methods base
other attached packages:
[1] BiocManager_1.30.13
loaded via a namespace (and not attached):
[1] compiler_4.1.0 tools_4.1.0
------
Professor Gordon K Smyth
Joint Head, Bioinformatics Division
Walter and Eliza Hall Institute of Medical Research
;)
> -Original Message-
> From: Gordon K Smyth
> Sent: Tuesday, 20 October 2020 7:58 AM
> To: Martin Morgan ; bioc-devel@r-project.org
> Subject: RE: [Bioc-devel] R 4.0.3 for Windows R CMD check finds 'abort'
>
> If you're interested, here is a small reproducible examp
compiler_4.0.3desc_1.2.0
[29] backports_1.1.10 prettyunits_1.1.1
----------
Professor Gordon K Smyth
Joint Head, Bioinformatics Division
Walter and Eliza Hall Institute of Medical Research
> -Original Message-
> From: Martin Morgan
> Sent: Tuesday,
I ignore it?
I also wonder whether this Note will cause the CRAN maintainers to not accept
my package submissions, but that is perhaps a question for another forum.
Thanks for any insights
Gordon
--
Professor Gordon K Smyth
Joint Head, Bioinformatics
at is attached to R-4.1.0
for Windows on the CRAN download page. There's no similar note attached to
R-4.0.0 RC, but I may have jumped to the wrong conclusion.
Gordon
> -Original Message-
> From: Hervé Pagès
> Sent: Tuesday, 21 April 2020 6:51 PM
> To: Gordon K Smyth ;
is afterall what the Rtools webpage says).
Thanks
Gordon
> -Original Message-
> From: Hervé Pagès
> Sent: Tuesday, 21 April 2020 2:55 PM
> To: Gordon K Smyth ; Martin Morgan
> ; bioc-devel@r-project.org
> Cc: Yunshun Chen
> Subject: Re: [Bioc-devel] R-devel for
ithout any proper justification. Maybe Rtools4.0 supports both the
4.0.0 and 4.1.0 pipelines.
Thanks
Gordon
> -Original Message-
> From: Hervé Pagès
> Sent: Tuesday, 21 April 2020 12:01 PM
> To: Gordon K Smyth ; Martin Morgan
> ; bioc-devel@r-project.org
> Cc: Yunshun Chen
t;
- R Session with R 4.0.0 for Windows --
> -Original Message-
> From: Martin Morgan
> Sent: Monday, 20 April 2020 7:44 PM
> To: Gordon K Smyth ; bioc-devel@r-project.org
> Cc: Yunshun Chen
> Subject: Re: [Bioc-devel] R-devel for Win
downtime.
Is there a time frame for how long the work will take? It would be good to know
so we can stay off until then and not keep trying.
Thanks
Gordon
--
Professor Gordon K Smyth
Joint Head, Bioinformatics Division
Walter and Eliza Hall Institute
limma by
library(BiocManager)
install("limma")
Then everything will work correctly.
Best wishes
Gordon
--
Professor Gordon K Smyth
Joint Head, Bioinformatics Division
Walter and Eliza Hall Institute of Medical Research
From: Lan Huong Ng
> -Original Message-
> From: Pages, Herve
> Sent: Saturday, 16 March 2019 3:15 AM
> To: Gordon K Smyth ; bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] Can I use .Rbuildignore to ignore .BBSoptions?
>
> Hi Gordon,
>
> My understanding is that adding .BBSo
Thanks. I confirm that it installs for me now in R-3.5.0alpha for Windows.
Gordon
> -Original Message-
> From: Hervé Pagès <hpa...@fredhutch.org>
> Sent: Thursday, 29 March 2018 3:42 PM
> To: Gordon K Smyth <sm...@wehi.edu.au>; bioc-devel@r-project.org
&g
is the ETA for a Windows version? I notice there haven't been any commits
to GenomicRanges since 27 Feb.
Gordon
--
Professor Gordon K Smyth
Head, Bioinformatics Division
Walter and Eliza Hall Institute of Medical Research
languages ['en']!"
I have checked the message at the source level and there appears to be no
language setting. The error persists even if I delete all the text and replace
it with new text or if I don't edit the text at all.
Any ideas?
Gordon
------
Prof
.mtime(dest) > file.mtime(lib) && :
missing value where TRUE/FALSE needed
> -Original Message-----
> From: Gordon K Smyth
> Sent: Tuesday, 11 April 2017 6:26 PM
> To: bioc-devel@r-project.org
> Subject: Using BiocInstaller with R 3.4.0 beta
>
> I thought I would te
ror in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) && :
missing value where TRUE/FALSE needed
---------
Professor Gordon K Smyth,
Head, Bioinformatics Division,
Walter and Eliza Hall Institute of
in the publication schedule? Are there still plans
for a June 2016 issue?
