-11-23 20:21, Iain Gallagher wrote: > Hi Karl > > Are you using Ubuntu? I just looked at my installation and see the same four libs. I wonder if this is due to initially installing R from the official Ubuntu repos and then updating R (to the current version) using the CRAN repos? > > Just a thought. > > Best > > Iain > > > > ________________________________ > From: Martin Morgan<mtmorgan at="" fhcrc.org=""> > To: Karl Brand<k.brand at="" erasmusmc.nl=""> > Cc: bioconductor at r-project.org > Sent: Wednesday, 23 November 2011, 17:39 > Subject: Re: [BioC] package ???DAVIDQuery??? is not available (for R version 2.14.0) > > On 11/23/2011 08:34 AM, Karl Brand wrote: >> >> Esteemed BioC UseRs and Devs, >> >> I'm trying (and failing) to install the BioC package "DAVIDQuery". There >> must be a simple way to solve this issue, but my googling failed to >> solve this issue. >> >> Within (ESS/Emacs) R --vanilla i tried: >> >> ?> install.packages("DAVIDQuery", dependencies=TRUE) >> Installing package(s) into >> ???/home/kbrand/R/x86_64-pc-linux-gnu-library/2.13??? >> (as ???lib??? is unspecified) >> --- Please select a CRAN mirror for use in this session --- >> Loading Tcl/Tk interface ... done >> Warning message: >> In getDependencies(pkgs, dependencies, available, lib) : >> package ???DAVIDQuery??? is not available (for R version 2.14.0) > > DAVIDQuery is a Bioconductor package, but it sounds like you're choosing > a 'CRAN' archive. The recommended installation process is > > ? source("http://bioconductor.org/biocLite.R") > ? biocLite("DAVIDQuery") > > >> ?> >> >> This makes me wonder if i need to specify a different library (path). If >> so, which one? >> >> ?> .libPaths() >> [1] "/home/kbrand/R/x86_64-pc-linux-gnu-library/2.13" >> [2] "/usr/local/lib/R/site-library" >> [3] "/usr/lib/R/site-library" >> [4] "/usr/lib/R/library" > > That there are four is due to someone / thing other than R; see ?Startup > for hints on how these libraries are identified. > > Martin > >> >> (This is a bigger area of ignorance for me - why has R set up four >> separate libraries by default? Where some require use of sudo to >> install/update packages, whilst others do not? And what are the >> implications when it comes time to upgrade to the next version of R? I >> have obtained some advice on this before - >> https://stat.ethz.ch/pipermail/ess-help/2011-September/007120.html - but >> have failed to implement this given my focus on just using R, neglecting >> its proper maintenance, and all round inexperience with linux). >> >> I'd really appreciate responses on getting "DAVIDQuery" running on my >> currently installed R 2.14.0 (as well as any tips on 'good practice' >> when it comes to R library management on linux (ubuntu)). >> >> Sincerely, >> >> Karl >> >> ?> sessionInfo() >> R version 2.14.0 (2011-10-31) >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_DK.UTF-8" LC_COLLATE=en_AU.UTF-8 >> [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> loaded via a namespace (and not attached): >> [1] tcltk_2.14.0 tools_2.14.0 >> ?> >> > > > > > _______________________________________________ > 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 -- Karl Brand <k.brand at="" erasmusmc.nl=""> Department of Genetics Erasmus MC Dr Molewaterplein 50 3015 GE Rotterdam P +31 (0)10 704 3455 | F +31 (0)10 704 4743 | M +31 (0)642 777 268
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Thank you Dan, James, Martin re. DAVIDQuery. Ok, install.packages() was NOT a good start, but a lesson i think i'll remember thanks to the surprisingly restrained pointers :) But within either emacs/ess or a terminal running "sudo R --vanilla" i fail to install "DAVIDQueary" using: source("http://www.bioconductor.org/biocLite.R") biocLite("DAVIDQuery"). FWIW, the output from the emacs/ess session, and below that, from the terminal (near identical) at the bottom of this message. To my inexperienced eye - this seems to be where the problems begin: checking for curl-config... no Cannot find curl-config ERROR: configuration failed for package ?RCurl? I found this with google: http://www.omegahat.org/RCurl/FAQ.html Which suggests that i verify the presence of libcurl on my system, and if present, point R to it. 