Bug report: Help pages for degree (package graph) not displayed
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@martin-morgan-1513
Last seen 3 days ago
United States
Thanks Kevin, I think this is a problem with our build system here in Seattle, and it'll be corrected before the release. Martin "Zembower, Kevin" <kzembowe at="" jhuccp.org=""> writes: > I just installed Windows version 2.7.0 of R, and version 1.17.17 of > graph. When I typed "?degree" after loading the graph library, I got the > error: 'Error in > print.help_files_with_topic("C:/R/R-2.7.0/library/graph/chm/graph- class" > ) : CHM file could not be displayed' > > The output of these steps is shown below. Please let me know if you have > any questions. The maintainer of the 'graph' package suggested I report > this bug to the BioC list, to allow testing in a Windows environment. > > -Kevin > > Kevin Zembower > Internet Services Group manager > Center for Communication Programs > Bloomberg School of Public Health > Johns Hopkins University > 111 Market Place, Suite 310 > Baltimore, Maryland 21202 > 410-659-6139 > ======================================= >> biocLite("graph") > Running biocinstall version 2.2.7 with R version 2.7.0 Your version of R > requires version 2.2 of BioConductor. > trying URL > 'http://bioconductor.org/packages/2.2/bioc/bin/windows/contrib/2.7/g raph > _1.17.17.zip' > Content type 'application/zip' length 811763 bytes (792 Kb) opened URL > downloaded 792 Kb > > package 'graph' successfully unpacked and MD5 sums checked > > The downloaded packages are in > C:\Documents and Settings\KZEMBOWE\Local > Settings\Temp\RtmpLl91qQ\downloaded_packages > updating HTML package descriptions > > <snip installing="" snadata="" and="" rbgl=""> > >> library("graph") >> ?degree > Error in > print.help_files_with_topic("C:/R/R-2.7.0/library/graph/chm/graph- class" > ) : > CHM file could not be displayed >> help("degree", package="graph") > Error in > print.help_files_with_topic("C:/R/R-2.7.0/library/graph/chm/graph- class" > ) : > CHM file could not be displayed >> 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] stats graphics grDevices utils datasets methods base > > > other attached packages: > [1] SNAData_1.8.0 graph_1.17.17 > > loaded via a namespace (and not attached): > [1] cluster_1.11.10 tools_2.7.0 >> > > _______________________________________________ > 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793
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@patrick-aboyoun-6734
Last seen 8.4 years ago
United States
Kevin, Thanks for pointing out this problem! It turns out that most of the BioC 2.2 Windows binary packages had corrupt Windows compressed HTML files. I am not sure what the cause was, but I do know they have been corrupt for about 1 week. For the Windows users out there, please remove all of the Windows binary packages for BioC 2.2 (just to be safe) and reinstall the latest Windows binary packages from the BioC repository. Thanks, Patrick Martin Morgan wrote: > Thanks Kevin, I think this is a problem with our build system here in > Seattle, and it'll be corrected before the release. Martin > > "Zembower, Kevin" <kzembowe at="" jhuccp.org=""> writes: > > >> I just installed Windows version 2.7.0 of R, and version 1.17.17 of >> graph. When I typed "?degree" after loading the graph library, I got the >> error: 'Error in >> print.help_files_with_topic("C:/R/R-2.7.0/library/graph/chm/graph- class" >> ) : CHM file could not be displayed' >> >> The output of these steps is shown below. Please let me know if you have >> any questions. The maintainer of the 'graph' package suggested I report >> this bug to the BioC list, to allow testing in a Windows environment. >> >> -Kevin >> >> Kevin Zembower >> Internet Services Group manager >> Center for Communication Programs >> Bloomberg School of Public Health >> Johns Hopkins University >> 111 Market Place, Suite 310 >> Baltimore, Maryland 21202 >> 410-659-6139 >> ======================================= >> >>> biocLite("graph") >>> >> Running biocinstall version 2.2.7 with R version 2.7.0 Your version of R >> requires version 2.2 of BioConductor. >> trying URL >> 'http://bioconductor.org/packages/2.2/bioc/bin/windows/contrib/2.7/ graph >> _1.17.17.zip' >> Content type 'application/zip' length 811763 bytes (792 Kb) opened URL >> downloaded 792 Kb >> >> package 'graph' successfully unpacked and MD5 sums checked >> >> The downloaded packages are in >> C:\Documents and Settings\KZEMBOWE\Local >> Settings\Temp\RtmpLl91qQ\downloaded_packages >> updating HTML package descriptions >> >> <snip installing="" snadata="" and="" rbgl=""> >> >> >>> library("graph") >>> ?degree >>> >> Error in >> print.help_files_with_topic("C:/R/R-2.7.0/library/graph/chm/graph- class" >> ) : >> CHM file could not be displayed >> >>> help("degree", package="graph") >>> >> Error in >> print.help_files_with_topic("C:/R/R-2.7.0/library/graph/chm/graph- class" >> ) : >> CHM file could not be displayed >> >>> 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] stats graphics grDevices utils datasets methods base >> >> >> other attached packages: >> [1] SNAData_1.8.0 graph_1.17.17 >> >> loaded via a namespace (and not attached): >> [1] cluster_1.11.10 tools_2.7.0 >> >> _______________________________________________ >> 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 >> > >
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