I will add "..." to the httpGet call. On Tue, Jun 30, 2015 at 10:10 AM, Marc Carlson <mcarl...@fredhutch.org> wrote: > Hi Arne, > > So this time when I look at the bioc-devel email list, I don't see a record > for this last name (or this email). In fact the only way I could be sure it > was you was that your post was the same... ;) If you want to post from > gmail, then you will need to subscribe the gmail address to the list here: > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > Marc > > > > On 06/30/2015 02:26 AM, Arne Müller wrote: >> >> Hello, >> >> >> I think there’s a problem in UCSCSession initializer in rtracklayer: >> >> setMethod("initialize", "UCSCSession", >> >> function(.Object, url =http://genome.ucsc.edu/cgi-bin/", >> >> user =ULL, session = NULL, force = FALSE, ...) >> >> { >> >> .Object@url <- url >> >> .Object@views <- new.env() >> >> gwURL <- ucscURL(.Object, "gateway") >> >> if (force) { >> >> gwURL <- paste0(gwURL, '?redirect=anual"') >> >> } >> >> gw <- httpGet(gwURL, cookiefile =empfile(), header = TRUE, >> >> .parseúLSE) >> >> if (grepl("redirectTd", gw)) { >> >> url <- sub(".*?a href=h([^[:space:]]+cgi-bin/).*", >> "h\\1", gw) >> >> return(initialize(.Object, url, user=er, session=session, >> >> force=UE, ...)) >> >> } >> >> cookie <- grep("Set-[Cc]ookie: hguid[^==", gw) >> >> if (!length(cookie)) >> >> stop("Failed to obtain 'hguid' cookie") >> >> hguid <- sub(".*Set-Cookie: (hguid[^==[^;]*);.*", "\\1", gw) >> >> .Object@hguid <- hguid >> >> if (!is.null(user) && !is.null(session)) { ## bring in other >> session >> >> ucscGet(.Object, "tracks", >> >> list(hgS_doOtherUser =submit", hgS_otherUserName >> user, >> >> hgS_otherUserSessionName =ession)) >> >> } >> >> .Object >> >> }) >> >> >> >> Shouldn’t ‘…’ be passed to httpGet that in turn is passed to >> RCURL, I.e. >> >> >> gw <- httpGet(gwURL, cookiefile =empfile(), header = TRUE, >> >> .parseúLSE, …) ? >> >> We run an internal instance of the UCSC genome browser and need to pass a >> cookie to all http-requests. The problem is that >> >> session =ew ('UCSCSession', url=myInternalURL, cookie=myAuthCookie) >> >> >> Does not pass the ‘cookie’ argument to httpGet. >> >> >> Regards, >> >> >> Arne >> >> [[alternative HTML version deleted]] >> > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel
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