Re: [Bioc-devel] Question regarding new ssh key

Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Jessie Maier via Bioc-devel Sent: Wednesday, December 18, 2024 7:17 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] Question regarding new

[Bioc-devel] Question regarding new ssh key

Hello all, I recently opened a new issue in Bioconductor Contributions with my package TrIdent. I need to push updates but realized that I forgot my ssh key passphrase! Since I am on Windows, there is unfortunately no way to recover the passphrase. I made a new ssh key and added it to my GitHub. A

Re: [Bioc-devel] Question relating to extending a class and inclusion of data

I replied the wrong email sorry. Please ignore. On 5/23/24 11:40, Hervé Pagès wrote: > > Ok I downloaded the SecureLink Connection Manager (file > connection-manager.run) on my Linux laptop (got a big warning from > Chrome that this kind of file is dangerous, I found this pretty ironic). > > The

Re: [Bioc-devel] Question relating to extending a class and inclusion of data

Ok I downloaded the SecureLink Connection Manager (file connection-manager.run) on my Linux laptop (got a big warning from Chrome that this kind of file is dangerous, I found this pretty ironic). Then I started it with   bash connection-manager.run (you have to kind of figure out these things

Re: [Bioc-devel] Question relating to extending a class and inclusion of data

On 5/22/24 02:16, Vincent Carey wrote: > ... > > > Q4: Do you think a separate ExperimentData package satisfying > the specifications laid out in Background 2 is warranted? This > could be included in a future version with > SummarizedExperiment/MetaboExperiment support. >

Re: [Bioc-devel] Question relating to extending a class and inclusion of data

, Laurent [1] https://rformassspectrometry.github.io/MsDataHub/ From: Bioc-devel on behalf of Vincent Carey Sent: 22 May 2024 11:16 To: Hervé Pagès Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Question relating to extending a class and inclusion

Re: [Bioc-devel] Question relating to extending a class and inclusion of data

> > ... > > > Q4: Do you think a separate ExperimentData package satisfying the > specifications laid out in Background 2 is warranted? This could be > included in a future version with SummarizedExperiment/MetaboExperiment > support. > It depends on the size of the data. For a software package, we

Re: [Bioc-devel] Question relating to extending a class and inclusion of data

Dear Vilhelm, notame seems to be an interesting package filling some gaps that currently exist in the untargeted metabolomics workflow. I would strongly suggest to support the SummarizedExperiment classes (in future). I would maybe suggest to keep it as generic as possible without dedicated add

Re: [Bioc-devel] Question relating to extending a class and inclusion of data

Hi, On 5/21/24 01:58, Vilhelm Suksi wrote: > Hi! > > Excuse the long email, but there are a number of things to be clarified in > preparation for submitting the notame package which I have been developing to > meet Bioconductor guidelines. As of now it passes almost all of the automatic > check

[Bioc-devel] Question relating to extending a class and inclusion of data

Hi! Excuse the long email, but there are a number of things to be clarified in preparation for submitting the notame package which I have been developing to meet Bioconductor guidelines. As of now it passes almost all of the automatic checks, with the exception of formatting and some functions

Re: [Bioc-devel] Question about cstack usage error

can you build a reprex for gplots? we are stretched very thin right now and i am sorry to say i don't see this as actionable in our group. On Tue, Feb 27, 2024 at 2:36 AM Johannes Griss < johannes.gr...@meduniwien.ac.at> wrote: > Hi, > > We've been encountering a cstack related error on the buil

[Bioc-devel] Question about cstack usage error

Hi, We've been encountering a cstack related error on the build systems on random occasions (https://master.bioconductor.org/checkResults/3.18/bioc-LATEST/ReactomeGSA/nebbiolo2-checksrc.html): Error: C stack usage 7970308 is too close to the limit I know, that the limit can be adapted using

Re: [Bioc-devel] [question about class extension]

Pleased to try also: ``` sapply(c("SummarizedExperiment", "MultiAssayExperiment"), library, character.only = T) new <- SummarizedExperiment() metadata(new) <- list(MultiAssayExperiment()) new ``` Again, it is a preference. kind regards, Sean On Wed, Jan 24, 2024 at 6:06 AM migdal migdal wrote

Re: [Bioc-devel] [question about class extension]

Hi Delphine, I had a similar dilemma while developing midasHLA package. There, we wanted to have unique features names across all experiments and colData as well as mandatory metadata. To this end I wrote a new class specific to my package that extends MAE.

