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Question: Problems installing bioconductor on ubuntu
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gravatar for Rebecca Griffiths
8.8 years ago by
Rebecca Griffiths20 wrote:
Hello everyone I have been trying to install bioconductor on ubuntu 7.10 gutsy using R version 2.5.1, and getting a lot of error messages: Here are a few: 1: package âxtableâ is not available in: install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... 2: dependency âsurvivalâ is not available in: install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... 3: installation of package 'affyio' had non-zero exit status in: install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... 4: installation of package 'lattice' had non-zero exit status in: install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... 5: installation of package 'KernSmooth' had non-zero exit status in: install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, ... I have installed r-base-core, build-essential, g77, reflas3, reflas3-dev, r-base-dev, and r-recommended. When I tried to install affyio by itself, I got the following error message: > biocLite(c("affyio")) Running biocinstall version 2.0.8 with R version 2.5.1 Your version of R requires version 2.0 of Bioconductor. Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, : argument 'lib' is missing: using '/usr/local/lib/R/site- library' trying URL 'http://bioconductor.org/packages/2.0/bioc/src/contrib/affyio_1.4.1.ta r.gz' Content type 'application/x-gzip' length 59104 bytes opened URL ================================================== downloaded 57Kb * Installing *source* package 'affyio' ... creating cache ./config.cache checking how to run the C preprocessor... cc -E checking for main in -lz... no updating cache ./config.cache creating ./config.status creating src/Makevars ** libs gcc-4.2 -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -fpic -g -O2 -c read_abatch.c -o read_abatch.o /bin/bash: gcc-4.2: command not found make: *** [read_abatch.o] Error 127 chmod: cannot access `/usr/local/lib/R/site-library/affyio/libs/*': No such file or directory ERROR: compilation failed for package 'affyio' ** Removing '/usr/local/lib/R/site-library/affyio' The downloaded packages are in /tmp/RtmpowXclV/downloaded_packages Warning message: installation of package 'affyio' had non-zero exit status in: install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, If anyone can offer suggestions or help, it would be appreciated. Thanks, R [[alternative HTML version deleted]]
ADD COMMENTlink modified 8.8 years ago by Wolfgang Huber13k • written 8.8 years ago by Rebecca Griffiths20
0
gravatar for Steve Lianoglou
8.8 years ago by
Genentech
Steve Lianoglou12k wrote:
Hi, On Jul 10, 2008, at 3:52 PM, Rebecca Griffiths wrote: > Hello everyone > > I have been trying to install bioconductor on ubuntu 7.10 gutsy > using R > version 2.5.1, and getting a lot of error messages: <snip> I'd suggest trying to install a newer version of R, the latest one is 2.7.1 Check out the instructions here: http://cran.r-project.org/bin/linux/ubuntu/README.html If you're still having problems installing the newest release, I think it would then be worth trying to figure out what's going wrong. -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Cornell Medical College http://cbio.mskcc.org/~lianos
ADD COMMENTlink written 8.8 years ago by Steve Lianoglou12k
0
gravatar for Wolfgang Huber
8.8 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
Dear Rebecca, please see below > I have been trying to install bioconductor on ubuntu 7.10 gutsy using R > version 2.5.1, and getting a lot of error messages: > > > > Here are a few: > > 1: package ?xtable? is not available in: install.packages(pkgs = pkgs, repos > = repos, dependencies = dependencies, ... > > 2: dependency ?survival? is not available in: install.packages(pkgs = pkgs, > repos = repos, dependencies = dependencies, ... > > 3: installation of package 'affyio' had non-zero exit status in: > install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, > ... > > 4: installation of package 'lattice' had non-zero exit status in: > install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, > ... > > 5: installation of package 'KernSmooth' had non-zero exit status in: > install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, > ... > > > > I have installed