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
[[alternative HTML version deleted]]
___
Bioc-devel@r-p
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 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 of
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 in
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)),
+ pos=1
th 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:
>
> library("Bi
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
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 Bioinformatics
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 platform
Hi Dan,
Thank you for your answer. I hope I can update to Mavericks but our help
desk just ask me to hold on current OS.
Yours Sincerely,
Jianhong Ou
TEL: 508-856-5379
LRB 608
Bioinformatician of Bioinformatics core at
Department of Molecular, Cell and Cancer Biology
364 Plantation Street Worce
kages 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 PM, Ou, Jianhong wrote:
>
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]:
a
Thank you for the quick fix. Have a good weekend.
Yours Sincerely,
Jianhong Ou
TEL: 508-856-5379
LRB 608
Bioinformatician of Bioinformatics core at
Department of Molecular, Cell and Cancer Biology
364 Plantation Street Worcester,
MA 01605
On 4/1/16 5:57 PM, "Dan Tenenbaum" wrote:
>Should
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
"/extra/svndata/gentleman/svnroot/bioconductor/hooks/DESCRIPTION_hook/check_for_bad_version
l/bioc/html/ChIPpeakAnno.html) and
release (http://bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html)
looks to be properly populated now, so this must be fixed.
On Mon, Mar 7, 2016 at 9:34 AM, Ou, Jianhong
mailto:jianhong...@umassmed.edu>> wrote:
Hi,
The test coverag
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
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" wrote:
>Welcom
Hi,
How could we mask the warnings when we check a package which imports on
BiocGenerics, AnnotationDbi and GenomeInfoDb.
The warning messages are:
Warning: multiple methods tables found for �species�
Warning: multiple methods tables found for �organism�
Yours Sincerely,
Jianhong Ou
TEL: 508-
nhong,
>
>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 re
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
[[alternat
Thanks Martin,
I am using \thanks now. It works.
Yours sincerely,
Jianhong Ou
LRB 670A
Program in Gene Function and Expression
364 Plantation Street Worcester,
MA 01605
On 12/19/13 5:53 PM, "Martin Morgan" wrote:
>On 12/19/2013 01:44 PM, Ou, Jianhong wrote:
>> Hi Al
t;> attached base packages:
>> [1] parallel stats graphics grDevices utils datasets methods
>>base
>>
>> other attached packages:
>> [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.10.1 GenomicFeatures_1.15.4
>> [3] AnnotationDbi_1.25.9 B
e(tx <- transcripts(TxDb.Hsapiens.UCSC.hg19.knownGene))
> # user system elapsed
> # 1.424 0.008 1.436
> system.time(tx <- transcripts(TxDb.Hsapiens.UCSC.hg19.knownGene))
> # user system elapsed
> # 0.776 0.012 0.790
>
>Less than 10 sec. to retriev
Dear all,
When I try to use intronsByTranscript to get introns for hg19 known genes, I
found it is unacceptable slow. Does any body has the same problem?
My code:
library(GenomicFeatures)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
introns <- intronsByTranscript(TxDb.Hsapiens.UCSC.hg19.knownGene)
t;
>
>> -Original Message-
>> From: bioc-devel-boun...@r-project.org [mailto:bioc-devel-bounces@r-
>> project.org] On Behalf Of Ou, Jianhong
>> Sent: December-19-13 1:53 PM
>> To: bioc-devel@r-project.org
>> Subject: [Bioc-devel] simple question abo
Hi all,
Maybe this is not a bioconductor question but R. However, I feel this is very
interesting.
I tried
> floor(29/50*50)
[1] 28
> floor(29*50/50)
[1] 29
Is this a floating-point problem? How could we explain this?
Yours sincerely,
Jianhong Ou
LRB 670A
Program in Gene Function and Expres
Hi All,
I tried to add \footnote in \author tag like
%\VignetteIndexEntry{MyPackage Vignette}
%\VignetteDepends{MyPackage}
%\VignetteKeywords{hello}
%\VignettePackage{MyPackage}
\documentclass[12pt]{article}
<>=
BiocStyle::latex()
@
\author{author1\footnote{a...@abc.com}} % could not work,
2:50 PM, "Hervé Pagès" 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, ŒGAlignmentP
Dear all,
When I try to renew Rsamtools, GenomicAlignments and rtracklayer, I got error
Error : objects GAlignments, GAlignmentPairs are not exported by
'namespace:GenomicRanges'
Does anybody know how to figure out this problem?
> biocValid()
* sessionInfo()
R Under development (unstable
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" wrote:
>
>
>- Original Message -
>> From: "Jianhong Ou"
>> To: bioc-devel@r-project.org
>> Sent: Fri
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 Worcest
slow in this situation, basically because the
>> underlying
>> seqselect is slow, due to this loop:
>>
>> x <- do.call(c, lapply(seq_len(length(ir)),
>> function(i)
>> window(x,
>> sta
Hi,
When I use big set of GrangesList, I found it become very slow when metadata
contain AtomicList. e.g.
> grll <- GRanges(seqnames="chr1", ranges=IRanges(start=1:500, width=2),
> someInfo=rep(RleList("*"), 500))
> grr <- split(grll, 1:500)
> grl <- as.list(grr)
> system.time(grl<- grl[500:1])
A
Program in Gene Function and Expression
364 Plantation Street Worcester,
MA 01605
On 7/26/13 2:48 AM, "Hervé Pagès" wrote:
>
>
>On 07/25/2013 11:32 PM, Maintainer wrote:
>> Hi Jianhong,
>>
>> On 07/24/2013 08:18 AM, Ou, Jianhong wrote:
>>> De
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" wrote:
>Hi,
>
>This
Hi,
I got "negative widths are not allowed" error when I use findOverlaps. Could
anybody help me to figure this out? Thanks. Here is the code:
> library("IRanges")
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: BiocGenerics
The following objects
Hi Martin,
This is a great package. When I insert the figure to the vignettes, the
codes will not run two times. Great!
One question is that how could I show "@" in the vignettes?
And is there any methods to draw multiple figures in one chunk and then
insert them separately?
Yours sincerely,
Ji
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