[BioC] Biobase/affy installation problem in linux

Mon Dec 5 07:12:25 CET 2005

It looks like affyPLM requires the BLAS library installed on your system.

http://www.netlib.org/blas/

hph

b.

On Sun, 4 Dec 2005, Frank Duan wrote:

> Many thanks, Benilton.
>
> After installed (gcc, g++, make, etc.), I finally got "Biobase" work.
> However, I met a new problem when I use "biocLite.R" to install "affyPLM".
> The compilation failed at the last step.
>
> Any suggestions are very welcomed and thanks ahead.
>
> Here is the problem.
>
>
> ...............................
> gcc -I/usr/lib/R/include     -fPIC  -g -O2 -c weightedkerneldensity.c -o
> weightedkerneldensity.o
> gcc -shared  -o affyPLM.so LESN.o PLM_modelmatrix.o SCAB.o avg_log.o
> biweight.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o
> do_PLMthreestep.o idealmismatch.o lm.o lm_threestep.o log_avg.o
> matrix_functions.o medianPM.o median_logPM.o medianpolish.o nthLargestPM.o
> preprocess.o psi_fns.o qnorm.o qnorm_probeset.o rlm.o rlm_PLM.o rlm_anova.o
> rlm_se.o rlm_threestep.o rmaPLM_pseudo.o rma_PLM.o rma_background2.o
> rma_common.o scaling.o threestep.o threestep_PLM.o threestep_common.o
> threestep_summary.o threestep_summary_methods.o transfns.o
> weightedkerneldensity.o -L/usr/lib/R/lib -lRlapack -lblas-3
> -L/usr/lib/R/lib -lR
> /usr/bin/ld: cannot find -lblas-3
> collect2: ld returned 1 exit status
> make: *** [affyPLM.so] Error 1
> ERROR: compilation failed for package 'affyPLM'
> ** Removing '/usr/local/lib/R/site-library/affyPLM'
>
> The downloaded packages are in
>        /tmp/Rtmpu89nBJ/downloaded_packages
> Warning message:
> installation of package 'affyPLM' had non-zero exit status in:
> install.packages(pkgs = "affyPLM", repos = c("
> http://www.bioconductor.org/packages/bioc/1.7"))
>
>
>
> On 12/4/05, Benilton Carvalho <bcarvalh at jhsph.edu> wrote:
>>
>> i'd guess you don't have the C compiler installed on your machine...
>>
>> install GCC and try it again.
>>
>> b.
>>
>> On Sun, 4 Dec 2005, Frank Duan wrote:
>>
>>> Hi Anjia and Hi Ting-Yuan,
>>>
>>> It's nice to see this topic has been discussed here. I have the similar
>> (or
>>> the same) problem as Anjia's even after installing R 2.2.0 on my ubuntu
>>> linux. Here are the details.
>>>
>>> The error under R 2.2.0 is:
>>>
>>>> source("http://www.bioconductor.org/biocLite.R")
>>>> biocLite("Biobase")
>>>
>>> Running bioCLite version 0.1  with R version  2.2.0
>>>
>>> Running biocinstall version 1.1  with R version  2.2.0
>>> trying URL
>>> '
>>>
>> http://www.bioconductor.org/packages/bioc/1.7/src/contrib/Biobase_1.8.0.tar.gz
>>> '
>>> Content type 'application/x-gzip' length 1285566 bytes
>>> opened URL
>>> ==================================================
>>> downloaded 1255Kb
>>>
>>> * Installing *source* package 'Biobase' ...
>>> ** libs
>>> /usr/lib/R/bin/SHLIB: line 102: make: command not found
>>> ERROR: compilation failed for package 'Biobase'
>>> ** Removing '/usr/local/lib/R/site-library/Biobase'
>>>
>>> The downloaded packages are in
>>>        /tmp/RtmpuiBzwp/downloaded_packages
>>> Warning message:
>>> installation of package 'Biobase' had non-zero exit status in:
>>> install.packages(pkgs = "Biobase", repos =
>>> c("http://www.bioconductor.org/packages/bioc/1.7",
>>>
>>> (Then I opened "/usr/lib/R/bin/SHLIB" and found the line 102)
>>>
>>> eval ${MAKE} ${makefiles} ${makeargs} ${makeobjs}
>>>
>>>
>>> I am a green hand to both Linux and C and can't fix the problem. My
>> guess is
>>> this is a problem specific to Linux Ubuntu Breezy Badger.
>>>
>>> Can anyone help me with it? Thanks ahead.
>>>
>>> Frank
>>>
>>>
>>> On 11/28/05, Ting-Yuan Liu <tliu at fhcrc.org> wrote:
>>>>
>>>>
>>>> Hi Anja,
>>>>
>>>> If you are using R 2.1.1, could you upgrade to R 2.2.0, which is the
>>>> latest versionof R, please?
>>>>
>>>> After you upgrade to R 2.2.0, you can use the biocLite script to
>> install
>>>> BioConductor for you.  In an R command window, type the following:
>>>>
>>>> source("http://www.bioconductor.org/biocLite.R")
>>>> biocLite()
>>>>
>>>> Please refer to the "Install - How To" page on the BioConductor
>> official
>>>> website.
>>>>
>>>> If you still have trouble in installing BioConductor, please report the
>>>> error/warning messages and the result of sessionInfo() to the list
>> again.
>>>>
>>>> HTH,
>>>> Ting-Yuan
>>>>
