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, experimentDat
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*{} to
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 is
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 is to have R bring up a menu listing all of th
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 wrote:
> Great. I was just wondering wheth
- Original Message -
> From: "Michael Lawrence"
> To: "Hervé Pagès"
> Cc: "Michael Lawrence" , bioc-devel@r-project.org,
> "James Macdonald"
>
> Sent: Wednesday, February 18, 2015 11:12:13 AM
> Subject: Re: [Bioc-devel] Documentation of GenomicRanges::follow etc. very
> hard to find
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.
On Wed, Feb 18, 2015 at 10:50 AM, Hervé Pagès wrote:
> Hi,
>
> Philip makes a very good point. This is exactly the reason wh
Hi,
Philip makes a very good point. This is exactly the reason why,
a few months ago, I started to alias method man pages with the
symbol of the generic. For example I've done it for findOverlaps
and all the intra- and inter- range methods (shift, resize, flank,
range, reduce, etc...). So after l
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
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 selecti
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 (GenomicR
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 th
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 to
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