Browse code

Code changes to free the package from depending on the GNU Scientific Library.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GSVA@63230 bc3139a8-67e5-0310-9ffc-ced21a209358

Robert Castelo authored on 27/02/2012 17:14:56
Showing 10 changed files

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@@ -1,6 +1,6 @@
1 1
 Package: GSVA
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-Version: 1.3.7
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-Date: 2012-02-22
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+Version: 1.3.8
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+Date: 2012-02-27
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 Title: Gene Set Variation Analysis
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 Author: Justin Guinney <justin.guinney@sagebase.org> (with contributions from Robert Castelo <robert.castelo@upf.edu> and Sonja Haenzelmann <shanzelmann@imim.es)
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 Maintainer: Justin Guinney <justin.guinney@sagebase.org>
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@@ -8,8 +8,7 @@ Depends: R (>= 2.13.0), methods
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 Imports: methods, Biobase, GSEABase
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 Enhances: snow, parallel
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 Suggests: limma, qpgraph, RBGL, graph, Rgraphviz, RColorBrewer, genefilter, GSVAdata
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-SystemRequirements: GNU Scientific Library >= 1.12
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-Description: Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner. Users on all platforms must install the GNU Scientific Library; see the README file, available in the source distribution of this file, for details.
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+Description: Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner.
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 License: GPL (>= 2)
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 LazyLoad: yes
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 biocViews: Bioinformatics, Microarray, Pathways
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@@ -97,14 +97,15 @@ setMethod("gsva", signature(expr="matrix", gset.idx.list="GeneSetCollection", an
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   verbose=TRUE,
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   mx.diff=TRUE)
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 {
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-  if (verbose)
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-    cat("Mapping identifiers between gene sets and feature names\n")
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-
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   ## map gene identifiers of the gene sets to the features in the matrix
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   mapped.gset.idx.list <- gset.idx.list
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-  if (!is.na(annotation))
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+  if (!is.na(annotation)) {
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+    if (verbose)
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+      cat("Mapping identifiers between gene sets and feature names\n")
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+
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     mapped.gset.idx.list <- mapIdentifiers(gset.idx.list,
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                                            AnnotationIdentifier(annotation))
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+  }
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   ## map to the actual features for which expression data is available
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   tmp <- lapply(geneIds(mapped.gset.idx.list),
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deleted file mode 100644
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@@ -1,150 +0,0 @@
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-The GSVA package calls functions from the GNU Scientific Library
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-and this README file discusses several steps to be taken to make
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-sure that this library is available to GSVA when installing it.
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-
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-Unix/Mac users
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-==============
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-
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-In order to successfully install and run GSVA in Unix/Mac
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-systems you need to install first the GNU Scientific Library
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-(GSL) which you can find in the following URL:
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-
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-http://www.gnu.org/software/gsl
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-
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-Follow the link to the FTP site and download the lastest tar ball or,
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-in any case, one with version >= 1.12, for instance, to your
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-'Desktop' directory. Then go to the shell (in a Mac computer you need
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-to open the Terminal window program under the Applications/Utilities
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-folder) and type the following instruccions for a system-wide installation
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-(assuming the tar ball has name 'gsl-1.15.tar.gz':
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-
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-$ cd Desktop
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-$ gzip -cd gsl-1.15.tar.gz | tar xvf -
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-$ cd gsl-1.15
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-$ ./configure
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-$ make
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-$ sudo make install
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-
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-The latter instruction will ask you for the system administration
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-password which may very well be the your own user password. If you
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-do not have system administration privileges, you can either ask your
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-sysadmin to make this system-wide installation of GSL or install GSL
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-yourself on another location of the filesystem where you have writing
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-permissions. This can be done by replacing the call to 'configure' by:
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-
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-$ ./configure --prefix=/home/myusername/gsl
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-
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-Then make sure that your PATH environment variable
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-allows you to execute the script 'gsl-config' located in the 'bin'
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-subdirectory of the GSL installation. This can be verified by writting 
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-n the shell:
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-
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-$ which gsl-config
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-
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-without obtaining an error. If you get an error, locate the path where
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-the 'gsl-config' script is and add it to the PATH environment variable.
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-Alternatively, you can set the environment variable GSL_CONFIG to this
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-path, thus avoiding to modify the PATH environment variable.
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-
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-After this, you can install GSVA in the usual way as with any other
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-Bioconductor package by writting the following instructions in the
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-R shell:
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-
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-source("http://www.bioconductor.org/biocLite.R")
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-biocLite("GSVA")
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-
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-Windows users
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-=============
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-
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-If you install the binary GSVA package for Windows that is available
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-through the Bioconductor website, then nothing needs to be done next
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-to a standard installation as a Bioconductor package, i.e.:
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-
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-source("http://www.bioconductor.org/biocLite.R")
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-biocLite("GSVA")
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-
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-since the binary GSVA package at Bioconductor already contains the
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-necessary GNU Scientific Library functions statically linked in the
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-package.
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-
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-If you want to install the package from source (not recommended for
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-standard users), then you need to install first the GNU Scientific
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-Library (GSL) which, in the case of windows, can be done in two ways,
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-from the GNUWIN32 site and from the CYGWIN site. Each option
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-requires slightly different configuration steps. Either is
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-equally good for having GSVA running under windows and the choice
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-is more a matter of whether incidentally you already have one of
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-the two installed in your windows machine. If not, just take any
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-of them.
