Dear Biocore Team (and users of GOstats): It appears that the Sanger URL format has changed for the Pfam site, which causes broken links when using summary() with option htmlLinks=TRUE. Below is a comparison of the old and new URLs for the same accession number. OLD http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF07974 NEW http://pfam.sanger.ac.uk/family?acc=PF07974 The latest development version of GOstats (2.17.1) that I looked at (below) shows the old form so I thought I would pass along. Thanks for all your hard work with Bioconductor. It is greatly appreciated! ---------------------------------------------------------------------- --- showMethods(summary, class = "PFAMHyperGResult", includeDefs = TRUE) Function: summary (package base) object="PFAMHyperGResult" function (object, ...) { .local <- function (object, pvalue = pvalueCutoff(object), categorySize = NULL, htmlLinks = FALSE) { PFAM_URL <- "http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?%s" df <- callNextMethod(object = object, pvalue = pvalue, categorySize = categorySize) if (nrow(df) == 0) { df$Term <- character(0) return(df) } pfamIds <- df[[1]] if (htmlLinks) { pfamIdUrls <- sapply(pfamIds, function(x) sprintf(PFAM_URL, x)) pfamTerms <- paste("", pfamIds, "", sep = "") } else { pfamTerms <- pfamIds } df$Term <- pfamTerms df } .local(object, ...) } ---------------------------------------------------------------------- ---- J. Wade Davis, PhD Assistant Professor 187 Galena DC 018.0 University of Missouri Columbia, MO 65212 Phone: (573) 882-0770 Fax: (573) 884-4196 MU Biostatistics Group<http: som.missouri.edu="" research="" biostat="" default.aspx=""> [[alternative HTML version deleted]]

Thank you Wade, The changes have been made and should propogate within a day or so. Marc On 02/23/2011 09:54 AM, Davis, Wade wrote: > Dear Biocore Team (and users of GOstats): > > It appears that the Sanger URL format has changed for the Pfam site, which causes broken links when using summary() with option htmlLinks=TRUE. Below is a comparison of the old and new URLs for the same accession number. > > OLD > http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF07974 > > NEW > http://pfam.sanger.ac.uk/family?acc=PF07974 > > The latest development version of GOstats (2.17.1) that I looked at (below) shows the old form so I thought I would pass along. > > Thanks for all your hard work with Bioconductor. It is greatly appreciated! > > > -------------------------------------------------------------------- ----- > > showMethods(summary, class = "PFAMHyperGResult", includeDefs = TRUE) > > Function: summary (package base) > object="PFAMHyperGResult" > function (object, ...) > { > .local <- function (object, pvalue = pvalueCutoff(object), > categorySize = NULL, htmlLinks = FALSE) > { > PFAM_URL <- "http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?%s" > df <- callNextMethod(object = object, pvalue = pvalue, > categorySize = categorySize) > if (nrow(df) == 0) { > df$Term <- character(0) > return(df) > } > pfamIds <- df[[1]] > if (htmlLinks) { > pfamIdUrls <- sapply(pfamIds, function(x) sprintf(PFAM_URL, > x)) > pfamTerms <- paste("", > pfamIds, "", sep = "") > } > else { > pfamTerms <- pfamIds > } > df$Term <- pfamTerms > df > } > .local(object, ...) > } > > > -------------------------------------------------------------------- ------ > > > J. Wade Davis, PhD > Assistant Professor > 187 Galena DC 018.0 > University of Missouri > Columbia, MO 65212 > Phone: (573) 882-0770 > Fax: (573) 884-4196 > MU Biostatistics Group<http: som.missouri.edu="" research="" biostat="" default.aspx=""> > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >