[R] [BioC] 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]]
>
> _______________________________________________
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>
>
> --
> 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]]
>
> ______________________________________________
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> PLEASE do read the posting guide
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> 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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