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-
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-** GNUWIN32
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-
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-You should download the GNUWIN32 GSL from:
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-
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-http://gnuwin32.sourceforge.net/packages/gsl.htm
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-
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-It is recommended that you download the file under the 'Setup'
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-link described as "Complete package, except sources'. You should
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-execute the downloaded file and perform the installation either
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-system-wide, for which you'll need system administration privileges,
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-or in some path where you have writting permissions.
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-
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-By default, this package installs GSL at 'C:\Program Files\GnuWin32'
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-and assume this is the case now. Go to the folder
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-
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-C:\Program Files\GnuWin32\bin
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-
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-and copy the file 'libgsl.dll' into 'libgsl-0.dll'. Then add the path
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-where these files are located to your PATH environment variable by
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-right-clicking on the "My PC" icon, select "Properties", go to the
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-"Advanced" tab, click on "Environment variables", select "Path" on the
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-"Environment variables" box, click on "Modify", and add to the end of
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-the current string:
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-
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-;C:/PROGRA~1/GNUWIN32/bin
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-
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-then press 'Ok' through out all previously opened dialog boxes and
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-you should be able to install GSVA in the usual way as with any other
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-Bioconductor package by writting the following instructions in the
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-R shell:
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-
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-source("http://www.bioconductor.org/biocLite.R")
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-biocLite("GSVA")
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-
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-
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-** CYGWIN
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-
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-You should have first Cygwin installed from:
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-
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-http://cygwin.com
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-
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-and follow the instructions to further install the GSL CYGWIN package.
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-Write down where the root of the GSL installation is in your hard disk.
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-Let's assume this path is C:\GSL. You should add an environment variable
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-called LIB_GSL that points to the root of this GSL installation, thus
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-setting in this example the value C:/GSL. Note that this path should be
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-set with slashes '/' instead of backslashes '\'. Then add the path
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-
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-C:/GSL/i383/bin
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-
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-to your PATH environment variable if your windows installation is 32bit
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-and add
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-
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-C:/GSL/x64/bin
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-
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-instead to your PATH environment variable if your windows installation
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-is 64bit.
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-
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-You can add and modify environment variables by right-clicking on the
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-"My PC" icon, select "Properties", go to the "Advanced" tab and click
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-on "Environment variables" where you'll be able to add and/or modify
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-these variables. Remember to separate paths of the filesystem with
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-a semicolon ';'.
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-
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-Once the environment variables are set you should press 'Ok' through
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-all previously opened dialog boxes and you should be able to install GSVA
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-in the usual way as with any other Bioconductor package by writting the
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-following instructions in the R shell:
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-
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-source("http://www.bioconductor.org/biocLite.R")
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-biocLite("GSVA")
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-
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-# Free Software Foundation, Inc.
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-# This file is free software; the Free Software Foundation
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-# gives unlimited permission to copy and/or distribute it,
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-# with or without modifications, as long as this notice is preserved.
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-
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-# This program is distributed in the hope that it will be useful,
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-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
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-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
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-# the Free Software Foundation; either version 2 of the License, or
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-# (at your option) any later version.
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-#
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-# This program is distributed in the hope that it will be useful, but
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-# WITHOUT ANY WARRANTY; without even the implied warranty of
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-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
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-# General Public License for more details.
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-#
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-# You should have received a copy of the GNU General Public License
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-# along with this program; if not, write to the Free Software
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-# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
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-#
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-# As a special exception to the GNU General Public License, if you
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-# distribute this file as part of a program that contains a
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-# configuration script generated by Autoconf, you may include it under
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-_PKG_TEXT
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-To get pkg-config, see <http://pkg-config.freedesktop.org/>.])],
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-else
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-])# PKG_CHECK_MODULES
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-AC_DEFUN([AM_PATH_GSL],
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-[
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-AC_ARG_WITH(gsl-prefix,[  --with-gsl-prefix=PFX   Prefix where GSL is installed (optional)],
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-            gsl_prefix="$withval", gsl_prefix="")
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-AC_ARG_WITH(gsl-exec-prefix,[  --with-gsl-exec-prefix=PFX Exec prefix where GSL is installed (optional)],
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-            gsl_exec_prefix="$withval", gsl_exec_prefix="")
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-AC_ARG_ENABLE(gsltest, [  --disable-gsltest       Do not try to compile and run a test GSL program],
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-		    , enable_gsltest=yes)
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-  if test "x${GSL_CONFIG+set}" != xset ; then
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-  else
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-
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-
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-      AC_TRY_RUN([
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-#include <stdio.h>
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-{
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-int main (void)
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-{
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-   }
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-   if (($gsl_major_version > major) ||
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-      (($gsl_major_version == major) && ($gsl_minor_version > minor)) ||
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-    {
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-      exit(0);
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-    }
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-  else
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-    {
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-      printf("\n*** 'gsl-config --version' returned %d.%d.%d, but the minimum version\n", $gsl_major_version, $gsl_minor_version, $gsl_micro_version);
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-      printf("*** of GSL required is %d.%d.%d. If gsl-config is correct, then it is\n", major, minor, micro);
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-      printf("*** best to upgrade to the required version.\n");
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-      printf("*** If gsl-config was wrong, set the environment variable GSL_CONFIG\n");
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-      printf("*** to point to the correct copy of gsl-config, and remove the file\n");
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-      printf("*** config.cache before re-running configure\n");
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-      exit(1);
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-    }
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-}
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-       CFLAGS="$ac_save_CFLAGS"
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-       LIBS="$ac_save_LIBS"
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-     fi
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-  fi
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-  if test "x$no_gsl" = x ; then
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-     AC_MSG_RESULT(yes)
296
-     ifelse([$2], , :, [$2])     
297
-  else
298
-     AC_MSG_RESULT(no)
299
-     if test "$GSL_CONFIG" = "no" ; then
300
-       echo "*** The gsl-config script installed by GSL could not be found"
301
-       echo "*** If GSL was installed in PREFIX, make sure PREFIX/bin is in"
302
-       echo "*** your path, or set the GSL_CONFIG environment variable to the"
303
-       echo "*** full path to gsl-config."
