[BioC] [R] BioC 2.3 standard installation

Hervé Pagès hpages at fhcrc.org
Mon Dec 1 23:42:56 CET 2008


Background: some CRAN or Bioconductor packages contain native code
that needs to be compiled and then linked against a system library.
Some of those libraries are not part of a standard Ubuntu installation
and need to be installed explicitly (sudo apt-get install
<somelib>-dev).

In the case of preprocessCore, the output below suggests that it
needs to be linked against the BLAS and LAPACK libraries. Not sure
but I think those are part of a default R installation unless R has
been configured with --with-blas and --with-lapack which might be
your case.

Not sure what's going on. Just a couple of suggestions:

   - Make sure you have Ubuntu pkg r-base-dev

   - Try to install KernSmooth (recommended pkg) from source:

       > install.packages('KernSmooth')

     This will replace the one you got when you installed
     Ubuntu pkg r-cran-kernsmooth
     KernSmooth also needs to be linked against BLAS so if
     this fails then it means something is wrong with your
     R installation (in that case R-help might be a better place
     to ask for help).

H.


Tiandao Li wrote:
> Thanks, Vincent. I installed XML. However, I still can't install 
> preprocessCore or other standard packages from BioC.
> 
>  > biocLite("preprocessCore")
> Running biocinstall version 2.3.9 with R version 2.8.0 
> Your version of R requires version 2.3 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/2.3/bioc/src/contrib/preprocessCore_1.4.0.tar.gz'
> Content type 'application/x-gzip' length 109921 bytes (107 Kb)
> opened URL
> ==================================================
> downloaded 107 Kb
> 
> * Installing *source* package 'preprocessCore' ...
> checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables... 
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ISO C89... none needed
> checking for pthread_create in -lpthread... yes
> checking if we can use pthreads... yes
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" 
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g 
> -O2 -c avg.c -o avg.o
> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" 
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g 
> -O2 -c avg_log.c -o avg_log.o
> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" 
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g 
> -O2 -c biweight.c -o biweight.o
> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" 
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g 
> -O2 -c init_package.c -o init_package.o
> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" 
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g 
> -O2 -c lm.c -o lm.o
> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" 
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g 
> -O2 -c log_avg.c -o log_avg.o
> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" 
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g 
> -O2 -c log_median.c -o log_median.o
> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" 
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g 
> -O2 -c matrix_functions.c -o matrix_functions.o
> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" 
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g 
> -O2 -c median.c -o median.o
> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" 
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g 
> -O2 -c median_log.c -o median_log.o
> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" 
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g 
> -O2 -c medianpolish.c -o medianpolish.o
> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" 
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g 
> -O2 -c plmd.c -o plmd.o
> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" 
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g 
> -O2 -c plmr.c -o plmr.o
> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" 
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g 
> -O2 -c psi_fns.c -o psi_fns.o
> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" 
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g 
> -O2 -c qnorm.c -o qnorm.o
> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" 
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g 
> -O2 -c R_colSummarize.c -o R_colSummarize.o
> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" 
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g 
> -O2 -c rlm_anova.c -o rlm_anova.o
> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" 
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g 
> -O2 -c rlm.c -o rlm.o
> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" 
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g 
> -O2 -c rlm_se.c -o rlm_se.o
> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" 
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g 
> -O2 -c rma_background4.c -o rma_background4.o
> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" 
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g 
> -O2 -c rma_common.c -o rma_common.o
> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" 
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g 
> -O2 -c R_plmd_interfaces.c -o R_plmd_interfaces.o
> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" 
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g 
> -O2 -c R_plmr_interfaces.c -o R_plmr_interfaces.o
> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" 
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g 
> -O2 -c R_rlm_interfaces.c -o R_rlm_interfaces.o
> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" 
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g 
> -O2 -c R_subColSummarize.c -o R_subColSummarize.o
> gcc -std=gnu99 -I/usr/share/R/include -g -O2 -DPACKAGE_NAME=\"\" 
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
> -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fpic -g 
> -O2 -c weightedkerneldensity.c -o weightedkerneldensity.o
> gcc -std=gnu99 -shared -o preprocessCore.so avg.o avg_log.o biweight.o 
> init_package.o lm.o log_avg.o log_median.o matrix_functions.o median.o 
> median_log.o medianpolish.o plmd.o plmr.o psi_fns.o qnorm.o 
> R_colSummarize.o rlm_anova.o rlm.o rlm_se.o rma_background4.o 
> rma_common.o R_plmd_interfaces.o R_plmr_interfaces.o R_rlm_interfaces.o 
> R_subColSummarize.o weightedkerneldensity.o -lpthread -lpthread 
> -lgfortran -lm -llapack -lf77blas -latlas -L/usr/lib/R/lib -lR
> /usr/bin/ld: cannot find -lf77blas
> collect2: ld returned 1 exit status
> make: *** [preprocessCore.so] Error 1
> chmod: cannot access 
> `/usr/local/lib/R/site-library/preprocessCore/libs/*': No such file or 
> directory
> ERROR: compilation failed for package 'preprocessCore'
> ** Removing '/usr/local/lib/R/site-library/preprocessCore'
> 
> The downloaded packages are in
>  /tmp/RtmpqCLrkQ/downloaded_packages
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, dependencies = 
> dependencies, :
>   installation of package 'preprocessCore' had non-zero exit status
>  > 
> 
> 
> 
> On Mon, Dec 1, 2008 at 2:34 PM, Vincent Goulet 
> <vincent.goulet at act.ulaval.ca <mailto:vincent.goulet at act.ulaval.ca>> wrote:
> 
>     Tiandao,
> 
>     According to
> 
>            http://packages.ubuntu.com/
> 
>     the file xml2-config is in the Ubuntu package libxml2-dev. I'd try
>     installing this package and then retry installing XML.
> 
>     HTH    Vincent
> 
>     Le lun. 1 déc. à 15:53, Tiandao Li a écrit :
> 
>         I always followed http://cran.r-project.org/bin/linux/ubuntu/ to
>         install R
>         on Ubuntu 8.1. I had no errors before!
> 
>             install.packages("XML")
> 
>         Warning in install.packages("XML") :
>          argument 'lib' is missing: using '/usr/local/lib/R/site-library'
>         --- Please select a CRAN mirror for use in this session ---
>         Loading Tcl/Tk interface ... done
>         trying URL 'http://cran.fhcrc.org/src/contrib/XML_1.98-1.tar.gz'
>         Content type 'application/x-gzip' length 648274 bytes (633 Kb)
>         opened URL
>         ==================================================
>         downloaded 633 Kb
> 
>         * Installing *source* package 'XML' ...
>         checking for gcc... gcc
>         checking for C compiler default output file name... a.out
>         checking whether the C compiler works... yes
>         checking whether we are cross compiling... no
>         checking for suffix of executables...
>         checking for suffix of object files... o
>         checking whether we are using the GNU C compiler... yes
>         checking whether gcc accepts -g... yes
>         checking for gcc option to accept ANSI C... none needed
>         checking how to run the C preprocessor... gcc -E
>         checking for sed... /bin/sed
>         checking for xml2-config... no
>         Cannot find xml2-config
>         ERROR: configuration failed for package 'XML'
>         ** Removing '/usr/local/lib/R/site-library/XML'
> 
>         The downloaded packages are in
>         /tmp/RtmpqCLrkQ/downloaded_packages
>         Warning message:
>         In install.packages("XML") :
>          installation of package 'XML' had non-zero exit status
> 
> 
> 
> 
> 
>         On Mon, Dec 1, 2008 at 1:42 PM, Hervé Pagès <hpages at fhcrc.org
>         <mailto:hpages at fhcrc.org>> wrote:
> 
>             Hi Tiandao,
> 
>             What OS do you have? How did you install R? It looks like
>             you cannot
>             install an R package with native code at all. Please try
> 
>                 install.packages("XML")
> 
> 
>             and show us the complete output.
>             You could also try the R-help mailing list
>             (r-help at r-project.org <mailto:r-help at r-project.org>)
>             since your problem doesn't seem to be Bioconductor-specific.
> 
>             Cheers,
