On Tue, Nov 15, 2016 at 7:34 PM, Martin Morgan wrote:
> On 11/15/2016 09:52 AM, Obenchain, Valerie wrote:
>> On 11/15/2016 03:32 AM, Pariksheet Nanda wrote:
>>>
>>> It would be great to have an OrganismDb package for
>>> Drosophila.melanogaster, s
SC "refGene" TxDb. I imagine one would query the UCSC public MySQL
server and then do the SQLite conversion. Although the conversion to
SQLite seems a bit finagly as the datatypes differ between MySQL and SQLite
and I'm having a hard time finding a well supported tool to do it; I don't
wa
Biobase_2.35.1
[9] matrixStats_0.52.1 Matrix_1.2-9
[11] GenomeInfoDbData_0.99.0bitops_1.0-6
[13] RCurl_1.95-4.8 DelayedArray_0.1.7
[15] compiler_3.5.0 Rsamtools_1.27.15
[17] XML_3.98-1.6
> BiocInstaller::biocValid()
[1] TRUE
>
---
Pariksheet Nanda
PhD Candida
On Fri, Apr 7, 2017 at 1:13 AM, Hervé Pagès wrote:
>
> This is the expected behavior.
>
> Some background: BSgenomeViews are list-like objects where the *list
> elements* (i.e. the elements one extracts with [[) are the DNA
> sequences from the views
--snip--
> The important
29.1
[41] matrixStats_0.52.2 GenomicAlignments_1.13.5
[43] ShortRead_1.35.1 assertthat_0.2.0
[45] SummarizedExperiment_1.7.5 stringi_1.1.5
[47] RCurl_1.95-4.8 VariantAnnotation_1.23.8
>
Pariksheet
---
Pariksheet Nanda
PhD Candidate in Genetics and Genomics
System Administrator, Storrs HPC Cl
ig2’ is not portable
> Warning: file stem ‘/fig3’ is not portable
Hmm... I think we'll have to look at the exact vignette to see what's
going on. Presumably that's a LaTeX vignette. Can you advise the
package name you are working on and/or link to the the source code?
> Anusha
Parikshee
Hi Anusha,
On Wed, Oct 18, 2017 at 2:30 PM, Anusha Nagari <
anusha.nag...@utsouthwestern.edu> wrote:
>
> Can you please let me know how to go about the following NOTE. Or if this
is something that should be really taken care of for a successful package
build and install:
>
> * checking
Hi Bhakti,
On Mon, Dec 11, 2017 at 12:19 PM, Dwivedi, Bhakti
wrote:
> Is there a way to parallelize ConsensusClusterPlus package?
> https://bioconductor.org/packages/release/bioc/html/
> ConsensusClusterPlus.html
> We are developing a R shiny tool that performs
Hi Adam,
On Wed, Apr 25, 2018 at 2:35 PM, Adam Price wrote:
>
> There are a few reasons why I'm using \dontrun{} for my examples and want
> to know if there is any way to actually run my examples.
>
> My package incorporates some automated data management and requires in
>
Hi Henrik,
On Thu, May 10, 2018 at 1:21 AM, Henrik Bengtsson <
henrik.bengts...@gmail.com> wrote:
>
>
> May I suggest the package name:
>
> * Bioconductor
>
> The potential downside would be possible confusions between the version of
> this package versus the actual Bioconductor repository.
Hi Levi,
Why not use devtools which already does this? Setting `dependencies =
TRUE` installs the packages listed in Imports and Suggests, and
BiocManager::repositories() like BiocInstaller::biocinstallRepos() returns
a list of repositories. See inline below:
On Mon, Jul 9, 2018 at 4:51 AM,
> disk efficient compression algorithm
Whoops, meant to say compression format.
Pariksheet
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Hi Claris,
On Sat, Mar 10, 2018 at 2:49 AM, Claris Baby via Bioc-devel <
bioc-devel@r-project.org> wrote:
>
> [1] "The following files are over 5MB in size:
> 'dataset/Caenorhabditis_elegans.WBcel235.dna.chromosome.I.fa'."
> This as well as other data like .gff files, that are being used
>
Hello,
R 3.0 added support for long vectors, but it's not yet possible to use them
with IRanges. Without long vector support it's not possible to construct
an IRanges object with more than 2^31 elements:
> ir <- IRanges(start = 1:(2^31 - 1), width = 1)
> ir <- IRanges(start = 1:2^31, width =
a GRanges is not as reasonable?
I don't even know of a sane way to mock a BSgenome object for writing
tests. It's irritating to have to use actual small genomes for tests.
Pariksheet
On Tue, May 28, 2019 at 3:35 AM Pages, Herve wrote:
> Hi Pariksheet,
>
> On 5/25/19 12:49, Pariksheet Nanda wrote:
&
Hi Patricia,
Whoops, my mistake! GLAD is indeed a Bioconductor package:
$ R -q
> BiocManager::available("glad")
[1] "GLAD" "GladiaTOX"
>
You don't need to purchase any software license.
You can install the package freely inside R.
See:
Hi Patricia,
You've got the wrong e-mail address.
Bioconductor doesn't sell proprietary software licenses.
This mailing list is for developers to discuss technical matters with the R
or Bioconductor software packages.
I don't know what the website or e-mail address you need for purchasing the
Hi all,
On 10/12/21 6:43 PM, Pariksheet Nanda wrote:
Error in `...`: internal logical NA value has been modified
In the R source code, this error is in src/main/memory.c so I was
thinking one way of investigating might be to run `R --debugger gdb`,
then running R to load the symbols
nning under valgrind, something like R -d valgrind -f
minimal_script.R.
Hope those suggestions help!
Martin
On 10/12/21, 6:43 PM, "Bioc-devel on behalf of Pariksheet Nanda"
wrote:
Hi folks,
I've been told to ask some of my more fun questions on this mailing list
i
AN suggestion, which requires the least
amount of work. I think I'd then try
R -d valgrind -f /tests/testthat.R
and then further into the weeds... actually from the section of R-exts
you mention
R_C_BOUNDS_CHECK=yes R -f /tests/testthat.R
might also be promising.
Martin
On 10/12/21, 1
Hi Hervé,
On 10/13/21 12:43 PM, Hervé Pagès wrote:
On 12/10/2021 15:43, Pariksheet Nanda wrote:
The function in question is:
replace_unstranded <- function (gr) {
idx <- strand(gr) == "*"
if (length(idx) == 0L)
^
Not related to the &
Hi folks,
I've been told to ask some of my more fun questions on this mailing list
instead of Slack. I'm climbing the ladder of submitting my first
Bioconductor package (https://gitlab.com/coregenomics/tsshmm) and feel
like there are gremlins that keep adding rungs to the top of the ladder.
Hi folks,
I'm wrapping up my dissertation and one of the chapters touches on a
summer of patching a Bioconductor package that currently lives as a
separate GitHub fork (the list of changes is here [1]). 2 of the
questions I've been asked by a member of my committee are whether to:
(1)
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