'locate libcurl' returns several lines of locations and files, including: /usr/lib32/libcurl.so Now i'm guessing pointing R's "PATH" variable to /usr/lib32 will solve my problems. What is the most appropriate way to do this? Presently i have: > Sys.getenv("PATH") [1] "/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/gam es" How do i add "/usr/lib32" to this? > help(Startup) Contains a lot of info that i don't feel experienced enough to act on (without buggering up what is otherwise working). Would anyone here at BioC care to share their thoughts on how to (persistently) add to R's search path? This is probably what's needed to close this thread, although i understand it may now be a Q for the general [R] forum. With thanks in advance for further patient responders, Karl ################# ess/emacs output ##################### > .help.ESS <- help > options(STERM='iESS', editor='emacsclient') > source("http://www.bioconductor.org/biocLite.R") BiocInstaller version 1.2.1, ?biocLite for help > biocLite("DAVIDQuery") BioC_mirror: 'http://www.bioconductor.org' Using R version 2.14, BiocInstaller version 1.2.1. Installing package(s) 'DAVIDQuery' Installing package(s) into ?/home/kbrand/R/x86_64-pc-linux-gnu- library/2.13? (as ?lib? is unspecified) also installing the dependency ?RCurl? trying URL 'http://cran.fhcrc.org/src/contrib/RCurl_1.7-0.tar.gz' Content type 'application/x-gzip' length 813252 bytes (794 Kb) opened URL ================================================== downloaded 794 Kb trying URL 'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/DAVIDQuery_ 1.14.0.tar.gz' Content type 'application/x-gzip' length 186887 bytes (182 Kb) opened URL ================================================== downloaded 182 Kb * installing *source* package ?RCurl? ... ** package ?RCurl? successfully unpacked and MD5 sums checked checking for curl-config... no Cannot find curl-config ERROR: configuration failed for package ?RCurl? * removing ?/home/kbrand/R/x86_64-pc-linux-gnu-library/2.13/RCurl? ERROR: dependency ?RCurl? is not available for package ?DAVIDQuery? * removing ?/home/kbrand/R/x86_64-pc-linux-gnu- library/2.13/DAVIDQuery? The downloaded packages are in ?/tmp/RtmpgNN770/downloaded_packages? Warning messages: 1: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package ?RCurl? had non-zero exit status 2: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package ?DAVIDQuery? had non-zero exit status > sessionInfo() R version 2.14.0 (2011-10-31) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_DK.UTF-8" LC_COLLATE=en_AU.UTF-8 [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.2.1 loaded via a namespace (and not attached): [1] tools_2.14.0 > ######################### terminal output ################## kbrand at kbrand:~$ sudo R --vanilla [sudo] password for kbrand: R version 2.14.0 (2011-10-31) Copyright (C) 2011 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > source("http://www.bioconductor.org/biocLite.R") BiocInstaller version 1.2.1, ?biocLite for help > biocLite("DAVIDQuery") BioC_mirror: 'http://www.bioconductor.org' Using R version 2.14, BiocInstaller version 1.2.1. Installing package(s) 'DAVIDQuery' Installing package(s) into ?/home/kbrand/R/x86_64-pc-linux-gnu- library/2.13? (as ?lib? is unspecified) also installing the dependency ?RCurl? trying URL 'http://cran.fhcrc.org/src/contrib/RCurl_1.7-0.tar.gz' Content type 'application/x-gzip' length 813252 bytes (794 Kb) opened URL ================================================== downloaded 794 Kb trying URL 'http://www.bioconductor.org/packages/2.9/bioc/src/contrib/DAVIDQuery_ 1.14.0.tar.gz' Content type 'application/x-gzip' length 186887 bytes (182 Kb) opened URL ================================================== downloaded 182 Kb * installing *source* package ?RCurl? ... ** package ?RCurl? successfully unpacked and MD5 sums checked checking for curl-config... no Cannot find curl-config ERROR: configuration failed for package ?RCurl? * removing ?/home/kbrand/R/x86_64-pc-linux-gnu-library/2.13/RCurl? ERROR: dependency ?RCurl? is not available for package ?DAVIDQuery? * removing ?/home/kbrand/R/x86_64-pc-linux-gnu- library/2.13/DAVIDQuery? The downloaded packages are in ?/tmp/RtmpI5FdwF/downloaded_packages? Warning messages: 1: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package ?RCurl? had non-zero exit status 2: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package ?DAVIDQuery? had non-zero exit status > sessionInfo() R version 2.14.0 (2011-10-31) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_DK.UTF-8" LC_COLLATE=en_AU.UTF-8 [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.2.1 loaded via a namespace (and not attached): [1] tools_2.14.0 > On 2011-11-23 18:39, Martin Morgan wrote: > On 11/23/2011 08:34 AM, Karl Brand wrote: >> >> Esteemed BioC UseRs and Devs, >> >> I'm trying (and failing) to install the BioC package "DAVIDQuery". There >> must be a simple way to solve this issue, but my googling failed to >> solve this issue. >> >> Within (ESS/Emacs) R --vanilla i tried: >> >> > install.packages("DAVIDQuery", dependencies=TRUE) >> Installing package(s) into >> ?/home/kbrand/R/x86_64-pc-linux-gnu-library/2.13? >> (as ?lib? is unspecified) >> --- Please select a CRAN mirror for use in this session --- >> Loading Tcl/Tk interface ... done >> Warning message: >> In getDependencies(pkgs, dependencies, available, lib) : >> package ?DAVIDQuery? is not available (for R version 2.14.0) > > DAVIDQuery is a Bioconductor package, but it sounds like you're choosing > a 'CRAN' archive. The recommended installation process is > > source("http://bioconductor.org/biocLite.R") > biocLite("DAVIDQuery") > > >> > >> >> This makes me wonder if i need to specify a different library (path). If >> so, which one? >> >> > .libPaths() >> [1] "/home/kbrand/R/x86_64-pc-linux-gnu-library/2.13" >> [2] "/usr/local/lib/R/site-library" >> [3] "/usr/lib/R/site-library" >> [4] "/usr/lib/R/library" > > That there are four is due to someone / thing other than R; see ?Startup > for hints on how these libraries are identified. > > Martin > >> >> (This is a bigger area of ignorance for me - why has R set up four >> separate libraries by default? Where some require use of sudo to >> install/update packages, whilst others do not? And what are the >> implications when it comes time to upgrade to the next version of R? I >> have obtained some advice on this before - >> https://stat.ethz.ch/pipermail/ess-help/2011-September/007120.html - but >> have failed to implement this given my focus on just using R, neglecting >> its proper maintenance, and all round inexperience with linux). >> >> I'd really appreciate responses on getting "DAVIDQuery" running on my >> currently installed R 2.14.0 (as well as any tips on 'good practice' >> when it comes to R library management on linux (ubuntu)). >> >> Sincerely, >> >> Karl >> >> > sessionInfo() >> R version 2.14.0 (2011-10-31) >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_DK.UTF-8" LC_COLLATE=en_AU.UTF-8 >> [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> loaded via a namespace (and not attached): >> [1] tcltk_2.14.0 tools_2.14.0 >> > >> > > -- Karl Brand <k.brand at="" erasmusmc.nl=""> Department of Genetics Erasmus MC Dr Molewaterplein 50 3015 GE Rotterdam P +31 (0)10 704 3455 | F +31 (0)10 704 4743 | M +31 (0)642 777 268
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Hi Karl, When I've encounted this problem with installing the RCurl package on Ubuntu I've found that the following installed the appropriate libraries: apt-get install libcurl4-openssl-dev I didn't have to change R's path or anything like that. Hope it helps, Mike On Thu, Nov 24, 2011 at 2:51 PM, Karl Brand <k.brand@erasmusmc.nl> wrote: > Thank you Dan, James, Martin re. DAVIDQuery. > > Ok, install.packages() was NOT a good start, but a lesson i think i'll > remember thanks to the surprisingly restrained pointers :) > > But within either emacs/ess or a terminal running "sudo R --vanilla" i > fail to install "DAVIDQueary" using: > > source("http://www.**bioconductor.org/biocLite.R<http: www.biocondu="" ctor.org="" bioclite.r=""> > ") > biocLite("DAVIDQuery"). > > FWIW, the output from the emacs/ess session, and below that, from the > terminal (near identical) at the bottom of this message. > > To my inexperienced eye - this seems to be where the problems begin: > > checking for curl-config... no > Cannot find curl-config > ERROR: configuration failed for package ‘RCurl’ > > I found this with google: http://www.omegahat.org/RCurl/**FAQ.html<h ttp:="" www.omegahat.org="" rcurl="" faq.html=""> > > Which suggests that i verify the presence of libcurl on my system, and if > present, point R to it. 