Hi, I'm having problems calling the help files for functions from the gcrma package. I haven't had this problem with getting help files from other packages (which I've done a LOT over the past week). Is it a bug? Thanks, Jenny > ?justGCRMA Error in print.help_files_with_topic("C:/PROGRA~1/R/R-27~1.0/library/gcrma/chm/ justGCRMA") : CHM file could not be displayed > ?gcrma Error in print.help_files_with_topic("C:/PROGRA~1/R/R-27~1.0/library/gcrma/chm/ gcrma") : CHM file could not be displayed > ?rma #works fine > sessionInfo() R version 2.7.0 (2008-04-22) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] canine2cdf_2.2.0 affyQCReport_1.18.0 geneplotter_1.18.0 [4] lattice_0.17-6 RColorBrewer_1.0-2 simpleaffy_2.16.0 [7] made4_1.14.0 ade4_1.4-7 affyPLM_1.16.0 [10] affycoretools_1.12.0 annaffy_1.12.0 KEGG.db_2.1.4 [13] gcrma_2.12.0 matchprobes_1.12.0 biomaRt_1.14.0 [16] RCurl_0.8-1 GOstats_2.6.0 Category_2.6.0 [19] genefilter_1.20.0 survival_2.34-1 RBGL_1.16.0 [22] annotate_1.18.0 xtable_1.5-2 GO.db_2.1.4 [25] AnnotationDbi_1.2.0 RSQLite_0.6-8 DBI_0.2-4 [28] graph_1.18.0 limma_2.14.0 affy_1.18.0 [31] preprocessCore_1.2.0 affyio_1.8.0 Biobase_2.0.0 [34] RWinEdt_1.7-9 loaded via a namespace (and not attached): [1] cluster_1.11.10 grid_2.7.0 KernSmooth_2.22-22 XML_1.94-0.1 > Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu

Jenny, Right now the compressed HTML help files in the Windows binary package builds of BioC 2.2 have been a bit flaky, and we are currently looking into correcting the problem. For now we recommend using the plain text or HTML version of the help files on Windows until this issue is fixed. To access the plain text help files, set chmhelp = FALSE in the help function call. For example, help(justGCRMA, chmhelp = FALSE) help(rma, chmhelp = FALSE) To access the HTML help files, set chmhelp = FALSE and htmlhelp = TRUE in the help function call. For example, help(justGCRMA, chmhelp = FALSE, htmlhelp = TRUE) help(rma, chmhelp = FALSE, htmlhelp = TRUE) Thanks for your patience. Patrick Jenny Drnevich wrote: > Hi, > > I'm having problems calling the help files for functions from the > gcrma package. I haven't had this problem with getting help files from > other packages (which I've done a LOT over the past week). Is it a bug? > > Thanks, > Jenny > > > ?justGCRMA > Error in > print.help_files_with_topic("C:/PROGRA~1/R/R-27~1.0/library/gcrma/ch m/justGCRMA") > : > CHM file could not be displayed > > ?gcrma > Error in > print.help_files_with_topic("C:/PROGRA~1/R/R-27~1.0/library/gcrma/ch m/gcrma") > : > CHM file could not be displayed > > ?rma > #works fine > > > sessionInfo() > R version 2.7.0 (2008-04-22) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] canine2cdf_2.2.0 affyQCReport_1.18.0 geneplotter_1.18.0 > [4] lattice_0.17-6 RColorBrewer_1.0-2 simpleaffy_2.16.0 > [7] made4_1.14.0 ade4_1.4-7 affyPLM_1.16.0 > [10] affycoretools_1.12.0 annaffy_1.12.0 KEGG.db_2.1.4 > [13] gcrma_2.12.0 matchprobes_1.12.0 biomaRt_1.14.0 > [16] RCurl_0.8-1 GOstats_2.6.0 Category_2.6.0 > [19] genefilter_1.20.0 survival_2.34-1 RBGL_1.16.0 > [22] annotate_1.18.0 xtable_1.5-2 GO.db_2.1.4 > [25] AnnotationDbi_1.2.0 RSQLite_0.6-8 DBI_0.2-4 > [28] graph_1.18.0 limma_2.14.0 affy_1.18.0 > [31] preprocessCore_1.2.0 affyio_1.8.0 Biobase_2.0.0 > [34] RWinEdt_1.7-9 > > loaded via a namespace (and not attached): > [1] cluster_1.11.10 grid_2.7.0 KernSmooth_2.22-22 XML_1.94-0.1 > > > > > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich at uiuc.edu > > _______________________________________________ > 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