Hi Tulip,
The R NEWS file says "Strict R headers are now the default. This
removes the legacy definitions of PI, Calloc, Realloc and Free: use
M_PI, R_Calloc, R_Realloc or R_Free instead" here:
https://cran.r-project.org/doc/manuals/r-devel/NEWS.html so the patch
below fixes the source compi
Hi Lluís,
> So your setter method `[<-` could have this call inside it, and this
> would prevent the creation of an invalid object.
Thank you for solving my issue! I wasn't successful trying something
similar earlier because I was passing no arguments to callNextMethod(),
but retrying your s
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) assoc
Hi folks,
The fault was my directly overwriting the value of an R object pointing
to NA with an integer value:
# ./R/TSSHMM-class.R
...
converged <- NA
.Call(C_train,
PACKAGE = "tsshmm",
converged,
...
# src/R_wrap_tsshmm.c
...
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 &
nt.
Actually, I liked Henrik's UBSAN 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
migh
You might have success running 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 o
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 and
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 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:
https://bioconductor.org/packages/release/bioc/html/GL
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
GLA
iring 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,
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 = 1)
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, Lev
Hi all,
> I want to compare a subset of GRanges for hits, but revert to
> the original GRanges indices when returning the results.
For now I will recreate the Hits object:
https://github.com/coregenomics/nascentrna/commit/e04e52b6db37bccde1dde7e85b262afe5c3d723c#diff-ee43ece522f0957d1699554637a9b
Hi folks,
I'm working on a package that does some trivial GRanges position
classifications; primarily to standardize nomenclature according to the
literature in workflows.
The API for S4Vectors::Hits() generally doesn't seem amenable to modify
Hits objects, except for the remapHits() feature (whi
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. Could
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
> practice that certain d
> 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
> for
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 consensus clustering in
> addition
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 re-building
e 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
Pariksheet
---
Pariksheet Nanda
P
Rsamtools_1.29.1
[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 Adm
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 difference is that wit
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 Ca
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, simil
at creating a
dm6 UCSC "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 too
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