'locate libcurl' returns several lines of locations > and files, including: /usr/lib32/libcurl.so > > Now i'm guessing pointing R's "PATH" variable to /usr/lib32 will solve my > problems. What is the most appropriate way to do this? Presently i have: > > > Sys.getenv("PATH") > [1] "/usr/local/sbin:/usr/local/**bin:/usr/sbin:/usr/bin:/sbin:/** > bin:/usr/games" > > How do i add "/usr/lib32" to this? > > > help(Startup) > > Contains a lot of info that i don't feel experienced enough to act on > (without buggering up what is otherwise working). Would anyone here at BioC > care to share their thoughts on how to (persistently) add to R's search > path? This is probably what's needed to close this thread, although i > understand it may now be a Q for the general [R] forum. > > With thanks in advance for further patient responders, > > Karl > > > > ################# ess/emacs output ##################### > > > .help.ESS <- help > > options(STERM='iESS', editor='emacsclient') > > source("http://www.**bioconductor.org/biocLite.R<http: www.biocon="" ductor.org="" bioclite.r=""> > ") > BiocInstaller version 1.2.1, ?biocLite for help > > biocLite("DAVIDQuery") > BioC_mirror: 'http://www.bioconductor.org' > Using R version 2.14, BiocInstaller version 1.2.1. > Installing package(s) 'DAVIDQuery' > > Installing package(s) into ‘/home/kbrand/R/x86_64-pc-** > linux-gnu-library/2.13’ > (as ‘lib’ is unspecified) > also installing the dependency ‘RCurl’ > > trying URL 'http://cran.fhcrc.org/src/**contrib/RCurl_1.7-0.tar.gz<h ttp:="" cran.fhcrc.org="" src="" contrib="" rcurl_1.7-0.tar.gz=""> > ' > Content type 'application/x-gzip' length 813252 bytes (794 Kb) > opened URL > ==============================**==================== > downloaded 794 Kb > > trying URL 'http://www.bioconductor.org/**packages/2.9/bioc/src/contrib/** > DAVIDQuery_1.14.0.tar.gz<http: www.bioconductor.org="" packages="" 2.9="" bi="" oc="" src="" contrib="" davidquery_1.14.0.tar.gz=""> > ' > Content type 'application/x-gzip' length 186887 bytes (182 Kb) > opened URL > ==============================**==================== > downloaded 182 Kb > > * installing *source* package ‘RCurl’ ... > ** package ‘RCurl’ successfully unpacked and MD5 sums checked > checking for curl-config... no > Cannot find curl-config > ERROR: configuration failed for package ‘RCurl’ > * removing ‘/home/kbrand/R/x86_64-pc-**linux-gnu-library/2.13/RCurl’ > ERROR: dependency ‘RCurl’ is not available for package ‘DAVIDQuery’ > * removing ‘/home/kbrand/R/x86_64-pc-**linux-gnu-library/2.13/** > DAVIDQuery’ > > The downloaded packages are in > ‘/tmp/RtmpgNN770/downloaded_**packages’ > Warning messages: > 1: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package ‘RCurl’ had non-zero exit status > 2: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package ‘DAVIDQuery’ had non-zero exit status > > > sessionInfo() > R version 2.14.0 (2011-10-31) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_DK.UTF-8" LC_COLLATE=en_AU.UTF-8 > [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.2.1 > > > loaded via a namespace (and not attached): > [1] tools_2.14.0 > > > ######################### terminal output ################## > > kbrand@kbrand:~$ sudo R --vanilla > [sudo] password for kbrand: > > R version 2.14.0 (2011-10-31) > Copyright (C) 2011 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > Platform: x86_64-pc-linux-gnu (64-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > > > source("http://www.**bioconductor.org/biocLite.R<http: www.biocon="" ductor.org="" bioclite.r=""> > ") > BiocInstaller version 1.2.1, ?biocLite for help > > biocLite("DAVIDQuery") > BioC_mirror: 'http://www.bioconductor.org' > Using R version 2.14, BiocInstaller version 1.2.1. > Installing package(s) 'DAVIDQuery' > > Installing package(s) into ‘/home/kbrand/R/x86_64-pc-** > linux-gnu-library/2.13’ > (as ‘lib’ is unspecified) > also installing the dependency ‘RCurl’ > > trying URL 'http://cran.fhcrc.org/src/**contrib/RCurl_1.7-0.tar.gz<h ttp:="" cran.fhcrc.org="" src="" contrib="" rcurl_1.7-0.tar.gz=""> > ' > Content type 'application/x-gzip' length 813252 bytes (794 Kb) > opened URL > ==============================**==================== > downloaded 794 Kb > > trying URL 'http://www.bioconductor.org/**packages/2.9/bioc/src/contrib/** > DAVIDQuery_1.14.0.tar.gz<http: www.bioconductor.org="" packages="" 2.9="" bi="" oc="" src="" contrib="" davidquery_1.14.0.tar.gz=""> > ' > Content type 'application/x-gzip' length 186887 bytes (182 Kb) > opened URL > ==============================**==================== > downloaded 182 Kb > > * installing *source* package ‘RCurl’ ... > ** package ‘RCurl’ successfully unpacked and MD5 sums checked > checking for curl-config... no > Cannot find curl-config > ERROR: configuration failed for package ‘RCurl’ > * removing ‘/home/kbrand/R/x86_64-pc-**linux-gnu-library/2.13/RCurl’ > ERROR: dependency ‘RCurl’ is not available for package ‘DAVIDQuery’ > * removing ‘/home/kbrand/R/x86_64-pc-**linux-gnu-library/2.13/** > DAVIDQuery’ > > The downloaded packages are in > ‘/tmp/RtmpI5FdwF/downloaded_**packages’ > Warning messages: > 1: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package ‘RCurl’ had non-zero exit status > 2: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package ‘DAVIDQuery’ had non-zero exit status > > > sessionInfo() > R version 2.14.0 (2011-10-31) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_DK.UTF-8" LC_COLLATE=en_AU.UTF-8 > [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.2.1 > > > loaded via a namespace (and not attached): > [1] tools_2.14.0 > > > > > > > > > On 2011-11-23 18:39, Martin Morgan wrote: > >> On 11/23/2011 08:34 AM, Karl Brand wrote: >> >>> >>> Esteemed BioC UseRs and Devs, >>> >>> I'm trying (and failing) to install the BioC package "DAVIDQuery". There >>> must be a simple way to solve this issue, but my googling failed to >>> solve this issue. >>> >>> Within (ESS/Emacs) R --vanilla i tried: >>> >>> > install.packages("DAVIDQuery", dependencies=TRUE) >>> Installing package(s) into >>> ‘/home/kbrand/R/x86_64-pc-**linux-gnu-library/2.13’ >>> (as ‘lib’ is unspecified) >>> --- Please select a CRAN mirror for use in this session --- >>> Loading Tcl/Tk interface ... done >>> Warning message: >>> In getDependencies(pkgs, dependencies, available, lib) : >>> package ‘DAVIDQuery’ is not available (for R version 2.14.0) >>> >> >> DAVIDQuery is a Bioconductor package, but it sounds like you're choosing >> a 'CRAN' archive. The recommended installation process is >> >> source("http://bioconductor.**org/biocLite.R<http: bioconductor.or="" g="" bioclite.r=""> >> ") >> biocLite("DAVIDQuery") >> >> >> > >>> >>> This makes me wonder if i need to specify a different library (path). If >>> so, which one? >>> >>> > .libPaths() >>> [1] "/home/kbrand/R/x86_64-pc-**linux-gnu-library/2.13" >>> [2] "/usr/local/lib/R/site-**library" >>> [3] "/usr/lib/R/site-library" >>> [4] "/usr/lib/R/library" >>> >> >> That there are four is due to someone / thing other than R; see ?Startup >> for hints on how these libraries are identified. >> >> Martin >> >> >>> (This is a bigger area of ignorance for me - why has R set up four >>> separate libraries by default? Where some require use of sudo to >>> install/update packages, whilst others do not? And what are the >>> implications when it comes time to upgrade to the next version of R? I >>> have obtained some advice on this before - >>> https://stat.ethz.ch/**pipermail/ess- help/2011-**September/007120.html<https: stat.ethz.ch="" pipermail="" ess-="" help="" 2011-september="" 007120.html="">- but >>> have failed to implement this given my focus on just using R, neglecting >>> its proper maintenance, and all round inexperience with linux). >>> >>> I'd really appreciate responses on getting "DAVIDQuery" running on my >>> currently installed R 2.14.0 (as well as any tips on 'good practice' >>> when it comes to R library management on linux (ubuntu)). >>> >>> Sincerely, >>> >>> Karl >>> >>> > sessionInfo() >>> R version 2.14.0 (2011-10-31) >>> Platform: x86_64-pc-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_DK.UTF-8" LC_COLLATE=en_AU.UTF-8 >>> [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 >>> [7] LC_PAPER=C LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> loaded via a namespace (and not attached): >>> [1] tcltk_2.14.0 tools_2.14.0 >>> > >>> >>> >> >> > -- > Karl Brand <k.brand@erasmusmc.nl> > Department of Genetics > Erasmus MC > Dr Molewaterplein 50 > 3015 GE Rotterdam > P +31 (0)10 704 3455 | F +31 (0)10 704 4743 | M +31 (0)642 777 268 > > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > -- Mike Smith PhD Student Computational Biology Group Cambridge University [[alternative HTML version deleted]]
