[BioC] BioC 2.3 standard installation
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 d?c. ? 15:53, Tiandao Li a ?crit :
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, Herv? Pag?s <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
Bioconductor at stat.math.ethz.ch
<mailto: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
--
Herv? Pag?s
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.
Herv? Pag?s 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