[Bioc-devel] rtracklayer bug?
I will add "..." to the httpGet call.
On Tue, Jun 30, 2015 at 10:10 AM, Marc Carlson <mcarlson at 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 M?ller 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 at url <- url .Object at views <- new.env() gwURL <- ucscURL(.Object, "gateway") if (force) { gwURL <- paste0(gwURL, '?redirect=anual"') } gw <- httpGet(gwURL, cookiefile =empfile(), header = TRUE, .parse?LSE) 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 at 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, .parse?LSE, ???) ? 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 at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel