[BioC] problem installing package GLAD under R-2.10.0

Thu Dec 17 10:01:02 CET 2009

Hello Wolfgang,

First you need to have the GSl library installed on your system.

On my debian, I have the following packages:
gsl-bin
libgsl0-dev
libgsl0ldbl

During the installation, the script need to know where gsl-config
program is installed. Normally this is located in standard path but  if
it is not the case to need to do the following in a bash:
export PATH=$PATH:/your/path/to/gsl-config and the installation will
proceed.

 For windows, just follows the README of the package:

You need the GNU Scientific Library (GSL) for the GLAD package. Make
sure it is installed on your machine if you want to use GLAD. GSL is
free and can be downloaded at http://www.gnu.org/software/gsl/ for unix
distributions and at http://gnuwin32.sourceforge.net/packages/gsl.htm
for Windows.

Windows users
=============

To install a pre-built binary of GLAD and to load the package
successfully you need to tell R where to link GSL. You can do that by
adding /path/to/libgsl.dll to the Path environment variable. To add this
you may right click on "My Computer", choose "Properties", select the
"Advanced" tab, and click the button "Environment Variables". In the
dialog box that opens, click "Path" in the variable list, and then click
"Edit". Add /path/to/libgsl.dll to the Variable value field. It is
important that the file path does not contain any space characters; to
avoid this you may simply use the short forms (8.3 DOS file names) found
by typing "dir /x" at the Windows command line. For example, I added the
following on my Windows machine:
C:/PROGRA~1/GNUWIN32/bin
and used ";" to separate it from existing paths.

To build the GLAD package from source (using Rtools), in addition to
adding /path/to/libgsl.dll to Path, you need to tell GLAD where your GSL
library and header files are. You can do that by setting up two
environment variables GSL_LIB and GSL_INC with the correct path to the
library files and header files respectively. You can do this by going to
the "Environment Variables" dialog box as instructed above and then
clicking the "New" button. Enter "GSL_LIB" in the Variable name field,
and /path/to/your/gsl/lib/directory in the Variable value field.
Likewise, do this for GSL_INC and /path/to/your/gsl/include/directory.
Remember to use "/" instead of "\" as the directory delimiter.

You can download Rtools at http://www.murdoch-sutherland.com/Rtools/
which provides the resources for building R and R packages. You should
add to the Path variable the paths to the various components of Rtools.
Please read the "Windows Toolset" appendix at
http://cran.r-project.org/doc/manuals/R-admin.html#The-Windows-toolset
for more details.

Let me know if any problem.

hth.

