[BioC] problem installing package GLAD under R-2.10.0

Laurent Gatto laurent.gatto at gmail.com
Wed Dec 16 18:38:39 CET 2009


Dear Wolfgang,

I would say that you need to install the Gnu Scientific Library in a
first time to install the package. On my ubuntu system, the package is
'libgsl0-dev' if I remember well (GLAD installs at least flawlessly
with libgsl0-dev installed).
I can't help with the installation on Windows.

Hope this helps.

Laurent

On Tue, Dec 15, 2009 at 2:33 PM, Wolfgang Raffelsberger <wraff at igbmc.fr> wrote:
> 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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