Re: [Bioc-devel] [question about class extension]

There aren't strict standards imposed on many of the packages in Bioconductor introducing classes, but many other packages extend and impose standards and constraints for given areas/fields/subjects. If you are considering this route, something like the following could work to determine if introd

[Bioc-devel] [question about class extension]

Dear Bioc developer, We are developing a package and have used the MultiAssayExperiment class to manage our data. We need to impose a particular structure on the slot metadata of the MAE object (list => named list) because we havec defined methods that depend on this named list. Is it good pract

Re: [Bioc-devel] Question on prospective Bioc package

Seems like this would be a great contribution. Best Regards Sutirtha On Wednesday, 22 February 2023, 03:02:52 PM IST, Wolfgang Huber wrote: Dear Greg This sounds like a typical use case for a Bioconductor package. Simplicity is a not a bad thing—robust, well-engineered building blocks

Re: [Bioc-devel] Question on prospective Bioc package

Dear Greg This sounds like a typical use case for a Bioconductor package. Simplicity is a not a bad thing—robust, well-engineered building blocks that do one thing really well are IMHO often more useful to many than big integrated complex jack of all trades. Thanks and best wishes Wolfgang

[Bioc-devel] Question on prospective Bioc package

Dear Bioconductor Developer team, I�m part of a team at the NCI that is looking at developing a Bioconductor package, but I want to be sure it is a good fit with the goals of the Bioconductor project. The core of the package is a custom data object that allows users to query predicted drug per

Re: [Bioc-devel] Question on GPL2 license copyright

seems to be problematic to me. Sincerely, Ji-Ping Wang From: Bioc-devel on behalf of Levi Waldron Date: Wednesday, July 27, 2022 at 1:41 PM To: Vincent Carey Cc: bioc-devel Subject: Re: [Bioc-devel] Question on GPL2 license copyright Sections 1-2 of the GPL-2.0 license ( https

Re: [Bioc-devel] Question on GPL2 license copyright

ions or import functions from my package, that’s not an issue. > But instead they just copied my codes and made their package. > > From: Jianhong Ou, Ph.D. > Date: Wednesday, July 27, 2022 at 10:15 AM > To: Jiping Wang , bioc-devel@r-project.org < > bioc-devel@r-project.org>

Re: [Bioc-devel] Question on package update and version bump

Bioc-devel on behalf of Jiping Wang Sent: Monday, June 6, 2022 7:46:14 AM To: Anestis Gkanogiannis; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Question on package update and version bump ***ATTENTION: This email came from an external source. Do not open attachments or click on links from unk

Re: [Bioc-devel] Question on tasks after successfully building a package

t; Elm & Carlton Streets > > Buffalo, New York 14263 > > > From: Bioc-devel on behalf of Keita > Iida > Sent: Monday, March 28, 2022 10:54 AM > To: bioc-devel@r-project.org > Subject: [Bioc-devel] Question on tasks after successfully building a > package > > Dea

[Bioc-devel] Question on tasks after successfully building a package

Dear Bioc-devel, I am Keita Iida from Osaka University, Japan. I appreciate your supports for developing our package ASURAT, which is under process in Bioconductor issue #2524. Our package was successfully built by Bioconductor Single Package Builder 24 days ago, and we have been waiting for you

Re: [Bioc-devel] Question on copyright in Bioc vignette

o re-use it (with credit). A licence would make that > straightforward. > > Best wishes, > > Laurent > > > From: Bioc-devel on behalf of Fabricio de > Almeida > Sent: 01 July 2021 19:20 > To: bioc-devel@r-project.o

