graphics grDevices utils datasets 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
;)
> -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 rep
fs_1.5.0 ps_1.4.0 testthat_2.3.2
[25] memoise_1.1.0 glue_1.4.2 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
packages.
My questions are:
1. Does anyone know what is causing this Note.
2. Can I fix the note? If not, can 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 i
ols40." that 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
>
which 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
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
mpy8bFkk\downloaded_packages
Old packages: 'backports', 'BiocFileCache', 'BiocNeighbors', 'BiocStyle',
'broom', 'dbplyr',
'foreign', 'GenomeInfoDb', 'GenomeInfoDbData', 'gtools', 'isoband'
eased, will it be the rtools40 toolchain or
rtools35?
Thanks
Gordon
--
Professor Gordon K Smyth
Joint Head, Bioinformatics Division
Walter and Eliza Hall Institute of Medical Research
___
The information in this
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 of
nd install 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: La
> -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
ell R CMD
check to ignore the .BBSoptions file, or will that cause problems for the
Bioconductor management routines, i.e., will it make the .BBSoptions file
invisible to Bioconductor as well?
Thanks
Gordon
--
Professor Gordon K Smyth
Joint Head, Bioinform
Thanks. I confirm that it installs for me now in R-3.5.0alpha for Windows.
Gordon
> -Original Message-
> From: Hervé Pagès
> Sent: Thursday, 29 March 2018 3:42 PM
> To: Gordon K Smyth ; bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] No Windows binary for Genomi
What 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 Medica
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
--------
I restarted my PC this morning and the problem disappeared.
I probably should have tried that last night, but it was late ...
Thanks
Gordon
> -Original Message-
> From: Martin Morgan [mailto:martin.mor...@roswellpark.org]
> Sent: Tuesday, 11 April 2017 7:20 PM
> To: Go
.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
staller 1.25.3), ?biocLite for help
> BiocInstaller::biocValid()
Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) && :
missing value where TRUE/FALSE needed
-
Professor Gordon K Smy
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
To: Peng Yu
Cc: Bioconductor Package Maintainer ,
"bioc
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
ty
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 supe
geR. Can
you add that one, too ?
--
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia
From: Gordon K Smyth
Sent: Friday, 27 June 2014 9:32 AM
To: Dario Strbenac
Cc: bioc-devel@r-project.org
Date: Thu, 26 Jun 2014 04:00:11 +
From: Dario Strbenac
To: "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 estimateGLMRobustDisp,
leading to an error :
Err
organ wrote:
On 10/20/2013 10:36 PM, Gordon K Smyth wrote:
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 b
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 playin
Dear Ryan,
See contrastAsCoef() in limma 3.17.23.
Best wishes
Gordon
-
Professor Gordon K Smyth,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.
http://www.statsci.org
Dear Miguel,
From: "Miguel Moreno-Risueno"
To: "'James W. MacDonald'"
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Can I analyze with bioconductor a microarray
experiement where the distribution of probes intesisties follow a
bimodal distribution?
Hi James
Thank you v
respected by subsetting and cbinding. voom() now
stores the (effective) lib.size as a column of the targets data.frame
rather than as a separate component.
Best wishes
Gordon
-
Professor Gordon K Smyth,
Bioinformatics Division,
Walter and Eliza Hall
Dear Rory,
Sorry, I didn't intend to make this change to the release version. I
over-looked it amongst some documentation updates that I did want to make.
I have fixed the release code (version 3.2.2) so that DGEList() will
accept a NULL value again for lib.size.
Just a note on terminology.
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 T
On Mon, 10 Dec 2012, Ryan C. Thompson wrote:
What about this more limited proposal?
I don't see a proposal below, only a question.
Suppose one is studying an additive model, but only one factor (or
equivalently, one set of interacting factors) is of interest and the
rest are blocking facto
Dear Ryan,
Thanks for your suggestion. I think though that the attribute that you
are thinking of implementing is not actually something that exists in
general.
On Mon, 10 Dec 2012, Ryan C. Thompson wrote:
Hi Gordon and list,
I've been thinking about how to make it easier to specify what
-
Professor Gordon K Smyth,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.
http://www.statsci.org/smyth
On Wed, 21 Nov 2012, Gordon K Smyth wrote:
Dear Ryan,
Thank you for
Dear Ryan,
Thank you for raising the issue with all zero counts and glmQLFTest(). I
am not sure why you are running the code with all zero cases, since we
advise against it, but I agree that it would be better for the code to
handle such cases more gracefully.
Rather than posting your own f
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