r-base-core, build-essential, g77, reflas3, reflas3-dev, > r-base-dev, and r-recommended. > > > > When I tried to install affyio by itself, I got the following error message: > >> biocLite(c("affyio")) > > Running biocinstall version 2.0.8 with R version 2.5.1 > > Your version of R requires version 2.0 of Bioconductor. > > Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > > argument 'lib' is missing: using '/usr/local/lib/R/site- library' > > trying URL > 'http://bioconductor.org/packages/2.0/bioc/src/contrib/affyio_1.4.1. tar.gz' > > Content type 'application/x-gzip' length 59104 bytes > > opened URL > > ================================================== > > downloaded 57Kb > > > > * Installing *source* package 'affyio' ... > > creating cache ./config.cache > > checking how to run the C preprocessor... cc -E > > checking for main in -lz... no > > updating cache ./config.cache > > creating ./config.status > > creating src/Makevars > > ** libs > > gcc-4.2 -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -fpic > -g -O2 -c read_abatch.c -o read_abatch.o > > /bin/bash: gcc-4.2: command not found > ^^^^^^^^^^ This is the first problem. To install packages from source (which is the common thing to do in Linux) you will need to install various compilers and software development tools into your Ubuntu. Note that this is not a Bioconductor "problem" but a general property of R. MacOSX and Windows versions of R and Bioconductor make it a bit easier by offering "precompiled" packages, but in Linux you (and your computer) are expected to build "from source code". I am afraid that this will require some iterations and careful reading of the output of attempts at installation, in order to see which Ubuntu packages you need to add. As Steve pointed out, it is also recommendable that you install R 2.7 rather than 2.5.1, and you can do this on your "old" Ubuntu, just not with the Ubuntu package manager, but rather by also building R 2.7 "from source". Some general help can be found here: http://cran.r-project.org/doc/manuals/R-admin.html Hope this helps Wolfgang > make: *** [read_abatch.o] Error 127 > > chmod: cannot access `/usr/local/lib/R/site-library/affyio/libs/*': No such > file or directory > > ERROR: compilation failed for package 'affyio' > > ** Removing '/usr/local/lib/R/site-library/affyio' > > > > The downloaded packages are in > > /tmp/RtmpowXclV/downloaded_packages > > Warning message: > > installation of package 'affyio' had non-zero exit status in: > install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, > > > > > > If anyone can offer suggestions or help, it would be appreciated. > > > > Thanks, > > R > > > [[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 -- ---------------------------------------------------- Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber
ADD COMMENTlink written 8.8 years ago by Wolfgang Huber13k
Hi again, On Jul 10, 2008, at 6:22 PM, Wolfgang Huber wrote: > Dear Rebecca, > > > please see below > > >> I have been trying to install bioconductor on ubuntu 7.10 gutsy >> using R >> version 2.5.1, and getting a lot of error messages: >> Here are a few: >> 1: package ?xtable? is not available in: install.packages(pkgs = >> pkgs, repos >> = repos, dependencies = dependencies, ... >> 2: dependency ?survival? is not available in: install.packages(pkgs >> = pkgs, >> repos = repos, dependencies = dependencies, ... >> 3: installation of package 'affyio' had non-zero exit status in: >> install.packages(pkgs = pkgs, repos = repos, dependencies = >> dependencies, >> ... >> 4: installation of package 'lattice' had non-zero exit status in: >> install.packages(pkgs = pkgs, repos = repos, dependencies = >> dependencies, >> ... >> 5: installation of package 'KernSmooth' had non-zero exit status in: >> install.packages(pkgs = pkgs, repos = repos, dependencies = >> dependencies, >> ... >> I have installed r-base-core, build-essential, g77, reflas3, >> reflas3-dev, >> r-base-dev, and r-recommended. >> When I tried to install affyio by itself, I got the following error >> message: >>> biocLite(c("affyio")) >> Running biocinstall version 2.0.8 with R version 2.5.1 >> Your version of R requires version 2.0 of Bioconductor. >> Warning in install.packages(pkgs = pkgs, repos = repos, >> dependencies = >> dependencies, : >> argument 'lib' is missing: using '/usr/local/lib/R/site- >> library' >> trying URL >> 'http://bioconductor.org/packages/2.0/bioc/src/contrib/affyio_1.4.1 .tar.gz' >> Content