Re: [Bioc-devel] Question on copyright in Bioc vignette

Sent: 01 July 2021 19:20 To: bioc-devel@r-project.org Subject: [Bioc-devel] Question on copyright in Bioc vignette Hi, all. I am writing a vignette for a package I plan to submit next week, and I would like to include a figure explaining the package's algorithm. However, I would also like

Re: [Bioc-devel] Question on copyright in Bioc vignette

___ From: Bioc-devel on behalf of Fabricio de Almeida Sent: 01 July 2021 19:20 To: bioc-devel@r-project.org Subject: [Bioc-devel] Question on copyright in Bioc vignette Hi, all. I am writing a vignette for a package I plan to submit next week, and I would like to include a figure explaining the

Re: [Bioc-devel] Question on copyright in Bioc vignette

sion to re-use it (with credit). A licence would make that straightforward. Best wishes, Laurent From: Bioc-devel on behalf of Fabricio de Almeida Sent: 01 July 2021 19:20 To: bioc-devel@r-project.org Subject: [Bioc-devel] Question on copyright in Bio

[Bioc-devel] Question on copyright in Bioc vignette

Hi, all. I am writing a vignette for a package I plan to submit next week, and I would like to include a figure explaining the package's algorithm. However, I would also like to include this figure in the paper that describes the package. Does anyone know if including the same figure in the vig

[Bioc-devel] Question about IRanges for coordinates greater than 536870912

Hi All, Recently I encountered issues with IRanges that the coordinates greater than 536870912. Is there any easy solution to extract the information from bam file for the range greater than 2^29 via Rsamtools or GenomicAlignments? And does Rsamtools support CRAI or CSI index formats? Thank yo

Re: [Bioc-devel] Question with push to remote repository

uot; Date: Monday, March 22, 2021 at 4:52 PM To: Nitesh Turaga Subject: Re: [Bioc-devel] Question with push to remote repository Hi Nitesh, Thank you for the reply! t.triche (Tim) is the registered maintainer, but I had him add my ssh key using this (https://git.bioconductor.org/BiocCredentials). S

Re: [Bioc-devel] Question with push to remote repository

Hi, It's possible you aren't using the correct SSH key? Why does it show t.triche as the key user? Best, Nitesh On 3/22/21, 2:28 PM, "Bioc-devel on behalf of Harmon, Lauren" wrote: Hello, I have a quick question! I accidentally committed a large file to a bioconductor repositor

[Bioc-devel] Question with push to remote repository

Hello, I have a quick question! I accidentally committed a large file to a bioconductor repository, and I am trying to remove it from the history with bfg. That works fine, but when I try to push my changes, I get this error: lauren.harmon@C02CG5WTLVDL spiky.git % git push Enter passphrase f

Re: [Bioc-devel] Question reg devtools in MacOS High Sierra

Thank you very much Martin, that was very helpful ! I had failed to catch that. When I ran "brew install openssl", it was already present in my mac, but I had to run install.packages("openssl") again for it to work. In case this is helpful to anyone, here is a full list of things I did to get t

Re: [Bioc-devel] Question reg devtools in MacOS High Sierra

The error says unable to load shared object '/Library/Frameworks/R.framework/Versions/4.1/Resources/library/openssl/libs/openssl.so': so it's having trouble loading the openssl R package. There are installation instructions for this package at https://github.com/jeroen/openssl#readme (I fo

Re: [Bioc-devel] Question reg devtools in MacOS High Sierra

Hi Nitesh, Thanks for your reply. I managed to get libgit2 installed. But having trouble with its other dependencies - ‘gert’ Please see attached txt which is a full information of the error. Do you have an installation of R 4.1 that is more stable where devtools is working ? If yes, are you ab

Re: [Bioc-devel] Question reg devtools in MacOS High Sierra

Hi, Could you provide more information about the error you face with `brew install libgit2` ?? Without knowing what error message you see, it's hard to speculate about why devtools or gert didn’t work. Best, On 2/11/21, 12:00 AM, "Bioc-devel on behalf of Krithika Bhuvaneshwar" wrote:

[Bioc-devel] Question reg devtools in MacOS High Sierra

Hello, We are the package maintainers of the CINdex package. Our package is giving build errors and we are investigating why. I'm currently working on setting up the environment so I can replicate the error. I have a MacOS High Sierra. Here is what I did: * downloaded R 4.1 from https://mac.r-pr

Re: [Bioc-devel] Question for scheduled release

rk 14263 From: Bioc-devel on behalf of Yang,Peng Sent: Friday, October 9, 2020 10:11 PM To: bioc-devel Subject: [Bioc-devel] Question for scheduled release Dear Bioconductor team, I am the maintainer for DeMixT package (1.5.0 in devel, 1.4.0 in release currently)

[Bioc-devel] Question for scheduled release

Dear Bioconductor team, I am the maintainer for DeMixT package (1.5.0 in devel, 1.4.0 in release currently). Here I have a question for release schedule. I notice the scheduled new devel Bioc 3.13 is Oct 13th, does that mean if I want to push a new version 1.7.0 on devel, I need to wait for the

Re: [Bioc-devel] Question about org.Dr.eg.db package

ngton.edu" > *Date: *Thursday, August 13, 2020 at 5:41 PM > *To: *"Margolin, Gennady (NIH/NICHD) [C]" > *Cc: *Vincent Carey , " > bioc-devel@r-project.org" > *Subject: *Re: [Bioc-devel] Question about org.Dr.eg.db package > > > > Hi Gennady,

Re: [Bioc-devel] Question about org.Dr.eg.db package

: "James W. MacDonald" Reply-To: "jmac...@u.washington.edu" Date: Thursday, August 13, 2020 at 5:41 PM To: "Margolin, Gennady (NIH/NICHD) [C]" Cc: Vincent Carey , "bioc-devel@r-project.org" Subject: Re: [Bioc-devel] Question about org.Dr.eg.db package Hi Ge

Re: [Bioc-devel] Question about org.Dr.eg.db package

> 26ENSOURCEURL > ftp://ftp.ensembl.org/pub/current_fasta > 27 UPSOURCENAME > Uniprot > 28 UPSOURCEURL > http://www.UniProt.org/ > 29 UPSOURCEDATE Mon Oct 21 > 14:32:30 2019 > > From: Vincent Car

Re: [Bioc-devel] Question about org.Dr.eg.db package

ATE Mon Oct 21 14:32:30 2019 From: Vincent Carey Date: Thursday, August 13, 2020 at 2:46 PM To: "Margolin, Gennady (NIH/NICHD) [C]" Cc: "bioc-devel@r-project.org" Subject: Re: [Bioc-devel] Question about org.Dr.eg.db package This should probably

Re: [Bioc-devel] Question about org.Dr.eg.db package

This should probably be posed to the support site. What version of the package are you using? Where are you seeing coordinates? I would expect those to be obtained from the TxDb package, or perhaps from AnnotationHub. > columns(org.Dr.eg.db) [1] "ACCNUM" "ALIAS""ENSEMBL" "E

[Bioc-devel] Question about org.Dr.eg.db package

Hello, I have a short question – how do I figure the genome version for org.Dr.eg.db package? I couldn’t see it in the DESCRIPTION and also it’s not in org.Dr.eg_dbInfo() output. It would be nice to know if this is danRer11/GRCz11 or some other assembly, as there are coordinates present in the

Re: [Bioc-devel] Question about "Warning: '.local' is deprecated."

Thank you! Found it: "flowCore::description" is old, "flowCore::keyword" is replacement. Best regards Jakob From: Martin Morgan Sent: 27 April 2020 10:28 To: Jakob Theorell ; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Question about &

Re: [Bioc-devel] Question about "Warning: '.local' is deprecated."

I would suggest forcing warnings to errors options(warn=2) and then when the now-error occurs using traceback() to see what is wrong -- I think this is a call to a deprecated S4 method, and what you'd really like is the method signature. Martin On 4/27/20, 2:58 AM, "Bioc-devel on be

[Bioc-devel] Question about "Warning: '.local' is deprecated."

