[Bioc-devel] Merging or renaming a fork, and appropriate journal for package updates

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)

Re: [Bioc-devel] Strange "internal logical NA value has been modified" error

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 &

Re: [Bioc-devel] [External] Re: Strange "internal logical NA value has been modified" error

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

Re: [Bioc-devel] Strange "internal logical NA value has been modified" error

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

Re: [Bioc-devel] Strange "internal logical NA value has been modified" error

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

[Bioc-devel] Strange "internal logical NA value has been modified" error

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.

Re: [Bioc-devel] GLAD quotation

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:

Re: [Bioc-devel] GLAD quotation

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

Re: [Bioc-devel] IRanges should support long vectors

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: &

[Bioc-devel] IRanges should support long vectors

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 =

Re: [Bioc-devel] BiocManager to install Depends/Imports/Suggests

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,

Re: [Bioc-devel] BiocInstaller: next generation

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.

Re: [Bioc-devel] Including data for @examples to run

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 >

Re: [Bioc-devel] BiocCheck - warning: files are over 5MB

> disk efficient compression algorithm Whoops, meant to say compression format. Pariksheet [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] BiocCheck - warning: files are over 5MB

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 >

Re: [Bioc-devel] parallel processing in R?

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

Re: [Bioc-devel] Help with R CMD check NOTEs

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: [Bioc-devel] Help with R CMD check NOTEs

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

[Bioc-devel] Cannot install Bioconductor packages with biocLite() after loading QuasR

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

Re: [Bioc-devel] Iterating over BSgenomeViews returns DNAString instead of BSgenomeViews

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

[Bioc-devel] Iterating over BSgenomeViews returns DNAString instead of BSgenomeViews

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

Re: [Bioc-devel] OrganismDb package for Drosophila.melanogaster

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

[Bioc-devel] OrganismDb package for Drosophila.melanogaster

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