304
-     else
305
-       if test -f conf.gsltest ; then
306
-        :
307
-       else
308
-          echo "*** Could not run GSL test program, checking why..."
309
-          CFLAGS="$CFLAGS $GSL_CFLAGS"
310
-          LIBS="$LIBS $GSL_LIBS"
311
-          AC_TRY_LINK([
312
-#include <stdio.h>
313
-],      [ return 0; ],
314
-        [ echo "*** The test program compiled, but did not run. This usually means"
315
-          echo "*** that the run-time linker is not finding GSL or finding the wrong"
316
-          echo "*** version of GSL. If it is not finding GSL, you'll need to set your"
317
-          echo "*** LD_LIBRARY_PATH environment variable, or edit /etc/ld.so.conf to point"
318
-          echo "*** to the installed location  Also, make sure you have run ldconfig if that"
319
-          echo "*** is required on your system"
320
-	  echo "***"
321
-          echo "*** If you have an old version installed, it is best to remove it, although"
322
-          echo "*** you may also be able to get things to work by modifying LD_LIBRARY_PATH"],
323
-        [ echo "*** The test program failed to compile or link. See the file config.log for the"
324
-          echo "*** exact error that occured. This usually means GSL was incorrectly installed"
325
-          echo "*** or that you have moved GSL since it was installed. In the latter case, you"
326
-          echo "*** may want to edit the gsl-config script: $GSL_CONFIG" ])
327
-          CFLAGS="$ac_save_CFLAGS"
328
-          LIBS="$ac_save_LIBS"
329
-       fi
330
-     fi
331
-#     GSL_CFLAGS=""
332
-#     GSL_LIBS=""
333
-     ifelse([$3], , :, [$3])
334
-  fi
335
-  AC_SUBST(GSL_CFLAGS)
336
-  AC_SUBST(GSL_LIBS)
337
-  rm -f conf.gsltest
338
-])
339
-
340
-
341
-
342
-AC_DEFUN([ACX_BLAS], [
343
-AC_PREREQ(2.50)
344
-AC_REQUIRE([AC_F77_LIBRARY_LDFLAGS])
345
-acx_blas_ok=no
346
-
347
-AC_ARG_WITH(blas,
348
-        [AC_HELP_STRING([--with-blas=<lib>], [use BLAS library <lib>])])
349
-case $with_blas in
350
-        yes | "") ;;
351
-        no) acx_blas_ok=disable ;;
352
-        -* | */* | *.a | *.so | *.so.* | *.o) BLAS_LIBS="$with_blas" ;;
353
-        *) BLAS_LIBS="-l$with_blas" ;;
354
-esac
355
-
356
-# Get fortran linker names of BLAS functions to check for.
357
-AC_F77_FUNC(sgemm)
358
-AC_F77_FUNC(dgemm)
359
-
360
-acx_blas_save_LIBS="$LIBS"
361
-LIBS="$LIBS $FLIBS"
362
-
363
-# First, check BLAS_LIBS environment variable
364
-if test $acx_blas_ok = no; then
365
-if test "x$BLAS_LIBS" != x; then
366
-        save_LIBS="$LIBS"; LIBS="$BLAS_LIBS $LIBS"
367
-        AC_MSG_CHECKING([for $sgemm in $BLAS_LIBS])
368
-        AC_TRY_LINK_FUNC($sgemm, [acx_blas_ok=yes], [BLAS_LIBS=""])
369
-        AC_MSG_RESULT($acx_blas_ok)
370
-        LIBS="$save_LIBS"
371
-fi
372
-fi
373
-
374
-# BLAS linked to by default?  (happens on some supercomputers)
375
-if test $acx_blas_ok = no; then
376
-        save_LIBS="$LIBS"; LIBS="$LIBS"
377
-        AC_CHECK_FUNC($sgemm, [acx_blas_ok=yes])
378
-        LIBS="$save_LIBS"
379
-fi
380
-
381
-# BLAS in ATLAS library? (http://math-atlas.sourceforge.net/)
382
-if test $acx_blas_ok = no; then
383
-        AC_CHECK_LIB(atlas, ATL_xerbla,
384
-                [AC_CHECK_LIB(f77blas, $sgemm,
385
-                [AC_CHECK_LIB(cblas, cblas_dgemm,
386
-                        [acx_blas_ok=yes
387
-                         BLAS_LIBS="-lcblas -lf77blas -latlas"],
388
-                        [], [-lf77blas -latlas])],
389
-                        [], [-latlas])])
390
-fi
391
-
392
-# BLAS in PhiPACK libraries? (requires generic BLAS lib, too)
393
-if test $acx_blas_ok = no; then
394
-        AC_CHECK_LIB(blas, $sgemm,
395
-                [AC_CHECK_LIB(dgemm, $dgemm,
396
-                [AC_CHECK_LIB(sgemm, $sgemm,
397
-                        [acx_blas_ok=yes; BLAS_LIBS="-lsgemm -ldgemm -lblas"],
398
-                        [], [-lblas])],
399
-                        [], [-lblas])])
400
-fi
401
-
402
-# BLAS in Alpha CXML library?