Dear all, In one of my packages, flowSpecs, I have over the last weeks gotten this warning message: * checking examples ... WARNING Found the following significant warnings: Warning: '.local' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecat

Re: [Bioc-devel] Question for building error

statistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Yang,Peng Sent: Friday, April 17, 2020 12:26 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] Question for building error Dear Bioconductor team, I met

[Bioc-devel] Question for building error

Dear Bioconductor team, I met a building errors for our package, DeMixT 1.3.6, under Mac OS planform on Apr 16th. And it shows failed to create vignettes. Since R 4.0.0 no longer support OpenMP, I disabled OpenMP under Mac version and it passed the building process after I committed the change

Re: [Bioc-devel] Question regarding the error from build report

Try resending the email as plain text. The list strips HTML content, so if the message has no text part, there will be no message. On Thu, Mar 26, 2020 at 9:35 PM Hervé Pagès wrote: > > What is the question? > > On 3/26/20 17:36, 유도영 wrote: > > > > ___

Re: [Bioc-devel] Question regarding the error from build report

What is the question? On 3/26/20 17:36, 유도영 wrote: ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0W

[Bioc-devel] Question regarding the error from build report

___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Question about passphrase for SSH key

Sorry, please ignore my previous email. I remember my passphrase and pushed the updates successfully. On Tue, Feb 18, 2020 at 12:02 PM Xu Ren wrote: > Hi, > > I'm the package maintainer of Bioconductor package methylGSA > https://bioconductor.org/packages/devel/bioc/html/methylGSA.html. I have >

[Bioc-devel] Question about passphrase for SSH key

Hi, I'm the package maintainer of Bioconductor package methylGSA https://bioconductor.org/packages/devel/bioc/html/methylGSA.html. I have some issues when updating the package, and I'd appreciate it if someone could help. When I was trying to update the package, I followed the guideline here: htt

Re: [Bioc-devel] Question about github repo

:49:49 To: bioc-devel@r-project.org Subject: [Bioc-devel] Question about github repo Hi Bioconductor dev team, I am ready to submit my first package to bioconductor. It is currently on a private github and I wish to start the process of submission. Do I need to make my github repo public prior t

[Bioc-devel] Question about github repo

Hi Bioconductor dev team, I am ready to submit my first package to bioconductor. It is currently on a private github and I wish to start the process of submission. Do I need to make my github repo public prior to sending it to the bioconductor contributions github repo. I understand that the co

Re: [Bioc-devel] Question regarding pruning release of large files

Hi Saskia, Mike is correct, you cannot force push to the Bioconductor git repo. If you point me to the GitHub location, and you are confident that you want your repo overwritten, let me know I'll force push it for you. Best, Nitesh > On Dec 19, 2019, at 8:49 AM, Mike Smith wrote: > > Hi

Re: [Bioc-devel] Question regarding pruning release of large files

Hi Saskia, There's some documentation on this at https://bioconductor.org/developers/how-to/git/remove-large-data/ I guess the most pertinent part is "The Bioconductor git server does not allow -f or to force push to the git.bioconductor.org location. Please email bioc-devel@r-project.org explain

[Bioc-devel] Question regarding pruning release of large files

Hi, I stupidly added and tracked some large files in my package repo at the start. I have since deleted these files and would like to permanently remove them form my GitHub history. I have been able to this locally. However when I try to do ‘git push upstream RELEASE_3_10’, it asks me to fetch

Re: [Bioc-devel] Question about package dependency

put ggplot2 in Suggests: see 1.1.3 of https://cran.r-project.org/doc/manuals/r-release/R-exts.html The ‘Suggests’ field uses the same syntax as ‘Depends’ and lists packages that are not necessarily needed. This includes packages used only in examples, tests or vignettes (see Writing package vigne

Re: [Bioc-devel] Question about package dependency

___ From: Bioc-devel on behalf of Xu Ren Sent: Tuesday, February 19, 2019 10:01:54 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Question about package dependency Hi everyone, I'm developing a Bioconductor package and I have a question about package dependency. The functions in my p