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Hi Mike, "sudo apt-get install libcurl4-openssl-dev" Solved the problem :) I now have: > library("DAVIDQuery") Loading required package: RCurl Loading required package: bitops This is DAVIDQuery Version 1.14.0 2010-06-10 > Many thanks! I'd still appreciate a tip on appropriate ways to add to R's PATH if and when the time comes (must be inevitable...) Karl On 2011-11-24 17:04, Mike Smith wrote: > Hi Karl, > > When I've encounted this problem with installing the RCurl package on > Ubuntu I've found that the following installed the appropriate libraries: > > apt-get install libcurl4-openssl-dev > > I didn't have to change R's path or anything like that. > > Hope it helps, > Mike > > On Thu, Nov 24, 2011 at 2:51 PM, Karl Brand <k.brand at="" erasmusmc.nl=""> <mailto:k.brand at="" erasmusmc.nl="">> wrote: > > Thank you Dan, James, Martin re. DAVIDQuery. > > Ok, install.packages() was NOT a good start, but a lesson i think > i'll remember thanks to the surprisingly restrained pointers :) > > But within either emacs/ess or a terminal running "sudo R --vanilla" > i fail to install "DAVIDQueary" using: > > source("http://www.__bioconductor.org/biocLite.R > <http: www.bioconductor.org="" bioclite.r="">") > biocLite("DAVIDQuery"). > > FWIW, the output from the emacs/ess session, and below that, from > the terminal (near identical) at the bottom of this message. > > To my inexperienced eye - this seems to be where the problems begin: > > checking for curl-config... no > Cannot find curl-config > ERROR: configuration failed for package ?RCurl? > > I found this with google: http://www.omegahat.org/RCurl/__FAQ.html > <http: www.omegahat.org="" rcurl="" faq.html=""> > > Which suggests that i verify the presence of libcurl on my system, > and if present, point R to it. 'locate libcurl' returns several > lines of locations and files, including: /usr/lib32/libcurl.so > > Now i'm guessing pointing R's "PATH" variable to /usr/lib32 will > solve my problems. What is the most appropriate way to do this? > Presently i have: > > > Sys.getenv("PATH") > [1] > "/usr/local/sbin:/usr/local/__bin:/usr/sbin:/usr/bin:/sbin:/__bi n:/usr/games" > > How do i add "/usr/lib32" to this? > > > help(Startup) > > Contains a lot of info that i don't feel experienced enough to act > on (without buggering up what is otherwise working). Would anyone > here at BioC care to share their thoughts on how to (persistently) > add to R's search path? This is probably what's needed to close this > thread, although i understand it may now be a Q for the general [R] > forum. > > With thanks in advance for further patient responders, > > Karl > > > > ################# ess/emacs output ##################### > > > .help.ESS <- help > > options(STERM='iESS', editor='emacsclient') > > source("http://www.__bioconductor.org/biocLite.R > <http: www.bioconductor.org="" bioclite.r="">") > BiocInstaller version 1.2.1, ?biocLite for help > > biocLite("DAVIDQuery") > BioC_mirror: 'http://www.bioconductor.org' > Using R version 2.14, BiocInstaller version 1.2.1. > Installing package(s) 'DAVIDQuery' > > Installing package(s) into > ?/home/kbrand/R/x86_64-pc-__linux-gnu-library/2.13? > (as ?lib? is unspecified) > also installing the dependency ?RCurl? > > trying URL 'http://cran.fhcrc.org/src/__contrib/RCurl_1.7-0.tar.gz > <http: cran.fhcrc.org="" src="" contrib="" rcurl_1.7-0.tar.gz="">' > Content type 'application/x-gzip' length 813252 bytes (794 Kb) > opened URL > ==============================__==================== > downloaded 794 Kb > > trying URL > 'http://www.bioconductor.org/__packages/2.9/bioc/src/contrib/__D AVIDQuery_1.14.0.tar.gz > <http: www.bioconductor.org="" packages="" 2.9="" bioc="" src="" contrib="" david="" query_1.14.0.tar.gz="">' > Content type 'application/x-gzip' length 186887 bytes (182 Kb) > opened URL > ==============================__==================== > downloaded 182 Kb > > * installing *source* package ?RCurl? ... > ** package ?RCurl? successfully unpacked and MD5 sums checked > checking for curl-config... no > Cannot find curl-config > ERROR: configuration failed for package ?RCurl? > * removing ?/home/kbrand/R/x86_64-pc-__linux-gnu- library/2.13/RCurl? > ERROR: dependency ?RCurl? is not available for package ?DAVIDQuery? > * removing > ?/home/kbrand/R/x86_64-pc-__linux-gnu-library/2.13/__DAVIDQuery? > > The downloaded packages are in > ?/tmp/RtmpgNN770/downloaded___packages? > Warning messages: > 1: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package ?RCurl? had non-zero exit status > 2: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package ?DAVIDQuery? had non-zero exit status > > > sessionInfo() > R version 2.14.0 (2011-10-31) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_DK.UTF-8" LC_COLLATE=en_AU.UTF-8 > [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.2.1 > > > loaded via a namespace (and not attached): > [1] tools_2.14.0 > > > ######################### terminal output ################## > > kbrand at kbrand:~$ sudo R --vanilla > [sudo] password for kbrand: > > R version 2.14.0 (2011-10-31) > Copyright (C) 2011 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > Platform: x86_64-pc-linux-gnu (64-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > > > source("http://www.