403
-if test $acx_blas_ok = no; then
404
-        AC_CHECK_LIB(cxml, $sgemm, [acx_blas_ok=yes;BLAS_LIBS="-lcxml"])
405
-fi
406
-
407
-# BLAS in Alpha DXML library? (now called CXML, see above)
408
-if test $acx_blas_ok = no; then
409
-        AC_CHECK_LIB(dxml, $sgemm, [acx_blas_ok=yes;BLAS_LIBS="-ldxml"])
410
-fi
411
-
412
-# BLAS in Sun Performance library?
413
-if test $acx_blas_ok = no; then
414
-        if test "x$GCC" != xyes; then # only works with Sun CC
415
-                AC_CHECK_LIB(sunmath, acosp,
416
-                        [AC_CHECK_LIB(sunperf, $sgemm,
417
-                                [BLAS_LIBS="-xlic_lib=sunperf -lsunmath"
418
-                                 acx_blas_ok=yes],[],[-lsunmath])])
419
-        fi
420
-fi
421
-
422
-# BLAS in SCSL library?  (SGI/Cray Scientific Library)
423
-if test $acx_blas_ok = no; then
424
-        AC_CHECK_LIB(scs, $sgemm, [acx_blas_ok=yes; BLAS_LIBS="-lscs"])
425
-fi
426
-
427
-# BLAS in SGIMATH library?
428
-if test $acx_blas_ok = no; then
429
-        AC_CHECK_LIB(complib.sgimath, $sgemm,
430
-                     [acx_blas_ok=yes; BLAS_LIBS="-lcomplib.sgimath"])
431
-fi
432
-
433
-# BLAS in IBM ESSL library? (requires generic BLAS lib, too)
434
-if test $acx_blas_ok = no; then
435
-        AC_CHECK_LIB(blas, $sgemm,
436
-                [AC_CHECK_LIB(essl, $sgemm,
437
-                        [acx_blas_ok=yes; BLAS_LIBS="-lessl -lblas"],
438
-                        [], [-lblas $FLIBS])])
439
-fi
440
-
441
-# Generic BLAS library?
442
-if test $acx_blas_ok = no; then
443
-        AC_CHECK_LIB(blas, $sgemm, [acx_blas_ok=yes; BLAS_LIBS="-lblas"])
444
-fi
445
-
446
-AC_SUBST(BLAS_LIBS)
447
-
448
-LIBS="$acx_blas_save_LIBS"
449
-
450
-# Finally, execute ACTION-IF-FOUND/ACTION-IF-NOT-FOUND:
451
-if test x"$acx_blas_ok" = xyes; then
452
-        ifelse([$1],,AC_DEFINE(HAVE_BLAS,1,[Define if you have a BLAS library.]),[$1])
453
-        :
454
-else
455
-        acx_blas_ok=no
456
-        $2
457
-fi
458
-])dnl ACX_BLAS
459 0
deleted file mode 100755
... ...
@@ -1,4327 +0,0 @@
1
-#! /bin/sh
2
-# Guess values for system-dependent variables and create Makefiles.
3
-# Generated by GNU Autoconf 2.63.
4
-#
5
-# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
6
-# 2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
7
-# This configure script is free software; the Free Software Foundation
8
-# gives unlimited permission to copy, distribute and modify it.
9
-## --------------------- ##
10
-## M4sh Initialization.  ##
11
-## --------------------- ##
12
-
13
-# Be more Bourne compatible
14
-DUALCASE=1; export DUALCASE # for MKS sh
15
-if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
16
-  emulate sh
17
-  NULLCMD=:
18
-  # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
19
-  # is contrary to our usage.  Disable this feature.
20
-  alias -g '${1+"$@"}'='"$@"'
21
-  setopt NO_GLOB_SUBST
22
-else
23
-  case `(set -o) 2>/dev/null` in
24
-  *posix*) set -o posix ;;
25
-esac
26
-
27
-fi
28
-
29
-
30
-
31
-
32
-# PATH needs CR
33
-# Avoid depending upon Character Ranges.
34
-as_cr_letters='abcdefghijklmnopqrstuvwxyz'
35
-as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
36
-as_cr_Letters=$as_cr_letters$as_cr_LETTERS
37
-as_cr_digits='0123456789'
38
-as_cr_alnum=$as_cr_Letters$as_cr_digits
39
-
40
-as_nl='
41
-'
42
-export as_nl
43
-# Printing a long string crashes Solaris 7 /usr/bin/printf.
44
-as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
45
-as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
46
-as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
47
-if (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
48
-  as_echo='printf %s\n'
49
-  as_echo_n='printf %s'
50
-else
51
-  if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then
52
-    as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'
53
-    as_echo_n='/usr/ucb/echo -n'
54
-  else
55
-    as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
56
-    as_echo_n_body='eval
57
-      arg=$1;
58
-      case $arg in
59
-      *"$as_nl"*)
60
-	expr "X$arg" : "X\\(.*\\)$as_nl";
61
-	arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
62
-      esac;
63
-      expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl"
64
-    '
65
-    export as_echo_n_body
66
-    as_echo_n='sh -c $as_echo_n_body as_echo'
67
-  fi
68
-  export as_echo_body
69
-  as_echo='sh -c $as_echo_body as_echo'
70
-fi
71
-
72
-# The user is always right.
