Laura [guest] | 6 May 20:17 2013

Install \"xps\" package


Hello,

I have little knowledge about R and informatics in general. I am trying to download and install the "xps"
bioconductor package but I get this error:

xps configuration error:

   You must set the shell variable ROOTSYS to the
   directory where ROOT resides and re-run R CMD INSTALL
   e.g., (using Bourne shell syntax):

      export ROOTSYS=/opt/root
      export "PATH=$ROOTSYS/bin:$PATH" 
      R CMD INSTALL xps

   Please consult the README file for more information

I have read the README file and downloaded root and unzipped it. According to the README file the two
following steps are:

2. set ROOTSYS to the `root' directory:

            sh family:
              export ROOTSYS=<path>/root
            csh family
              setenv ROOTSYS <path>/root

   3. now type the build commands:

            all shells:
              ./configure --help    [optional, shows e.g. <arch> for supported architectures]
              ./configure [<arch>]  [e.g. <arch>= linux or macosx (32bit) or macosx64 (64bit)]
              make                  [or, make -j2 for dual CPU machines]

            Note: ./configure should automatically detect the architecture, if not use e.g.
              ./configure linux (32bit) ot linuxx8664gcc (64bit)

Now, the root directory is the directory downloads. In downloads I tiped "export ROOTSYS=root" (step two)
Then I tried typing "./configure [<arch>]" (step 3) but I get this answer:
bash: arch: No such file or directory

Does anybody know what's wrong and what I should do? I know little or nothing about linux so I don't really
understand what's being done at each step...

Thanks!

 -- output of sessionInfo(): 

R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=es_ES.UTF-8       LC_NUMERIC=C               LC_TIME=es_ES.UTF-8       
 [4] LC_COLLATE=es_ES.UTF-8     LC_MONETARY=es_ES.UTF-8    LC_MESSAGES=es_ES.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] splines   stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] survival_2.36-14        Matrix_1.0-6            lattice_0.20-6         
 [4] BiocInstaller_1.8.3     rpart_3.1-54            rstudio_0.97.246       
 [7] pdInfoBuilder_1.22.0    affxparser_1.30.2       pd.huex.1.0.st.v2_3.8.0
[10] RSQLite_0.11.3          DBI_0.2-6               oligo_1.22.0           
[13] oligoClasses_1.20.0     nnet_7.3-4              nlme_3.1-104           
[16] mgcv_1.7-18             KernSmooth_2.23-8       GenomicRanges_1.10.7   
[19] IRanges_1.16.6          foreign_0.8-50          cluster_1.14.2         
[22] class_7.3-4             affyPLM_1.34.0          preprocessCore_1.20.0  
[25] gcrma_2.30.0            affy_1.36.1             Biobase_2.18.0         
[28] BiocGenerics_0.4.0     

loaded via a namespace (and not attached):
 [1] affyio_1.26.0     Biostrings_2.26.3 bit_1.1-10        codetools_0.2-8   ff_2.2-11        
 [6] foreach_1.4.0     grid_2.15.1       iterators_1.0.6   parallel_2.15.1   tools_2.15.1     
[11] zlibbioc_1.4.0  

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