type 'application/x-gzip' length 59104 bytes >> opened URL >> ================================================== >> downloaded 57Kb >> * Installing *source* package 'affyio' ... >> creating cache ./config.cache >> checking how to run the C preprocessor... cc -E >> checking for main in -lz... no >> updating cache ./config.cache >> creating ./config.status >> creating src/Makevars >> ** libs >> gcc-4.2 -std=gnu99 -I/usr/share/R/include -I/usr/share/R/ >> include -fpic >> -g -O2 -c read_abatch.c -o read_abatch.o >> /bin/bash: gcc-4.2: command not found > > > ^^^^^^^^^^ This is the first problem. To install packages from > source (which is the common thing to do in Linux) you will need to > install various compilers and software development tools into your > Ubuntu. Note that this is not a Bioconductor "problem" but a general > property of R. > > MacOSX and Windows versions of R and Bioconductor make it a bit > easier by offering "precompiled" packages, but in Linux you (and > your computer) are expected to build "from source code". > > I am afraid that this will require some iterations and careful > reading of the output of attempts at installation, in order to see > which Ubuntu packages you need to add. > As Steve pointed out, it is also recommendable that you install R > 2.7 rather than 2.5.1, and you can do this on your "old" Ubuntu, > just not with the Ubuntu package manager, but rather by also > building R 2.7 "from source". Some general help can be found here: > http://cran.r-project.org/doc/manuals/R-admin.html Ah! Sorry! I didn't look through the entire error dump and just tried to pick at the "low hanging fruit" first. Maybe I can be more helpful this time. Typically to get the development tools in ubuntu, you'll just have to install the "build-essential" package. From the terminal, you'd do it like so: sudo apt-get install build-essential That should get you gcc, make and other stuff (listed here: http://packages.ubuntu.com/gutsy/devel/build-essential) Hope that helps, -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Cornell Medical College http://cbio.mskcc.org/~lianos
ADD REPLYlink written 8.8 years ago by Steve Lianoglou12k
Hi Rebecca, as a big fan of Ubuntu and Bioconductor, I've gone through a number of installs, and run into many similar headaches. As Steve pointed out, you are missing gcc and associated libraries, which you can get from build-essentials. This will get many packages working, but I typically also run into many additional missing requirements when I try to install other components of Bioconductor using the biocLite() script. To avoid these problems, I usually go through a checklist of steps to get R/Bioconductor working smoothly. 1. Install dependencies: This command will install most of the Ubuntu package that R/Bioconductor will need later. You can also use Synaptic Package Manager and install each one (I haven't updated this list for a few months, so some might have newer versions, also this list was compiled for ubuntu 7.10.): sudo apt-get install sun-java6-jdk libgtk2.0-dev graphviz-dev libgtk1.2-dev curl ggobi libxml2-dev mesa-common-dev libglu1-mesa-dev libgd2-xpm-dev libmysqlclient15-dev gfortran-4.2 refblas3-dev libcurl4-gnutls-dev libboost-dev g++-4.2 unixodbc-dev build-essential 2. I then add the Cran Ubuntu repository as explained here: http://cran.r-project.org/bin/linux/ubuntu/ This ensures that I'm running the latest version of R, which usually isn't available from the Ubuntu software repositories. I have had very good luck with this repository in the ~2 years I've been using it. 3. Install R: After adding the repository above, I install the following packages using either the command line "apt-get install" or Synaptic Package Manager: r-base-core r-base-html r-base-latex r-base-dev r-base-core r-cran-rgtk2 r-cran-rggobi r-cran-rgl 4: Fix Java To make sure that R will use the Sun version of java installed above (sun-java6-jdk) run: R CMD javareconf 5: run biocLite() After doing this, you should be able to install most packages from the Cran/Bioconductor repositories without any problems with missing dependencies. Again, some of these steps might not be necessary depending on which Bioconductor packages you plan to use (although build-essential is essential), but if you run into problems installing the packages above might help. Sam
ADD REPLYlink written 8.8 years ago by Bio Sam60
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