73
-if test "${PATH_SEPARATOR+set}" != set; then
74
-  PATH_SEPARATOR=:
75
-  (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && {
76
-    (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 ||
77
-      PATH_SEPARATOR=';'
78
-  }
79
-fi
80
-
81
-# Support unset when possible.
82
-if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then
83
-  as_unset=unset
84
-else
85
-  as_unset=false
86
-fi
87
-
88
-
89
-# IFS
90
-# We need space, tab and new line, in precisely that order.  Quoting is
91
-# there to prevent editors from complaining about space-tab.
92
-# (If _AS_PATH_WALK were called with IFS unset, it would disable word
93
-# splitting by setting IFS to empty value.)
94
-IFS=" ""	$as_nl"
95
-
96
-# Find who we are.  Look in the path if we contain no directory separator.
97
-case $0 in
98
-  *[\\/]* ) as_myself=$0 ;;
99
-  *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
100
-for as_dir in $PATH
101
-do
102
-  IFS=$as_save_IFS
103
-  test -z "$as_dir" && as_dir=.
104
-  test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
105
-done
106
-IFS=$as_save_IFS
107
-
108
-     ;;
109
-esac
110
-# We did not find ourselves, most probably we were run as `sh COMMAND'
111
-# in which case we are not to be found in the path.
112
-if test "x$as_myself" = x; then
113
-  as_myself=$0
114
-fi
115
-if test ! -f "$as_myself"; then
116
-  $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
117
-  { (exit 1); exit 1; }
118
-fi
119
-
120
-# Work around bugs in pre-3.0 UWIN ksh.
121
-for as_var in ENV MAIL MAILPATH
122
-do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var
123
-done
124
-PS1='$ '
125
-PS2='> '
126
-PS4='+ '
127
-
128
-# NLS nuisances.
129
-LC_ALL=C
130
-export LC_ALL
131
-LANGUAGE=C
132
-export LANGUAGE
133
-
134
-# Required to use basename.
135
-if expr a : '\(a\)' >/dev/null 2>&1 &&
136
-   test "X`expr 00001 : '.*\(...\)'`" = X001; then
137
-  as_expr=expr
138
-else
139
-  as_expr=false
140
-fi
141
-
142
-if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
143
-  as_basename=basename
144
-else
145
-  as_basename=false
146
-fi
147
-
148
-
149
-# Name of the executable.
150
-as_me=`$as_basename -- "$0" ||
151
-$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
152
-	 X"$0" : 'X\(//\)$' \| \
153
-	 X"$0" : 'X\(/\)' \| . 2>/dev/null ||
154
-$as_echo X/"$0" |
155
-    sed '/^.*\/\([^/][^/]*\)\/*$/{
156
-	    s//\1/
157
-	    q
158
-	  }
159
-	  /^X\/\(\/\/\)$/{
160
-	    s//\1/
161
-	    q
162
-	  }
163
-	  /^X\/\(\/\).*/{
164
-	    s//\1/
165
-	    q
166
-	  }
167
-	  s/.*/./; q'`
168
-
169
-# CDPATH.
170
-$as_unset CDPATH
171
-
172
-
173
-if test "x$CONFIG_SHELL" = x; then
174
-  if (eval ":") 2>/dev/null; then
175
-  as_have_required=yes
176
-else
177
-  as_have_required=no
178
-fi
179
-
180
-  if test $as_have_required = yes &&	 (eval ":
181
-(as_func_return () {
182
-  (exit \$1)
183
-}
184
-as_func_success () {
185
-  as_func_return 0
186
-}
187
-as_func_failure () {
188
-  as_func_return 1
189
-}
190
-as_func_ret_success () {
191
-  return 0
192
-}
193
-as_func_ret_failure () {
194
-  return 1
195
-}
196
-
197
-exitcode=0
198
-if as_func_success; then
199
-  :
200
-else
201
-  exitcode=1
202
-  echo as_func_success failed.
203
-fi
204
-
205
-if as_func_failure; then
206
-  exitcode=1
207
-  echo as_func_failure succeeded.
208
-fi
209
-
210
-if as_func_ret_success; then
211
-  :
212
-else
213
-  exitcode=1
214
-  echo as_func_ret_success failed.
215
-fi
216
-
217
-if as_func_ret_failure; then
218
-  exitcode=1
219
-  echo as_func_ret_failure succeeded.
220
-fi
221
-
222
-if ( set x; as_func_ret_success y && test x = \"\$1\" ); then
223
-  :
224
-else
225
-  exitcode=1
226
-  echo positional parameters were not saved.
227
-fi
228
-
229
-test \$exitcode = 0) || { (exit 1); exit 1; }
230
-
231
-(
232
-  as_lineno_1=\$LINENO
233
-  as_lineno_2=\$LINENO
234
-  test \"x\$as_lineno_1\" != \"x\$as_lineno_2\" &&
235
-  test \"x\`expr \$as_lineno_1 + 1\`\" = \"x\$as_lineno_2\") || { (exit 1); exit 1; }
236
-") 2> /dev/null; then
237
-  :
238
-else
239
-  as_candidate_shells=
240
-    as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
241
-for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH
242
-do
243
-  IFS=$as_save_IFS
244
-  test -z "$as_dir" && as_dir=.
