Dear Hervé,
Is it possible to ignore minoverlap when people set maxgap greater than 0
and give a message for that?
Yours sincerely,
Jianhong Ou
LRB 670A
Program in Gene Function and Expression
364 Plantation Street Worcester,
MA 01605
On 7/23/13 5:35 PM, Hervé Pagès hpa...@fhcrc.org wrote:
and Expression
364 Plantation Street Worcester,
MA 01605
On 7/26/13 2:48 AM, Hervé Pagès hpa...@fhcrc.org wrote:
On 07/25/2013 11:32 PM, Maintainer wrote:
Hi Jianhong,
On 07/24/2013 08:18 AM, Ou, Jianhong wrote:
Dear Hervé,
Is it possible to ignore minoverlap when people set maxgap greater
than 0
compress=TRUE to the constructor.
On Wed, Aug 21, 2013 at 8:30 AM, Ou, Jianhong
jianhong...@umassmed.edu mailto:jianhong...@umassmed.edu
mailto:Jianhong.Ou@umassmed.__edu
mailto:jianhong...@umassmed.edu wrote:
Hi,
When I use big set
Hi,
When I check http://master.bioconductor.org/developers/new_packages/ recently,
I can not get new packages list. Is there any other methods to get the new
available packages? Thanks.
Yours sincerely,
Jianhong Ou
LRB 670A
Program in Gene Function and Expression
364 Plantation Street
Hi Dan,
Thanks a lot.
Yours sincerely,
Jianhong Ou
LRB 670A
Program in Gene Function and Expression
364 Plantation Street Worcester,
MA 01605
On 10/11/13 10:53 AM, Dan Tenenbaum dtene...@fhcrc.org wrote:
- Original Message -
From: Jianhong Ou jianhong...@umassmed.edu
To: bioc
PM, Hervé Pagès hpa...@fhcrc.org wrote:
Hi Jianhong,
On 12/13/2013 11:45 AM, Ou, Jianhong wrote:
Dear all,
When I try to renew Rsamtools, GenomicAlignments and rtracklayer, I got
error
Error : objects ŒGAlignments¹, ŒGAlignmentPairs¹ are not exported by
'namespace:GenomicRanges'
You didn't
] 29.
Steven McKinney
Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre
-Original Message-
From: bioc-devel-boun...@r-project.org [mailto:bioc-devel-bounces@r-
project.org] On Behalf Of Ou, Jianhong
Sent: December-19
(TxDb.Hsapiens.UCSC.hg19.knownGene))
# user system elapsed
# 0.776 0.012 0.790
Less than 10 sec. to retrieve all the exons and transcripts from disk
and compute the 659327 introns. It's actually not that bad.
Cheers,
H.
On 12/20/2013 08:25 AM, Ou, Jianhong wrote:
Dear all,
When I try to use
rtracklayer_1.23.6 stats4_3.1.0
tools_3.1.0
[13] XML_3.98-1.1 zlibbioc_1.9.0
cheers,
robert.
On 12/20/2013 06:31 PM, Ou, Jianhong wrote:
In my case, looks like never end.
I need to check my R first.
Yours sincerely,
Jianhong Ou
LRB 670A
Program in Gene
Hi,
When I run sample code for reduce, I got Warning message:
The 'with.mapping' argument is deprecated.
Please use the 'with.revmap' argument instead.
Yours Sincerely,
Jianhong Ou
LRB 670A
Program in Gene Function and Expression
364 Plantation Street Worcester,
MA 01605
,
On 03/21/2014 07:01 AM, Ou, Jianhong wrote:
Hi,
When I run sample code for reduce, I got Warning message:
The 'with.mapping' argument is deprecated.
Please use the 'with.revmap' argument instead.
Not really a bug, just a warning that the 'with.mapping' arg is being
replaced
Does that mean we will have a package store in the future?
