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 -- Sent via the guest posting facility at bioconductor.org.

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=/root > csh family > setenv ROOTSYS/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