[BioC] Install \"xps\" package

[James W. MacDonald]

Hi Laura,

On 5/6/2013 2:17 PM, Laura [guest] wrote:
> 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

You are supposed to type

./configure linux

not

./configure [<arch>]

And in addition, I doubt you put root where you said you did. What you 
want to do is type

export ROOTSYS=/path/to/root

where /path/to/root might be

/home/laura/root

or something else. It is supposed to be the directory where you 
installed all the files for root.

Best,

Jim


>
> 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
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099