I guess this is really an argument for having _all_ method man pages be
aliased with the symbol of the generic. I wonder if R should just be made
smarter and bring up a menu whenever help is requested on a generic,
listing all of the available methods, with the default method as the
default
On 02/18/2015 05:13 PM, Martin Morgan wrote:
On 02/18/2015 08:05 AM, Philip Lijnzaad wrote:
Dear all,
looking up the documentation on functions like follow() and
precede() is
very hard, since they are only documented under the topic
nearest-methods,
which currently
I agree with Michael. In my opinion, the help pages for S4 methods are
painfully obscure, and expecting anybody (let alone a newbie) to figure out
that they need to do something like method?follow,GenomicRanges,
GenomicRanges in order to get the help page for a method is a high hurdle
indeed.
In
- Original Message -
From: Michael Lawrence lawrence.mich...@gene.com
To: Hervé Pagès hpa...@fredhutch.org
Cc: Michael Lawrence lawrence.mich...@gene.com, bioc-devel@r-project.org,
James Macdonald
jmac...@u.washington.edu
Sent: Wednesday, February 18, 2015 11:12:13 AM
Subject:
What Michael suggests is obviously the way forward.
To be clear: what Herve is doing is somewhat simple though: if a man page
is for a specific method, it should also contain
\alias{$GENERIC}
Kasper
On Wed, Feb 18, 2015 at 2:12 PM, Michael Lawrence lawrence.mich...@gene.com
wrote:
Great.
By default, the menu could collapse the methods by man page, so there would
not be an imposing number of choices. Another idea (for extreme cases like
length) would be to have aliases that do not appear in the index, in the
same way that \keyword{internal} hides entire man pages. Maybe \alias*{}
On 02/18/2015 11:52 AM, Hervé Pagès wrote:
Hi Michael,
On 02/18/2015 11:12 AM, Michael Lawrence wrote:
Great. I was just wondering whether we could make the job of the
developer easier by having R find the methods, instead of needing to add
aliases to every method man page.
If the proposal
library(GEOquery)
gastricChina - getGEO(GSE65801, GSEMatrix = FALSE)
Generates warnings
head(warnings(), 1)
Warning message:
In readLines(con, n = chunksize) :
seek on a gzfile connection returned an internal error
Does it affect the correctness of the imported data ?
Also,
On 02/18/2015 08:05 AM, Philip Lijnzaad wrote:
Dear all,
looking up the documentation on functions like follow() and precede() is
very hard, since they are only documented under the topic nearest-methods,
which currently (GenomicRanges package 1.18.4) can only be found using the
Dear all,
looking up the documentation on functions like follow() and precede() is
very hard, since they are only documented under the topic nearest-methods,
which currently (GenomicRanges package 1.18.4) can only be found using the
?? operator (and having found the name of the
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