Yours Sincerely,
Jianhong Ou
TEL: 508-856-5379
LRB 608
Member of Bioinformatics core at
Department of Molecular, Cell and Cancer Biology
364 Plantation Street Worcester,
MA 01605
On 9/8/15 6:36 PM, "Michael Lawrence"
Hi,
The test coverage status for ChIPpeakAnno devel version is shown as unknown. I
tried covr::package_coverage(clean=FALSE), it reports:
ChIPpeakAnno Test Coverage: 40.49%
However, when I try codecov()
I got error: Error: running command ''git' 'rev-parse' '--abbrev-ref' 'HEAD''
had status 128
<james.f.hes...@gmail.com<mailto:james.f.hes...@gmail.com>>
Date: Monday, March 7, 2016 1:53 PM
To: Jianhong Ou <jianhong...@umassmed.edu<mailto:jianhong...@umassmed.edu>>
Cc: bioc-devel <bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>>
Subject: Re: [Bioc-devel
Hi,
When I try to commit new code to development version of ChIPpeakAnno, I got
error,
svn: E165001: Commit blocked by pre-commit hook (exit code 1) with output:
Traceback (most recent call last):
File
onger officially supported by R or Bioconductor (that's why a
>binary is not available).
>
>
>Dan
>
>
>- Original Message -
>> From: "Jianhong Ou" <jianhong...@umassmed.edu>
>> To: "bioc-devel" <bioc-devel@r-project.org>
>>
Hi,
I got error when I update S4Vectors in R 3.3 RC r70564 today. I also tried
r70549, same error like this
> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.21.6), R 3.3.0 RC (2016-04-28 r70564).
Old packages: 'S4Vectors'
Update all/some/none? [a/s/n]:
>updating R, all your packages should be re-installed. Most people
>don't do it because that takes a long time but there is no guarantee
>that packages installed under a previous version of R will still work
>properly with a new version of R.
>
>H.
>
>On 05/02/2016 12:00
Hi All,
I got some warnings when check. However, I could not see any details for that
warnings. How could I debug for these kind of warnings? Thank you.
* using log directory �/home/biocbuild/bbs-3.3-bioc/meat/ChIPpeakAnno.Rcheck�
* using R version 3.3.0 RC (2016-04-25 r70549)
* using
Hi Julie,
You could try to install windows 10 in a virtualBox for debugging.
virtualBox: https://www.virtualbox.org/wiki/Downloads
Windows 10: https://www.microsoft.com/en-us/software-download/windows10/
Yours Sincerely,
Jianhong Ou
TEL: 508-856-5379
LRB 608
Bioinformatician of
I got error when I try order for Rle object by following codes:
library("BiocGenerics")
library(XVector)
order(Rle(1))
## Error in match.arg(method) : 'arg' must be of length 1
> sessionInfo()
R Under development (unstable) (2017-05-10 r72667)
Platform: x86_64-apple-darwin16.5.0 (64-bit)
Running
el (aka BioC 3.6) with R devel.
This is not supported. Both, BioC 3.5 (current release) and
BioC 3.6 require R 3.4.0.
Cheers,
H.
On 05/11/2017 01:11 PM, Ou, Jianhong wrote:
> I got error when I try order for Rle object by following codes:
>
&
Hi, is this a bug in the development version of GenomicAlignments or
compressedList? Or I missed anything?
Here is how to repeat the error:
> library(GenomicAlignments)
> gal1 <- GAlignments(
+ seqnames=Rle(factor(c("chr1", "chr2", "chr1", "chr3")),
+ c(1, 3, 2, 4)),
+
Hi Herve,
The recent update of Rsamtools is using a new method of path. However, you did
not export this method. Will you export it? Or we should drop the dependence of
this method?
Yours Sincerely,
Jianhong Ou
TEL: 508-856-5379
LRB 608
Bioinformatician of Bioinformatics core at
Department
and destroy or permanently delete all copies of the original
message.
From: Obenchain, Valerie [valerie.obench...@roswellpark.org]
Sent: Friday, December 01, 2017 11:38 AM
To: Ou, Jianhong; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] a possible bug
and destroy or permanently delete all copies of the original
message.
From: Hervé Pagès [hpa...@fredhutch.org]
Sent: Tuesday, December 19, 2017 9:52 PM
To: Ou, Jianhong; bioc-devel@r-project.org
Subject: Re: Rsamtools does not export "path"
Hi Ji
Hi,
I got timeout for my package motifStack in machv2. But I don’t know what
caused the issue. Could you share me how to repeat this error? Thank you.
Best!
Your sincerely,
Jianhong Ou
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