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Question: bug in gcrma help CHM files?
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gravatar for Jenny Drnevich
9.6 years ago by
Jenny Drnevich2.2k
Jenny Drnevich2.2k 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/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
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ADD COMMENTlink modified 9.6 years ago by Patrick Aboyoun1.6k • written 9.6 years ago by Jenny Drnevich2.2k
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gravatar for Patrick Aboyoun
9.6 years ago by
Patrick Aboyoun1.6k
United States
Patrick Aboyoun1.6k wrote:
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
ADD COMMENTlink written 9.6 years ago by Patrick Aboyoun1.6k
A fresh build of the Windows binary packages for BioC 2.2 release are now on-line at bioconductor.org. These new builds contain corrected CHM help files. As have been noted on this bulletin board, a number of the old Windows binary package builds for the BioC 2.2 release have been corrupt. This new batch should be clear of this defect. New precautions have been put in place to prevent poorly built CHM files. If any more Windows binary packages are encountered with corrupt CHM files are encountered, please send me an e-mail so I can address the issue. If you have a build of a Windows binary package with a faulty CHM help file, please uninstall that version and grab the newly built version using biocLite(<<package name="">>) from within R. Thanks, Patrick
ADD REPLYlink written 9.6 years ago by Patrick Aboyoun1.6k
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