__bioconductor.org/biocLite.R > <http: www.bioconductor.org="" bioclite.r="">") > BiocInstaller version 1.2.1, ?biocLite for help > > biocLite("DAVIDQuery") > BioC_mirror: 'http://www.bioconductor.org' > Using R version 2.14, BiocInstaller version 1.2.1. > Installing package(s) 'DAVIDQuery' > > Installing package(s) into > ?/home/kbrand/R/x86_64-pc-__linux-gnu-library/2.13? > (as ?lib? is unspecified) > also installing the dependency ?RCurl? > > trying URL 'http://cran.fhcrc.org/src/__contrib/RCurl_1.7-0.tar.gz > <http: cran.fhcrc.org="" src="" contrib="" rcurl_1.7-0.tar.gz="">' > Content type 'application/x-gzip' length 813252 bytes (794 Kb) > opened URL > ==============================__==================== > downloaded 794 Kb > > trying URL > 'http://www.bioconductor.org/__packages/2.9/bioc/src/contrib/__D AVIDQuery_1.14.0.tar.gz > <http: www.bioconductor.org="" packages="" 2.9="" bioc="" src="" contrib="" david="" query_1.14.0.tar.gz="">' > Content type 'application/x-gzip' length 186887 bytes (182 Kb) > opened URL > ==============================__==================== > downloaded 182 Kb > > * installing *source* package ?RCurl? ... > ** package ?RCurl? successfully unpacked and MD5 sums checked > checking for curl-config... no > Cannot find curl-config > ERROR: configuration failed for package ?RCurl? > * removing ?/home/kbrand/R/x86_64-pc-__linux-gnu- library/2.13/RCurl? > ERROR: dependency ?RCurl? is not available for package ?DAVIDQuery? > * removing > ?/home/kbrand/R/x86_64-pc-__linux-gnu-library/2.13/__DAVIDQuery? > > The downloaded packages are in > ?/tmp/RtmpI5FdwF/downloaded___packages? > Warning messages: > 1: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package ?RCurl? had non-zero exit status > 2: In install.packages(pkgs = pkgs, repos = repos, ...) : > installation of package ?DAVIDQuery? had non-zero exit status > > > sessionInfo() > R version 2.14.0 (2011-10-31) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_DK.UTF-8" LC_COLLATE=en_AU.UTF-8 > [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.2.1 > > > loaded via a namespace (and not attached): > [1] tools_2.14.0 > > > > > > > > > On 2011-11-23 18:39, Martin Morgan wrote: > > On 11/23/2011 08:34 AM, Karl Brand wrote: > > > Esteemed BioC UseRs and Devs, > > I'm trying (and failing) to install the BioC package > "DAVIDQuery". There > must be a simple way to solve this issue, but my googling > failed to > solve this issue. > > Within (ESS/Emacs) R --vanilla i tried: > > > install.packages("DAVIDQuery", dependencies=TRUE) > Installing package(s) into > ?/home/kbrand/R/x86_64-pc-__linux-gnu-library/2.13? > (as ?lib? is unspecified) > --- Please select a CRAN mirror for use in this session --- > Loading Tcl/Tk interface ... done > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > package ?DAVIDQuery? is not available (for R version 2.14.0) > > > DAVIDQuery is a Bioconductor package, but it sounds like you're > choosing > a 'CRAN' archive. The recommended installation process is > > source("http://bioconductor.__org/biocLite.R > <http: bioconductor.org="" bioclite.r="">") > biocLite("DAVIDQuery") > > > > > > This makes me wonder if i need to specify a different > library (path). If > so, which one? > > > .libPaths() > [1] "/home/kbrand/R/x86_64-pc-__linux-gnu-library/2.13" > [2] "/usr/local/lib/R/site-__library" > [3] "/usr/lib/R/site-library" > [4] "/usr/lib/R/library" > > > That there are four is due to someone / thing other than R; see > ?Startup > for hints on how these libraries are identified. > > Martin > > > (This is a bigger area of ignorance for me - why has R set > up four > separate libraries by default? Where some require use of sudo to > install/update packages, whilst others do not? And what are the > implications when it comes time to upgrade to the next > version of R? I > have obtained some advice on this before - > https://stat.ethz.ch/__pipermail/ess- help/2011-__September/007120.html > <https: stat.ethz.ch="" pipermail="" ess-="" help="" 2011-september="" 007120.html=""> > - but > have failed to implement