[Bioc-devel] Question about package dependency

Hi everyone, I'm developing a Bioconductor package and I have a question about package dependency. The functions in my package do not depend on ggplot2 but I used ggplot2 to do some visualization in the package vignette. I'm wondering if I should import ggplot2 in the DESCRIPTION file. If ggplot2

Re: [Bioc-devel] Question: error in makeTxDbFromUCSC

Hi there, I answered this yesterday on the support site:   https://support.bioconductor.org/p/117265/#117346 Cheers, H. On 1/26/19 05:13, Vincent Carey wrote: > If I am not mistaken the same problem is on the support site and I provided > some > commentary at > https://urldefense.proofpoint.

Re: [Bioc-devel] Question: error in makeTxDbFromUCSC

If I am not mistaken the same problem is on the support site and I provided some commentary at https://support.bioconductor.org/p/117265/#117312 Let's keep the discussion there. The "problem" seems to be upstream at UCSC. There may be a design approach that avoids the risk of asynchrony between

[Bioc-devel] Question: error in makeTxDbFromUCSC

Hi GenomicFeatures support, I am Shihang Chen, a phD student at the University of Tokyo, using GenomicFeatures for ChIPSeeker. I run into a problem when I was using makeTxDbFromUCSC, and really need your help. After I run txdb=makeTxDbFromUCSC(genome="hg19",tablename="refGene") I got this error.

Re: [Bioc-devel] Question

Another concern with kent utils (as opposed to kent lib) is the non-open-source licensing. Michael On Sat, Aug 18, 2018 at 10:11 AM, Tim Triche, Jr. wrote: > Vince beat me to it. Don’t use Kent utils unless you have to. If you have > something like a bigBed parser, I could perhaps help clean it

Re: [Bioc-devel] Question

Vince beat me to it. Don’t use Kent utils unless you have to. If you have something like a bigBed parser, I could perhaps help clean it up. But if you’re doing anything that could possibly be done in Rsamtools or rtracklayer, I would join Vince in urging you to use their functions. You will have

Re: [Bioc-devel] Question

On Sat, Aug 18, 2018 at 12:17 PM, Ghiwa Khalil wrote: > Hello, > > We are writing a package with 2 main functions, one of these functions > requires kent utils to be installed. > > Since kent utils is supported by only specific operating systems, is it > recommended to have it in an R package? >

[Bioc-devel] Question

Hello, We are writing a package with 2 main functions, one of these functions requires kent utils to be installed. Since kent utils is supported by only specific operating systems, is it recommended to have it in an R package? If we remove this function then our package will only be based on one

Re: [Bioc-devel] Question

rk 14263 From: Bioc-devel on behalf of Ghiwa Khalil Sent: Monday, August 13, 2018 4:47:44 AM To: bioc-devel@r-project.org Subject: EXTERNAL: [Bioc-devel] Question To whom it may concern, We are a bioinformatics team from the American University of Beirut, we are currently working on our package t

[Bioc-devel] Question

To whom it may concern, We are a bioinformatics team from the American University of Beirut, we are currently working on our package to submit to bioconductor. We have a question which we hope you can help us with. We plan on writing a paper regarding our package, is it recommended to wait to

Re: [Bioc-devel] Question about package development

As Lori has noted Bioconductor users have access to many chain files through AnnotationHub -- please let us know if these are not sufficient for your needs. > library(AnnotationHub) > ah = AnnotationHub() > query(ah, "chain") AnnotationHub with 1513 records # snapshotDate(): 2018-08-01 # $dat

Re: [Bioc-devel] Question about package development

n Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Ghiwa Khalil Sent: Friday, August 3, 2018 4:23:35 AM To: bioc-devel@r-project.org Subject: EXTERNAL: [Bioc-devel] Question about package development To whom it may concern, I am Ghiwa a research assi

[Bioc-devel] Question about package development

To whom it may concern, I am Ghiwa a research assistant at Dr.Pierre Khoeuiry bioinformatic's lab at the American University of Beirut. We are currently building our package and we have a question, we hope you can help us with. While writing the documentation for the function(.Rd file) the