245
-  case $as_dir in
246
-	 /*)
247
-	   for as_base in sh bash ksh sh5; do
248
-	     as_candidate_shells="$as_candidate_shells $as_dir/$as_base"
249
-	   done;;
250
-       esac
251
-done
252
-IFS=$as_save_IFS
253
-
254
-
255
-      for as_shell in $as_candidate_shells $SHELL; do
256
-	 # Try only shells that exist, to save several forks.
257
-	 if { test -f "$as_shell" || test -f "$as_shell.exe"; } &&
258
-		{ ("$as_shell") 2> /dev/null <<\_ASEOF
259
-if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
260
-  emulate sh
261
-  NULLCMD=:
262
-  # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
263
-  # is contrary to our usage.  Disable this feature.
264
-  alias -g '${1+"$@"}'='"$@"'
265
-  setopt NO_GLOB_SUBST
266
-else
267
-  case `(set -o) 2>/dev/null` in
268
-  *posix*) set -o posix ;;
269
-esac
270
-
271
-fi
272
-
273
-
274
-:
275
-_ASEOF
276
-}; then
277
-  CONFIG_SHELL=$as_shell
278
-	       as_have_required=yes
279
-	       if { "$as_shell" 2> /dev/null <<\_ASEOF
280
-if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
281
-  emulate sh
282
-  NULLCMD=:
283
-  # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
284
-  # is contrary to our usage.  Disable this feature.
285
-  alias -g '${1+"$@"}'='"$@"'
286
-  setopt NO_GLOB_SUBST
287
-else
288
-  case `(set -o) 2>/dev/null` in
289
-  *posix*) set -o posix ;;
290
-esac
291
-
292
-fi
293
-
294
-
295
-:
296
-(as_func_return () {
297
-  (exit $1)
298
-}
299
-as_func_success () {
300
-  as_func_return 0
301
-}
302
-as_func_failure () {
303
-  as_func_return 1
304
-}
305
-as_func_ret_success () {
306
-  return 0
307
-}
308
-as_func_ret_failure () {
309
-  return 1
310
-}
311
-
312
-exitcode=0
313
-if as_func_success; then
314
-  :
315
-else
316
-  exitcode=1
317
-  echo as_func_success failed.
318
-fi
319
-
320
-if as_func_failure; then
321
-  exitcode=1
322
-  echo as_func_failure succeeded.
323
-fi
324
-
325
-if as_func_ret_success; then
326
-  :
327
-else
328
-  exitcode=1
329
-  echo as_func_ret_success failed.
330
-fi
331
-
332
-if as_func_ret_failure; then
333
-  exitcode=1
334
-  echo as_func_ret_failure succeeded.
335
-fi
336
-
337
-if ( set x; as_func_ret_success y && test x = "$1" ); then
338
-  :
339
-else
340
-  exitcode=1
341
-  echo positional parameters were not saved.
342
-fi
343
-
344
-test $exitcode = 0) || { (exit 1); exit 1; }
345
-
346
-(
347
-  as_lineno_1=$LINENO
348
-  as_lineno_2=$LINENO
349
-  test "x$as_lineno_1" != "x$as_lineno_2" &&
350
-  test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2") || { (exit 1); exit 1; }
351
-
352
-_ASEOF
353
-}; then
354
-  break
355
-fi
356
-
357
-fi
358
-
359
-      done
360
-
361
-      if test "x$CONFIG_SHELL" != x; then
362
-  for as_var in BASH_ENV ENV
363
-	do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var
364
-	done
365
-	export CONFIG_SHELL
366
-	exec "$CONFIG_SHELL" "$as_myself" ${1+"$@"}
367
-fi
368
-
369
-
370
-    if test $as_have_required = no; then
371
-  echo This script requires a shell more modern than all the
372
-      echo shells that I found on your system.  Please install a
373
-      echo modern shell, or manually run the script under such a
374
-      echo shell if you do have one.
375
-      { (exit 1); exit 1; }
376
-fi
377
-
378
-
379
-fi
380
-
381
-fi
382
-
383
-
384
-
385
-(eval "as_func_return () {
386
-  (exit \$1)
387
-}
388
-as_func_success () {
389
-  as_func_return 0
390
-}
391
-as_func_failure () {
392
-  as_func_return 1
393
-}
394
-as_func_ret_success () {
395
-  return 0
396
-}
397
-as_func_ret_failure () {
398
-  return 1
399
-}
400
-
401
-exitcode=0
402
-if as_func_success; then
403
-  :
404
-else
405
-  exitcode=1
406
-  echo as_func_success failed.
407
-fi
408
-
409
-if as_func_failure; then
410
-  exitcode=1
411
-  echo as_func_failure succeeded.
412
-fi
413
-
414
-if as_func_ret_success; then
415
-  :
416
-else
417
-  exitcode=1
418
-  echo as_func_ret_success failed.
419
-fi
420
-
421
-if as_func_ret_failure; then
422
-  exitcode=1
423
-  echo as_func_ret_failure succeeded.
424
-fi
425
-
426
-if ( set x; as_func_ret_success y && test x = \"\$1\" ); then
427
-  :
428
-else
429
-  exitcode=1
430
-  echo positional parameters were not saved.
431
-fi
432
-
433
-test \$exitcode = 0") || {
434
-  echo No shell found that supports shell functions.