>>>> ______________________________________
>>>> Ting-Yuan Liu
>>>> Program in Computational Biology
>>>> Division of Public Health Sciences
>>>> Fred Hutchinson Cancer Research Center
>>>> Seattle, WA, USA
>>>> ______________________________________
>>>>
>>>> On Sat, 26 Nov 2005, Anja Schiel wrote:
>>>>
>>>>> I have downloaded R version 2.1.1 via apt-get and have now a running R
>>>> under Ubuntu Breezy Badger. But now I would like to use the
>> Bioconductor
>>>> packages and tried to install with BioC().
>>>> No matter if I use the root account or my personal login, I always end
>>>> up with at least 11 to 14 warnings and always the problem that all
>>>> packages dependent on the Biobase package can not be installed.
>>>>
>>>> I should mention that I gave myself permission to all libraries and
>>>> anyhow, other libraries such as limma are not affected.
>>>>
>>>> Warning messages:
>>>> 1: installation of package 'Biobase' had non-zero exit status in:
>>>> install.packages(pkgs = c("affy", "affydata", "affyPLM",
>>>> "annaffy",   ...
>>>> 2: installation of package 'Biostrings' had non-zero exit status in:
>>>> install.packages(pkgs = c("affy", "affydata", "affyPLM",
>>>> "annaffy",   ...
>>>> 3: installation of package 'pamr' had non-zero exit status in:
>>>> install.packages(pkgs = c("affy", "affydata", "affyPLM",
>>>> "annaffy",   ...
>>>> 4: installation of package 'affy' had non-zero exit status in:
>>>> install.packages(pkgs = c("affy", "affydata", "affyPLM",
>>>> "annaffy",   ...
>>>> 5: installation of package 'annaffy' had non-zero exit status in:
>>>> install.packages(pkgs = c("affy", "affydata", "affyPLM",
>>>> "annaffy",   ...
>>>> 6: installation of package 'edd' had non-zero exit status in:
>>>> install.packages(pkgs = c("affy", "affydata", "affyPLM",
>>>> "annaffy",   ...
>>>> 7: installation of package 'genefilter' had non-zero exit status in:
>>>> install.packages(pkgs = c("affy", "affydata", "affyPLM",
>>>> "annaffy",   ...
>>>> 8: installation of package 'multtest' had non-zero exit status in:
>>>> install.packages(pkgs = c("affy", "affydata", "affyPLM",
>>>> "annaffy",   ...
>>>> 9: installation of package 'vsn' had non-zero exit status in:
>>>> install.packages(pkgs = c("affy", "affydata", "affyPLM",
>>>> "annaffy",   ...
>>>> 10: installation of package 'geneplotter' had non-zero exit status in:
>>>> install.packages(pkgs = c("affy", "affydata", "affyPLM",
>>>> "annaffy",   ...
>>>> 11: installation of package 'makecdfenv' had non-zero exit status in:
>>>> install.packages(pkgs = c("affy", "affydata", "affyPLM",
>>>> "annaffy",   ...
>>>> 12: installation of package 'matchprobes' had non-zero exit status in:
>>>> install.packages(pkgs = c("affy", "affydata", "affyPLM",
>>>> "annaffy",   ...
>>>> 13: installation of package 'gcrma' had non-zero exit status in:
>>>> install.packages(pkgs = c("affy", "affydata", "affyPLM",
>>>> "annaffy",   ...
>>>> 14: installation of package 'affyPLM' had non-zero exit status in:
>>>> install.packages(pkgs = c("affy", "affydata", "affyPLM",
>>>> "annaffy",   ...
>>>>
>>>> So when I try to open affy the following error message appears.
>>>>
>>>>> library(affy)
>>>> Loading required package: Biobase
>>>> Error in library.dynam(lib, package, package.lib) :
>>>>        shared library 'Biobase' not found
>>>> In addition: Warning messages:
>>>> 1: package 'Biobase' contains no R code in: loadNamespace(package,
>>>> c(which.lib.loc, lib.loc))
>>>> 2: S3 method 'as.data.frame.exprSet' was declared in NAMESPACE but not
>>>> found
>>>> Error: package 'Biobase' could not be loaded
>>>>
>>>> I used the woody URL to apt-get install, but I guess that should not
>>>> make a difference.
>>>>
>>>> I checked the mail archive, but somehow this particular problem was not
>>>> discussed. It seems that something goes wrong during compiling the
>>>> Biobase package.
>>>> Any suggestions would be very welcome, I am not necessarily an expert
>> on
>>>> Linux.
>>>>
>>>> Greetings and thanks in advance,
>>>> Anja Schiel
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor at stat.math.ethz.ch
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor at stat.math.ethz.ch
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>
>>>>
>>>>
>>>
>>>       [[alternative HTML version deleted]]
>>>
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>>>
>>
>