[Bioc-devel] Question about Wercker continuous integration

Dear all, I'm usually a big Travis CI fan, but I'm having a go at Wercker, using the bioconductor/devel_core2 docker (I have also tried the rocker 'parent' ones without further success). I am running into the following issue: [...] * creating vignettes ... ERROR Error: processing vignette 'NewPac

Re: [Bioc-devel] Question regarding potential package

On 01/16/2018 04:44 PM, Rupji, Manali wrote: Hello, I have recently developed a shiny R package to perform clustering analysis. It is currently in publication and under review. I wish to also create a bio-conductor package for the same. Does bio-conductor allow a shiny tool to be created as

[Bioc-devel] Question regarding potential package

Hello, I have recently developed a shiny R package to perform clustering analysis. It is currently in publication and under review. I wish to also create a bio-conductor package for the same. Does bio-conductor allow a shiny tool to be created as a bio-conductor package? Any help in this reg

Re: [Bioc-devel] Question about Access to Bioconductor through Git

Hi George, If you’ve had an SVN id before, then you would have to submit that. I’ve checked your submission and you have to submit just your SVN ID, not the password. Please try and check for this. Otherwise, there is no way for us to associate your package with your Github ID. Best, Nitesh

[Bioc-devel] Question about Access to Bioconductor through Git

Hi Bioc-Devel List, I am having trouble pushing to the git bioconductor repository, most likely due to not requesting for access correctly. I was able to follow the instructions to open a github account and link the github repository to the one on my local machine, and then sync both with the g..

Re: [Bioc-devel] Question about external algorithms to Bioconductor package

.org>> Cc: "A.E.S." mailto:adrian.salat...@conicet.gov.ar>>, Ryan Thompson mailto:r...@thompsonclan.org>>, "bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>" mailto:bioc-devel@r-project.org>> Subject: Re: [Bioc-devel] Question about ext

Re: [Bioc-devel] Question about external algorithms to Bioconductor package

Date: Sunday, November 26, 2017 at 9:30 PM To: Martin Morgan Cc: "A.E.S." , Ryan Thompson , "bioc-devel@r-project.org" , Wei Shi Subject: Re: [Bioc-devel] Question about external algorithms to Bioconductor package I used Rbowtie and the mapping was done in 7 minutes, the res

Re: [Bioc-devel] Question about external algorithms to Bioconductor package

I used Rbowtie and the mapping was done in 7 minutes, the results where fine too. Rsubread had been running for 2 days so I had to stop it. But anyway I can use Rbowtie which is nice :) Ioannis Vardaxis Stipendiat NTNU Sendt fra min iPhone 26. nov. 2017 kl. 04:14 skrev Martin Morgan mailto:mar

Re: [Bioc-devel] Question about external algorithms to Bioconductor package

.; Ryan Thompson Cc: bioc-devel@r-project.org; Wei Shi Subject: Re: [Bioc-devel] Question about external algorithms to Bioconductor package I think that generally Rsubread is 'fast' so you might make sure that there are not obvious problems, e.g., aligning reads to the wrong reference;

Re: [Bioc-devel] Question about external algorithms to Bioconductor package

Good day, > I have DNA data. Is there any other solution rather than Rsubread which is > extremely slow? How much of it do you have? If it's a large size, such as whole genome sequencing, then it would take longer than an RNA-seq experiment regardless of the algorithm you use. I have used Rsub

Re: [Bioc-devel] Question about external algorithms to Bioconductor package

I think that generally Rsubread is 'fast' so you might make sure that there are not obvious problems, e.g., aligning reads to the wrong reference; maybe Wei Shi will chime in. Martin On 11/24/2017 09:57 AM, Ioannis Vardaxis wrote: Hi, I tried the Rsubread package you suggested and the mappin