435
-  echo Please tell bug-autoconf@gnu.org about your system,
436
-  echo including any error possibly output before this message.
437
-  echo This can help us improve future autoconf versions.
438
-  echo Configuration will now proceed without shell functions.
439
-}
440
-
441
-
442
-
443
-  as_lineno_1=$LINENO
444
-  as_lineno_2=$LINENO
445
-  test "x$as_lineno_1" != "x$as_lineno_2" &&
446
-  test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2" || {
447
-
448
-  # Create $as_me.lineno as a copy of $as_myself, but with $LINENO
449
-  # uniformly replaced by the line number.  The first 'sed' inserts a
450
-  # line-number line after each line using $LINENO; the second 'sed'
451
-  # does the real work.  The second script uses 'N' to pair each
452
-  # line-number line with the line containing $LINENO, and appends
453
-  # trailing '-' during substitution so that $LINENO is not a special
454
-  # case at line end.
455
-  # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the
456
-  # scripts with optimization help from Paolo Bonzini.  Blame Lee
457
-  # E. McMahon (1931-1989) for sed's syntax.  :-)
458
-  sed -n '
459
-    p
460
-    /[$]LINENO/=
461
-  ' <$as_myself |
462
-    sed '
463
-      s/[$]LINENO.*/&-/
464
-      t lineno
465
-      b
466
-      :lineno
467
-      N
468
-      :loop
469
-      s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/
470
-      t loop
471
-      s/-\n.*//
472
-    ' >$as_me.lineno &&
473
-  chmod +x "$as_me.lineno" ||
474
-    { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2
475
-   { (exit 1); exit 1; }; }
476
-
477
-  # Don't try to exec as it changes $[0], causing all sort of problems
478
-  # (the dirname of $[0] is not the place where we might find the
479
-  # original and so on.  Autoconf is especially sensitive to this).
480
-  . "./$as_me.lineno"
481
-  # Exit status is that of the last command.
482
-  exit
483
-}
484
-
485
-
486
-if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
487
-  as_dirname=dirname
488
-else
489
-  as_dirname=false
490
-fi
491
-
492
-ECHO_C= ECHO_N= ECHO_T=
493
-case `echo -n x` in
494
--n*)
495
-  case `echo 'x\c'` in
496
-  *c*) ECHO_T='	';;	# ECHO_T is single tab character.
497
-  *)   ECHO_C='\c';;
498
-  esac;;
499
-*)
500
-  ECHO_N='-n';;
501
-esac
502
-if expr a : '\(a\)' >/dev/null 2>&1 &&
503
-   test "X`expr 00001 : '.*\(...\)'`" = X001; then
504
-  as_expr=expr
505
-else
506
-  as_expr=false
507
-fi
508
-
509
-rm -f conf$$ conf$$.exe conf$$.file
510
-if test -d conf$$.dir; then
511
-  rm -f conf$$.dir/conf$$.file
512
-else
513
-  rm -f conf$$.dir
514
-  mkdir conf$$.dir 2>/dev/null
515
-fi
516
-if (echo >conf$$.file) 2>/dev/null; then
517
-  if ln -s conf$$.file conf$$ 2>/dev/null; then
518
-    as_ln_s='ln -s'
519
-    # ... but there are two gotchas:
520
-    # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
521
-    # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
522
-    # In both cases, we have to default to `cp -p'.
523
-    ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
524
-      as_ln_s='cp -p'
525
-  elif ln conf$$.file conf$$ 2>/dev/null; then
526
-    as_ln_s=ln
527
-  else
528
-    as_ln_s='cp -p'
529
-  fi
530
-else
531
-  as_ln_s='cp -p'
532
-fi
533
-rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
534
-rmdir conf$$.dir 2>/dev/null
535
-
536
-if mkdir -p . 2>/dev/null; then
537
-  as_mkdir_p=:
538
-else
539
-  test -d ./-p && rmdir ./-p
540
-  as_mkdir_p=false
541
-fi
542
-
543
-if test -x / >/dev/null 2>&1; then
544
-  as_test_x='test -x'
545
-else
546
-  if ls -dL / >/dev/null 2>&1; then
547
-    as_ls_L_option=L
548
-  else
549
-    as_ls_L_option=
550
-  fi
551
-  as_test_x='
552
-    eval sh -c '\''
553
-      if test -d "$1"; then
554
-	test -d "$1/.";
555
-      else
556
-	case $1 in
557
-	-*)set "./$1";;
558
-	esac;
559
-	case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in
560
-	???[sx]*):;;*)false;;esac;fi
561
-    '\'' sh
562
-  '
563
-fi
564
-as_executable_p=$as_test_x
565
-
566
-# Sed expression to map a string onto a valid CPP name.
567
-as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
568
-
569
-# Sed expression to map a string onto a valid variable name.
570
-as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"
571
-
572
-
573
-
574
-exec 7<&0 </dev/null 6>&1
575
-
576
-# Name of the host.
577
-# hostname on some systems (SVR3.2, Linux) returns a bogus exit status,
578
-# so uname gets run too.
579
-ac_hostname=`(hostname || uname -n) 2>/dev/null | sed 1q`
580
-
581
-#
582
-# Initializations.
583
-#
584
-ac_default_prefix=/usr/local
585
-ac_clean_files=
586
-ac_config_libobj_dir=.
587
-LIBOBJS=
588
-cross_compiling=no
589
-subdirs=
590
-MFLAGS=
591
-MAKEFLAGS=
592
-SHELL=${CONFIG_SHELL-/bin/sh}
593
-
594
-# Identity of this package.