Thanks
Gordon
-
Professor Gordon K Smyth,
Head, Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
http://www.statsci.org/smyth
Hi Michael,
What aspect of the methods package causes the slowness?
There are many packages (limma for one) that depend on methods but load
quickly.
Regards
Gordon
Date: Wed, 31 Dec 2014 09:17:01 -0800
From: Michael Lawrence lawrence.mich...@gene.com
To: Peng Yu pengyu...@gmail.com
Cc:
Date: Thu, 13 Nov 2014 12:09:47 +0100
From: January Weiner january.wei...@gmail.com
To: r-devel r-devel@r-project.org
Subject: [Rd] Changing style for the Sweave vignettes
As a user, I am always annoyed beyond measure that Sweave vignettes
precede the code by a command line prompt. It makes
Hi Ryan,
On Fri, 11 Jul 2014, Ryan C. Thompson wrote:
Hello,
I think I may have found a bug in the code for aveLogCPM.default in the edgeR
package. Near the end of the function, the variable prior.count.scale is
conditionally assigned to, and never subsequently used. I assume this is a
edgeR knows about LargeDataObject. It's your package that doesn't.
Gordon
On Fri, 27 Jun 2014, Dario Strbenac wrote:
Hello,
I never explicitly use that class in my function. I did debugging and realised
what the problem is. DGEList is part of class hierarchy and it inherits from
the
Date: Thu, 26 Jun 2014 04:00:11 +
From: Dario Strbenac dstr7...@uni.sydney.edu.au
To: bioc-devel@r-project.org bioc-devel@r-project.org
Subject: [Bioc-devel] edgeR estimateGLMRobustDisp Fails when Called
From A Package
Hello,
I am writing a package that has a function that uses
Hi Martin,
Thanks for the heads-up. I think I've made the changes necessary, but am
having trouble confirming whether the changes are correct on a Windows
machine.
Could you tell me hows Bioconductor builds the Windows binaries of
Bioconductor packages?
To see how things work, I am
Hi Dan,
You say that the notes will be collated no later than Monday, but that
suggests it could be earlier. What's the latest day we can continue to
make edits for NEWS.Rd and other documentation for the coming release?
Thanks a lot
Gordon
Date: Tue, 26 Mar 2013 13:59:17 -0700
From: Dan
-
Professor Gordon K Smyth,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.
Tel: (03) 9345 2326, Fax (03) 9347 0852,
http://www.statsci.org/smyth
Thanks. Our package has LGPL (= 2) licence, so we'll copy with header
and proper acknowledgements.
Gordon
On Mon, 9 Jul 2012, Prof Brian Ripley wrote:
On Mon, 9 Jul 2012, Gordon K Smyth wrote:
Dear all,
I'm writing to ask for advice as to best practice. A PhD student working
with me
On Thu, 17 Mar 2011, peter dalgaard wrote:
On Mar 16, 2011, at 23:29 , Gordon K Smyth wrote:
Hi Peter and others,
If it helps, I wrote a small function glm.scoretest() for the statmod
package on CRAN to compute score tests from glm fits. The score test
for adding a covariate, or any set
already know that.
Regards
Gordon
-
Professor Gordon K Smyth,
NHMRC Senior Research Fellow,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.
sm...@wehi.edu.au
http
Rcmd check under R 2.10.0dev for Windows seems to be issuing a number of
spurious warning messages about Rd cross-references.
The following warning messages appear when checking the latest
(non-public) version of the Bioconductor package limma. They appear only
under Windows, not Unix or
this up with the
Bioconductor people.
The one exception is the self-reference to limma:00Index. This marked as
a missing link, under Windows only, although it works fine.
Gordon
On Mon, 28 Sep 2009, Gordon K Smyth wrote:
Rcmd check under R 2.10.0dev for Windows seems to be issuing a number
Date: Sat, 25 Mar 2006 16:57:50 -0400
From: Kjetil Brinchmann Halvorsen
[EMAIL PROTECTED]
Subject: Re: [Rd] How to capture t-score and p-values from t.test
To: Bernzweig, Bruce \(Exchange\) [EMAIL PROTECTED]
Cc: r-devel@r-project.org
Bernzweig, Bruce (Exchange) wrote:
When I do
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