[BioC] Install \"xps\" package

[cstrato]

Dear Laura,

As Jim already mentioned you need to do use 'linux' instead of 'arch'. 
Here are the steps you need to do after unzipping ROOT:

$ cd root
$ ./configure linux
$ make
$ . bin/thisroot.sh

However, before you need to create a '.bashrc' file in your home 
directory, as I have explained earlier in:
https://www.stat.math.ethz.ch/pipermail/bioconductor/2013-March/051785.html

Best regards,
Christian


On 5/6/13 8:41 PM, James W. MacDonald wrote:
> 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.
>>
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>