Re: [Bioc-devel] Question about external algorithms to Bioconductor package

On 11/24/2017 01:25 PM, Ioannis Vardaxis wrote: Hei, Both kalliston and salmon er for RNA data, I have DNA data. Is there any other solution rather than Rsubread which is extremely slow? I am making an algorithm where one of its steps should be to map the DNA reads to the reference genome. So I

Re: [Bioc-devel] Question about external algorithms to Bioconductor package

Maybe gmapR? 2017-11-24 16:25 GMT-02:00 Ioannis Vardaxis : > Hei, > > Both kalliston and salmon er for RNA data, I have DNA data. Is there any > other solution rather than Rsubread which is extremely slow? > I am making an algorithm where one of its steps should be to map the DNA > reads to the r

Re: [Bioc-devel] Question about external algorithms to Bioconductor package

On 11/24/2017 09:57 AM, Ioannis Vardaxis wrote: Hi, I tried the Rsubread package you suggested and the mapping is running. However it takes like forever to end. Even in parallel it needs some days to run while bowtie for example needs only a couple of hours in 4 cores. Is there any way of speedi

Re: [Bioc-devel] Question about external algorithms to Bioconductor package

Hei, Both kalliston and salmon er for RNA data, I have DNA data. Is there any other solution rather than Rsubread which is extremely slow? I am making an algorithm where one of its steps should be to map the DNA reads to the reference genome. So I would like for the user-convenience to do it in my

Re: [Bioc-devel] Question about external algorithms to Bioconductor package

Hi, I tried the Rsubread package you suggested and the mapping is running. However it takes like forever to end. Even in parallel it needs some days to run while bowtie for example needs only a couple of hours in 4 cores. Is there any way of speeding up Rsubread? Or else I don¹t see any reason usi

Re: [Bioc-devel] Question about external algorithms to Bioconductor package

On Sun, 12 Nov 2017 22:22:56 + Ryan Thompson wrote: > Hi, > > I don't know the Bioconductor policy for packages that rely on > external tools, but for the specific features you mention, there are > Bioconductor packages to accomplish most or all of them. You can use > samtools via Rsamtools,

Re: [Bioc-devel] Question about external algorithms to Bioconductor package

Hi, I don't know the Bioconductor policy for packages that rely on external tools, but for the specific features you mention, there are Bioconductor packages to accomplish most or all of them. You can use samtools via Rsamtools, you can use the Rsubread package in place of bowtie for alignment, an

[Bioc-devel] Question about external algorithms to Bioconductor package

Hi, I have developed a package and is current under review from Bioconductor. In the future I am considering of making some changes to the package, basically adding more functions etc. My package is currently a peak calling algorithm where the input it gets is either a BAM or SAM format. Because in

Re: [Bioc-devel] Question about inclusion in upcoming bioconductor

ics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Weirather, Jason L. Sent: Friday, September 15, 2017 10:45:18 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Question about inclusion in upcoming bio

Re: [Bioc-devel] Question about inclusion in upcoming bioconductor

45:18 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Question about inclusion in upcoming bioconductor Dear Bioconductor Team, I had a couple of quick questions 1) Is our package set to go into the next Bioconductor if it�s made it through the submission process and we have acces

[Bioc-devel] Question about inclusion in upcoming bioconductor

Dear Bioconductor Team, I had a couple of quick questions 1) Is our package set to go into the next Bioconductor if it’s made it through the submission process and we have access to the Bioconductor git repository? Is the master branch for that properly staged for the upcoming release, or do w

Re: [Bioc-devel] Question : GitHub-Commit changes to the released branch

M To: bioc-devel@r-project.org Subject: [Bioc-devel] Question : GitHub-Commit changes to the released branch Hi, I need to fix a bug in the development and released version of CRISPRseek. So far, I have successfully updated the dev version of CRISPRseek following the guides at https://www.bioconduc

Re: [Bioc-devel] Question : GitHub-Commit changes to the released branch

: Friday, August 25, 2017 1:41:52 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] Question : GitHub-Commit changes to the released branch Hi, I need to fix a bug in the development and released version of CRISPRseek. So far, I have successfully updated the dev version of CRISPRseek follo

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