this given my focus on just using > R, neglecting > its proper maintenance, and all round inexperience with linux). > > I'd really appreciate responses on getting "DAVIDQuery" > running on my > currently installed R 2.14.0 (as well as any tips on 'good > practice' > when it comes to R library management on linux (ubuntu)). > > Sincerely, > > Karl > > > sessionInfo() > R version 2.14.0 (2011-10-31) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_DK.UTF-8" LC_COLLATE=en_AU.UTF-8 > [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tcltk_2.14.0 tools_2.14.0 > > > > > > > -- > Karl Brand <k.brand at="" erasmusmc.nl="" <mailto:k.brand="" at="" erasmusmc.nl="">> > Department of Genetics > Erasmus MC > Dr Molewaterplein 50 > 3015 GE Rotterdam > P +31 (0)10 704 3455 <tel:%2b31%20%280%2910%20704%203455> | F +31 > (0)10 704 4743 <tel:%2b31%20%280%2910%20704%204743> | M +31 (0)642 > 777 268 <tel:%2b31%20%280%29642%20777%20268> > > _________________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/__listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: > http://news.gmane.org/gmane.__science.biology.informatics.__conductor <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > > > > > -- > Mike Smith > PhD Student > Computational Biology Group > Cambridge University > -- Karl Brand <k.brand at="" erasmusmc.nl=""> Department of Genetics Erasmus MC Dr Molewaterplein 50 3015 GE Rotterdam P +31 (0)10 704 3455 | F +31 (0)10 704 4743 | M +31 (0)642 777 268
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@james-w-macdonald-5106
Last seen 7 days ago
United States
Hi Karl, On 11/23/2011 11:34 AM, Karl Brand wrote: > > Esteemed BioC UseRs and Devs, > > I'm trying (and failing) to install the BioC package "DAVIDQuery". > There must be a simple way to solve this issue, but my googling failed > to solve this issue. > > Within (ESS/Emacs) R --vanilla i tried: > > > install.packages("DAVIDQuery", dependencies=TRUE) > Installing package(s) into > ?/home/kbrand/R/x86_64-pc-linux-gnu-library/2.13? > (as ?lib? is unspecified) > --- Please select a CRAN mirror for use in this session --- > Loading Tcl/Tk interface ... done > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > package ?DAVIDQuery? is not available (for R version 2.14.0) > > Tsk, tsk. What is this install.packages() of which you speak? I do believe you want source("http://www.bioconductor.org/biocLite.R") biocLite("DAVIDQuery") Which is guaranteed to (find and) install the right thing, whereas install.packages() most likely will not. > > This makes me wonder if i need to specify a different library (path). > If so, which one? > > > .libPaths() > [1] "/home/kbrand/R/x86_64-pc-linux-gnu-library/2.13" > [2] "/usr/local/lib/R/site-library" > [3] "/usr/lib/R/site-library" > [4] "/usr/lib/R/library" > > (This is a bigger area of ignorance for me - why has R set up four > separate libraries by default? Where some require use of sudo to > install/update packages, whilst others do not? And what are the > implications when it comes time to upgrade to the next version of R? I > have obtained some advice on this before - > https://stat.ethz.ch/pipermail/ess-help/2011-September/007120.html - > but have failed to implement this given my focus on just using R, > neglecting its proper maintenance, and all round inexperience with > linux). > > I'd really appreciate responses on getting "DAVIDQuery" running on my > currently installed R 2.14.0 (as well as any tips on 'good practice' > when it comes to R library management on linux (ubuntu)). I am not a fan of system-wide installs of R. I always just download the tarball to my personal directory, then do tar xvfz <r-tarballname> cd <r-whateverversion> ./configure && make Then you will only have one library, and will not require sudo to do anything with it. When you upgrade you should always be upgrading your BioC install as well, and there is no profit in doing anything but installing biocLite() (which now comes in a package called BiocInstaller), and then re-installing all the packages you use in the new version of R. Best, Jim > > Sincerely, > > Karl > > > sessionInfo() > R version 2.14.0 (2011-10-31) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_DK.UTF-8" LC_COLLATE=en_AU.UTF-8 > [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tcltk_2.14.0 tools_2.14.0 > > > -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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