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/GL AD_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 sp?cifi? 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 G?nomique Int?gratives IGBMC, 1 rue Laurent Fries, 67404 Illkirch Strasbourg, France Tel (+33) 388 65 3300 Fax (+33) 388 65 3276 wolfgang.raffelsberger (at) igbmc.fr

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.ta r.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 sp?cifi? 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 G?nomique Int?gratives > IGBMC, ?1 rue Laurent Fries, ?67404 Illkirch ?Strasbourg, ?France > Tel (+33) 388 65 3300 ? ? ? ? Fax (+33) 388 65 3276 > wolfgang.raffelsberger (at) igbmc.fr > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >

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 ?crit : > 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.ta r.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 sp?cifi? 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 G?nomique Int?gratives > IGBMC, 1 rue Laurent Fries, 67404 Illkirch Strasbourg, France > Tel (+33) 388 65 3300 Fax (+33) 388 65 3276 > wolfgang.raffelsberger (at) igbmc.fr > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- Philippe Hup? Institut Curie, CNRS UMR 144, INSERM U900 26 rue d'Ulm 75005 Paris - France Email : Philippe.Hupe at curie.fr T?l : +33 (0)1 56 24 69 91 Fax: +33 (0)1 56 24 69 11 website : http://bioinfo.curie.fr