595
-PACKAGE_NAME=
596
-PACKAGE_TARNAME=
597
-PACKAGE_VERSION=
598
-PACKAGE_STRING=
599
-PACKAGE_BUGREPORT=
600
-
601
-ac_unique_file="GSVA"
602
-ac_subst_vars='LTLIBOBJS
603
-LIBOBJS
604
-OBJEXT
605
-EXEEXT
606
-ac_ct_CC
607
-CPPFLAGS
608
-LDFLAGS
609
-CFLAGS
610
-CC
611
-GSL_CONFIG
612
-GSL_LIBS
613
-GSL_CFLAGS
614
-PKG_CONFIG
615
-target_alias
616
-host_alias
617
-build_alias
618
-LIBS
619
-ECHO_T
620
-ECHO_N
621
-ECHO_C
622
-DEFS
623
-mandir
624
-localedir
625
-libdir
626
-psdir
627
-pdfdir
628
-dvidir
629
-htmldir
630
-infodir
631
-docdir
632
-oldincludedir
633
-includedir
634
-localstatedir
635
-sharedstatedir
636
-sysconfdir
637
-datadir
638
-datarootdir
639
-libexecdir
640
-sbindir
641
-bindir
642
-program_transform_name
643
-prefix
644
-exec_prefix
645
-PACKAGE_BUGREPORT
646
-PACKAGE_STRING
647
-PACKAGE_VERSION
648
-PACKAGE_TARNAME
649
-PACKAGE_NAME
650
-PATH_SEPARATOR
651
-SHELL'
652
-ac_subst_files=''
653
-ac_user_opts='
654
-enable_option_checking
655
-with_blas
656
-with_gsl_prefix
657
-with_gsl_exec_prefix
658
-enable_gsltest
659
-'
660
-      ac_precious_vars='build_alias
661
-host_alias
662
-target_alias
663
-PKG_CONFIG
664
-GSL_CFLAGS
665
-GSL_LIBS
666
-CC
667
-CFLAGS
668
-LDFLAGS
669
-LIBS
670
-CPPFLAGS'
671
-
672
-
673
-# Initialize some variables set by options.
674
-ac_init_help=
675
-ac_init_version=false
676
-ac_unrecognized_opts=
677
-ac_unrecognized_sep=
678
-# The variables have the same names as the options, with
679
-# dashes changed to underlines.
680
-cache_file=/dev/null
681
-exec_prefix=NONE
682
-no_create=
683
-no_recursion=
684
-prefix=NONE
685
-program_prefix=NONE
686
-program_suffix=NONE
687
-program_transform_name=s,x,x,
688
-silent=
689
-site=
690
-srcdir=
691
-verbose=
692
-x_includes=NONE
693
-x_libraries=NONE
694
-
695
-# Installation directory options.
696
-# These are left unexpanded so users can "make install exec_prefix=/foo"
697
-# and all the variables that are supposed to be based on exec_prefix
698
-# by default will actually change.
699
-# Use braces instead of parens because sh, perl, etc. also accept them.
700
-# (The list follows the same order as the GNU Coding Standards.)
701
-bindir='${exec_prefix}/bin'
702
-sbindir='${exec_prefix}/sbin'
703
-libexecdir='${exec_prefix}/libexec'
704
-datarootdir='${prefix}/share'
705
-datadir='${datarootdir}'
706
-sysconfdir='${prefix}/etc'
707
-sharedstatedir='${prefix}/com'
708
-localstatedir='${prefix}/var'
709
-includedir='${prefix}/include'
710
-oldincludedir='/usr/include'
711
-docdir='${datarootdir}/doc/${PACKAGE}'
712
-infodir='${datarootdir}/info'
713
-htmldir='${docdir}'
714
-dvidir='${docdir}'
715
-pdfdir='${docdir}'
716
-psdir='${docdir}'
717
-libdir='${exec_prefix}/lib'
718
-localedir='${datarootdir}/locale'
719
-mandir='${datarootdir}/man'
720
-
721
-ac_prev=
722
-ac_dashdash=
723
-for ac_option
724
-do
725
-  # If the previous option needs an argument, assign it.
726
-  if test -n "$ac_prev"; then
727
-    eval $ac_prev=\$ac_option
728
-    ac_prev=
729
-    continue
730
-  fi
731
-
732
-  case $ac_option in
733
-  *=*)	ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;;
734
-  *)	ac_optarg=yes ;;
735
-  esac
736
-
737
-  # Accept the important Cygnus configure options, so we can diagnose typos.
738
-
739
-  case $ac_dashdash$ac_option in
740
-  --)
741
-    ac_dashdash=yes ;;
742
-
743
-  -bindir | --bindir | --bindi | --bind | --bin | --bi)
744
-    ac_prev=bindir ;;
745
-  -bindir=* | --bindir=* | --bindi=* | --bind=* | --bin=* | --bi=*)
746
-    bindir=$ac_optarg ;;
747
-
748
-  -build | --build | --buil | --bui | --bu)
749
-    ac_prev=build_alias ;;
750
-  -build=* | --build=* | --buil=* | --bui=* | --bu=*)
751
-    build_alias=$ac_optarg ;;
752
-
753
-  -cache-file | --cache-file | --cache-fil | --cache-fi \
754
-  | --cache-f | --cache- | --cache | --cach | --cac | --ca | --c)
755