Cheers,

Philippe

Wolfgang Raffelsberger a écrit :
> Dear list,
>
> all at sudden I have problems installing and/or loading the package
> "GLAD".  The installation part seems to work OK well on Windows XP but
> Linux tells me already at this level about a problem at the
> configuration level. Anyway, neither on Windows XP as in Fedora Linux
> can't load it afterwards !?
> With R-2.9.x I didn't have this problem (neither Linux or Win).
> Any suggestions ?
>
> Thank's in advance,
> Wolfgang Raffelsberger
>
>
> #### LINUX
> > source("http://www.bioconductor.org/biocLite.R")
> > biocLite("GLAD")
> Using R version 2.10.0, biocinstall version 2.5.8.
> Installing Bioconductor version 2.5 packages:
> [1] "GLAD"
> Please wait...
>
> trying URL
> 'http://bioconductor.org/packages/2.5/bioc/src/contrib/GLAD_2.6.0.tar.gz'
> Content type 'application/x-gzip' length 1297578 bytes (1.2 Mb)
> opened URL
> ==================================================
> downloaded 1.2 Mb
>
> * installing *source* package 'GLAD' ...
> checking for pkg-config... /usr/bin/pkg-config
> checking pkg-config is at least version 0.9.0... yes
> checking for GSL... no
> checking for gcc... gcc -std=gnu99
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc -std=gnu99 accepts -g... yes
> checking for gcc -std=gnu99 option to accept ISO C89... none needed
> checking for gsl-config... no
> checking for GSL - version >= 1.6... no
> *** The gsl-config script installed by GSL could not be found
> *** If GSL was installed in PREFIX, make sure PREFIX/bin is in
> *** your path, or set the GSL_CONFIG environment variable to the
> *** full path to gsl-config.
> configure: error: Cannot find Gnu Scientific Library >=1.6
> ERROR: configuration failed for package 'GLAD'
> * removing '/linux/local/lib64/R/library/GLAD'
>
> The downloaded packages are in
>        '/tmp/Rtmps5w1d6/downloaded_packages'
> Updating HTML index of packages in '.Library'
> Warning message:
> In install.packages(pkgs = pkgs, repos = repos, ...) :
>  installation of package 'GLAD' had non-zero exit status
> >
> > library(GLAD)
> Error in library(GLAD) : there is no package called 'GLAD'
> >
> > sessionInfo()
> R version 2.10.0 (2009-10-26)
> x86_64-unknown-linux-gnu
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base   
> loaded via a namespace (and not attached):
> [1] tools_2.10.0
>
>
> #### WINDOWS
> > source("http://www.bioconductor.org/biocLite.R")
> > biocLite("GLAD")
> Using R version 2.10.0, biocinstall version 2.5.8.
> Installing Bioconductor version 2.5 packages:
> [1] "GLAD"
> Please wait...
>
> trying URL
> 'http://bioconductor.org/packages/2.5/bioc/bin/windows/contrib/2.10/GLAD_2.6.0.zip'
>
> Content type 'application/zip' length 1773962 bytes (1.7 Mb)
> opened URL
> downloaded 1.7 Mb
>
> package 'GLAD' successfully unpacked and MD5 sums checked
>
> The downloaded packages are in
>        C:\Documents and Settings\wraff\Local
> Settings\Temp\RtmpJgMkmr\downloaded_packages
> >
> > library(GLAD)
> Error in inDL(x, as.logical(local), as.logical(now), ...) :
>  unable to load shared library
> 'C:/PROGRA~1/R/R-210~1.0/library/GLAD/libs/GLAD.dll':
>  LoadLibrary failure:  Le module spécifié est introuvable.
>
>
> Error: package/namespace load failed for 'GLAD'
>
> > ## translated to English : LoadLibrary failure:  The specified
> module can't be found.
> >
> > sessionInfo()
> R version 2.10.0 (2009-10-26)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252   
> LC_MONETARY=French_France.1252 LC_NUMERIC=C                 [5]
> LC_TIME=French_France.1252  
> attached base packages:
> [1] grDevices datasets  tools     splines   graphics  stats    
> tcltk     utils     methods   base   
> other attached packages:
> [1] svSocket_0.9-43 svMisc_0.9-56   TinnR_1.0.3     R2HTML_1.59-1  
> Hmisc_3.7-0     survival_2.35-7
>
> loaded via a namespace (and not attached):
> [1] cluster_1.12.1  grid_2.10.0     lattice_0.17-26
>
>
>
> . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
> Wolfgang Raffelsberger, PhD
> Laboratoire de BioInformatique et Génomique Intégratives
> IGBMC,  1 rue Laurent Fries,  67404 Illkirch  Strasbourg,  France
> Tel (+33) 388 65 3300         Fax (+33) 388 65 3276
> wolfgang.raffelsberger (at) igbmc.fr
>
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>
>

-- 
Philippe Hupé
Institut Curie, CNRS UMR 144, INSERM U900
26 rue d'Ulm
75005 Paris - France

Email :  Philippe.Hupe at curie.fr
Tél :	 +33 (0)1 56 24 69 91
Fax:     +33 (0)1 56 24 69 11
website : http://bioinfo.curie.fr