>             H.
> 
> 
>             Tiandao Li wrote:
> 
>                 Hello,
> 
>                 I tried to install BioC 2.3 on a new laptop (HP AMD
>                 Turion x2). However I
>                 constantly had the following warnings, I tried several
>                 times for the last
>                 few days. I never had this kind of errors before.
> 
>                 sudo R
> 
>                 source("http://bioconductor.org/biocLite.R")
> 
> 
> 
>                 biocLite()
> 
> 
> 
>                 warnings()
> 
> 
>                 Warning messages:
>                 1: In install.packages(pkgs = pkgs, repos = repos,
>                 dependencies =
>                 dependencies, ... :
>                 installation of package 'Matrix' had non-zero exit status
>                 2: In install.packages(pkgs = pkgs, repos = repos,
>                 dependencies =
>                 dependencies, ... :
>                 installation of package 'preprocessCore' had non-zero
>                 exit status
>                 3: In install.packages(pkgs = pkgs, repos = repos,
>                 dependencies =
>                 dependencies, ... :
>                 installation of package 'IRanges' had non-zero exit status
>                 4: In install.packages(pkgs = pkgs, repos = repos,
>                 dependencies =
>                 dependencies, ... :
>                 installation of package 'affy' had non-zero exit status
>                 5: In install.packages(pkgs = pkgs, repos = repos,
>                 dependencies =
>                 dependencies, ... :
>                 installation of package 'affydata' had non-zero exit status
>                 6: In install.packages(pkgs = pkgs, repos = repos,
>                 dependencies =
>                 dependencies, ... :
>                 installation of package 'Biostrings' had non-zero exit
>                 status
>                 7: In install.packages(pkgs = pkgs, repos = repos,
>                 dependencies =
>                 dependencies, ... :
>                 installation of package 'matchprobes' had non-zero exit
>                 status
>                 8: In install.packages(pkgs = pkgs, repos = repos,
>                 dependencies =
>                 dependencies, ... :
>                 installation of package 'vsn' had non-zero exit status
>                 9: In install.packages(pkgs = pkgs, repos = repos,
>                 dependencies =
>                 dependencies, ... :
>                 installation of package 'gcrma' had non-zero exit status
>                 10: In install.packages(pkgs = pkgs, repos = repos,
>                 dependencies =
>                 dependencies, ... :
>                 installation of package 'simpleaffy' had non-zero exit
>                 status
>                 11: In install.packages(pkgs = pkgs, repos = repos,
>                 dependencies =
>                 dependencies, ... :
>                 installation of package 'affyPLM' had non-zero exit status
>                 12: In install.packages(pkgs = pkgs, repos = repos,
>                 dependencies =
>                 dependencies, ... :
>                 installation of package 'affyQCReport' had non-zero exit
>                 status
> 
>                 sessionInfo()
> 
> 
>                 R version 2.8.0 (2008-10-20)
>                 i486-pc-linux-gnu
> 
>                 locale:
> 
>                 LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.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_2.8.0 tools_2.8.0
> 
>                      [[alternative HTML version deleted]]
> 
>                 _______________________________________________
>                 Bioconductor mailing list
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>                 Search the archives:
>                 http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
> 
>             --
>             Hervé Pagès
> 
>             Program in Computational Biology
>             Division of Public Health Sciences
>             Fred Hutchinson Cancer Research Center
>             1100 Fairview Ave. N, M2-B876
>             P.O. Box 19024
>             Seattle, WA 98109-1024
> 
>             E-mail: hpages at fhcrc.org <mailto:hpages at fhcrc.org>
>             Phone:  (206) 667-5791
>             Fax:    (206) 667-1319
> 
> 
>                [[alternative HTML version deleted]]
> 
>         ______________________________________________
>         R-help at r-project.org <mailto:R-help at r-project.org> mailing list
>         https://stat.ethz.ch/mailman/listinfo/r-help
>         PLEASE do read the posting guide
>         http://www.R-project.org/posting-guide.html
>         and provide commented, minimal, self-contained, reproducible code.
> 
> 
> 

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319



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