Hi, I downloaded the latest version of the snapCGH package, but it gives an error when I try to load it. Here is the error message: > library(snapCGH) Loading required package: limma Loading required package: tilingArray Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: pixmap Loading required package: DNAcopy Attaching package: 'DNAcopy' The following object(s) are masked from package:tilingArray : segment Loading required package: GLAD Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared library 'C:/PROGRA~1/R/library/GLAD/libs/GLAD.dll': LoadLibrary failure: The specified module could not be found. In addition: Warning messages: 1: package 'limma' was built under R version 2.8.0 and help will not work correctly Please re-install it 2: package 'Biobase' was built under R version 2.8.0 and help will not work correctly Please re-install it 3: package 'pixmap' was built under R version 2.10.1 Error: package 'GLAD' could not be loaded > sessionInfo() R version 2.10.0 (2009-10-26) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252 attached base packages: [1] tools stats graphics grDevices utils datasets methods base other attached packages: [1] DNAcopy_1.20.0 tilingArray_1.24.0 pixmap_0.4-10 Biobase_2.2.1 limma_2.16.3 loaded via a namespace (and not attached): [1] affy_1.20.0 affyio_1.10.1 annotate_1.20.1 AnnotationDbi_1.4.2 DBI_0.2-4 genefilter_1.22.0 grid_2.10.0 [8] lattice_0.17-26 preprocessCore_1.4.0 RColorBrewer_1.0-2 RSQLite_0.7-1 splines_2.10.0 strucchange_1.3-7 survival_2.35-7 [15] vsn_3.8.0 > Does anyone knows what seems to be the problem? Thanks in advance, Joao Fadista

Hi Joao, Looking at the code you reproduced below, I think the problem might be that the GLAD package is not installed correctly on your machine. Maybe if you reinstall GLAD that will help? Hope this is useful, John On Tue, Feb 9, 2010 at 10:34 AM, João Fadista <joao.fadista@agrsci.dk>wrote: > > Hi, > > I downloaded the latest version of the snapCGH package, but it gives an > error when I try to load it. Here is the error message: > > > library(snapCGH) > Loading required package: limma > Loading required package: tilingArray > Loading required package: Biobase > Loading required package: tools > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > Loading required package: pixmap > Loading required package: DNAcopy > > Attaching package: 'DNAcopy' > > > The following object(s) are masked from package:tilingArray : > > segment > > Loading required package: GLAD > Error in inDL(x, as.logical(local), as.logical(now), ...) : > unable to load shared library 'C:/PROGRA~1/R/library/GLAD/libs/GLAD.dll': > LoadLibrary failure: The specified module could not be found. > > > In addition: Warning messages: > 1: package 'limma' was built under R version 2.8.0 and help will not work > correctly > Please re-install it > 2: package 'Biobase' was built under R version 2.8.0 and help will not work > correctly > Please re-install it > 3: package 'pixmap' was built under R version 2.10.1 > Error: package 'GLAD' could not be loaded > > sessionInfo() > R version 2.10.0 (2009-10-26) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United > Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 > [4] LC_NUMERIC=C LC_TIME=English_United > Kingdom.1252 > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] DNAcopy_1.20.0 tilingArray_1.24.0 pixmap_0.4-10 Biobase_2.2.1 > limma_2.16.3 > > loaded via a namespace (and not attached): > [1] affy_1.20.0 affyio_1.10.1 annotate_1.20.1 > AnnotationDbi_1.4.2 DBI_0.2-4 genefilter_1.22.0 grid_2.10.0 > [8] lattice_0.17-26 preprocessCore_1.4.0 RColorBrewer_1.0-2 > RSQLite_0.7-1 splines_2.10.0 strucchange_1.3-7 > survival_2.35-7 > [15] vsn_3.8.0 > > > > > Does anyone knows what seems to be the problem? > Thanks in advance, > Joao Fadista > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- John Marioni, PhD Postdoctoral Scholar Department of Human Genetics University of Chicago [[alternative HTML version deleted]]

On Tue, Feb 9, 2010 at 11:34 AM, Jo?o Fadista <joao.fadista at="" agrsci.dk=""> wrote: > > Hi, > > I downloaded the latest version of the snapCGH package, but it gives an error when I try to load it. Here is the error message: > >> library(snapCGH) > Loading required package: limma > Loading required package: tilingArray > Loading required package: Biobase > Loading required package: tools > > Welcome to Bioconductor > > ?Vignettes contain introductory material. To view, type > ?'openVignette()'. To cite Bioconductor, see > ?'citation("Biobase")' and for packages 'citation(pkgname)'. > > Loading required package: pixmap > Loading required package: DNAcopy > > Attaching package: 'DNAcopy' > > > ? ? ? ?The following object(s) are masked from package:tilingArray : > > ? ? ? ? segment > > Loading required package: GLAD > Error in inDL(x, as.logical(local), as.logical(now), ...) : > ?unable to load shared library 'C:/PROGRA~1/R/library/GLAD/libs/GLAD.dll': > ?LoadLibrary failure: ?The specified module could not be found. > > > In addition: Warning messages: > 1: package 'limma' was built under R version 2.8.0 and help will not work correctly > Please re-install it > 2: package 'Biobase' was built under R version 2.8.0 and help will not work correctly > Please re-install it > 3: package 'pixmap' was built under R version 2.10.1 > Error: package 'GLAD' could not be loaded >> sessionInfo() > R version 2.10.0 (2009-10-26) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United Kingdom.1252 ?LC_CTYPE=English_United Kingdom.1252 ? ?LC_MONETARY=English_United Kingdom.1252 > [4] LC_NUMERIC=C ? ? ? ? ? ? ? ? ? ? ? ? ? ?LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] tools ? ? stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] DNAcopy_1.20.0 ? ? tilingArray_1.24.0 pixmap_0.4-10 ? ? ?Biobase_2.2.1 ? ? ?limma_2.16.3 > > loaded via a namespace (and not attached): > ?[1] affy_1.20.0 ? ? ? ? ?affyio_1.10.1 ? ? ? ?annotate_1.20.1 ? ? ?AnnotationDbi_1.4.2 ?DBI_0.2-4 ? ? ? ? ? ?genefilter_1.22.0 ? ?grid_2.10.0 > ?[8] lattice_0.17-26 ? ? ?preprocessCore_1.4.0 RColorBrewer_1.0-2 ? RSQLite_0.7-1 ? ? ? ?splines_2.10.0 ? ? ? strucchange_1.3-7 ? ?survival_2.35-7 > [15] vsn_3.8.0 >> > > > Does anyone knows what seems to be the problem? Hi, Joao. It looks like you have quite a mixture of packages from different releases and that the GLAD package may be broken. I'd suggest reinstalling at least the GLAD package (using biocLite). Probably better, though, is to upgrade to the newest version of R and reinstall all the packages of interest using biocLite(). Sean