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

You can log on directly to the BiocCredentials account to see if it is pulled automatically (as well as add any keys manually). There is no need to delete the old one unless you want to. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Bios

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

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

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

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

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

You need to increase your package version number to trigger a new build on the submission package. On Tue, Mar 29, 2022 at 7:03 AM Kern, Lori wrote: > You can modify your package at any time. Please remember to push to > git.bioconductor.org with any updates and fix any ERROR or Warnings that >

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

Hi Fabricio, Creative Commons has detailed instructions on how to apply the licenses: http://creativecommons.org/licenses/by-sa/4.0/ I'd rather add a section at the beginning of the document, not at the bottom. For instance, in Rnw documents, right after \tableofcontents I add \section*{License

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

Yes, that would be a sensible way, I think. Laurent From: Fabricio de Almeida Sent: 01 July 2021 19:42 To: Laurent Gatto; bioc-devel@r-project.org Subject: RE: Question on copyright in Bioc vignette Hi, Laurent. Thank you for your suggestion. How would

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

Hi, Laurent. Thank you for your suggestion. How would you mention that the vignette is licensed under CC-BY? A section named "License" at the bottom of the vignette? Best, = Fabrício de Almeida Silva Undergraduate degree in Biological Sciences (UENF) MSc. candidate

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

Dear Fabrício, As far as I know, there's no explicit license on the documentation of a package, and I'm not sure the the package/software licence applies to documentation. I would explicitly mention that the figure (and possibly the vignette) is released under a CC-BY (or any alternative) to be

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

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:

Re: [Bioc-devel] Question for scheduled release

The officially release will not be until October 28th. Today, commmits to release/ RELEASE_3_11 (1.4.0) will be frozen and there will be no more commits allowed to this branch every. You can still commit the the master/devel branch (1.5.0) . For version x.y.z , if you push to the devel you

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

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

Re: [Bioc-devel] Question for building error

The current ERROR "polygon edge not found" is a Bioconductor builder issue having to do with fonts not being found. We are working on a solution but for now you can ignore. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinforma

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

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 >

Re: [Bioc-devel] Question about github repo

Hi Krutik, You are looking at the "problem" from a wrong angle. If there are no any reasons raised by your PhD funding body to keep your repository closed, it's of your own benefit to have all the code public: a) There is chance that someone else in the world is working on something very sim

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

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

I believe this type of dependency belongs in the Suggests: field of the DESCRIPTION file. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bi

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

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? >

Re: [Bioc-devel] Question

I think it depends on the journal and your order of priority. Essentially they are separate tasks but it is always nice when submitting to a journal to link to the accepted package on Bioconductor rather than a github repository. Keep in mind the review process for a package to be accepted 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

You could see if there are any appropriate chain files provided in AnnotationHub (https://bioconductor.org/packages/release/bioc/html/AnnotationHub.html) library(AnnotationHub) ah = AnnotationHub( ) query(ah, "chain file") or investigate other packages that do similar functions or address a

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

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

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

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

Hi Jason, Note that https://bioconductor.org/developers/how-to/git/ has a collection of documents that cover all the aspects of maintaining a Bioconductor package via git/GitHub. In particular see "New package workflow" for what to do after package acceptance and "Push to GitHub and Bioconductor

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

1. Yes. If you package was accepted and is on g...@git.bioconductor.org then it is set to be included in the next release version of Bioconductor. You do not need to do anything; the Bioconductor team will handle making appropriate branches to the repository. 2. You can add changes to Bio

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

Thanks so much, Lori! Best, Julie From: "Shepherd, Lori" Date: Friday, August 25, 2017 at 1:58 PM To: "Zhu, Lihua (Julie)" , "bioc-devel@r-project.org" Subject: Re: Question : GitHub-Commit changes to the released branch The current release is RELEASE_3_5 Lori Shepherd Bioconductor Cor

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

The current release is RELEASE_3_5 Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Zhu, Lihua (Julie) Sent: Friday,

Re: [Bioc-devel] Question about creating a bulleted list without bullets in rstudio

On 06/09/2017 11:08 AM, Aimin Yan wrote: I have a question about making R package documentation. I use rstudio to make this package. In my test.R file, I have code like the following: ... #' @return Returns a dataframe with several following variables (columns) #' \itemize{ #' \item gen

Re: [Bioc-devel] Question about creating a bulleted list without bullets in rstudio

https://stackoverflow.com/questions/9267584/when-documenting-in-roxygen-how-do-i-make-an-itemized-list-in-details See last answer. It's not clear to me if you can have bulletted lists in all of the sections of an Rd file or not, so it may be that the 'value' section can't have bulletted lists. I d

Re: [Bioc-devel] question regarding timeout

Hi, I'm not sure what's going on here. It looks there haven't been any changes to the vignette and the package doesn't have the timeout in devel. I went on the release builder and was able to build the vignette which confirms that the vignette doesn't hang, it just takes a long time. When I ran

Re: [Bioc-devel] Question about BiocGeneric::order

Thanks for noticing that. I'll fix that in R soon. I'm going through and generalizing many of the stats default methods so that they work automatically with Rle. For order,Rle(), I fixed the method argument default and added a fast path for the single arg case. I guess we'll keep it around. On Th

Re: [Bioc-devel] Question about BiocGeneric::order

On 05/11/2017 06:44 PM, Hervé Pagès wrote: Hi Michael, On 05/11/2017 03:27 PM, Michael Lawrence wrote: There is a bug in S4Vectors, but thanks to an R 3.4 bug in the methods package (recently fixed in devel), the bug is masked. So, we should fix S4Vectors. The problem is that order,Rle has a de

Re: [Bioc-devel] Question about BiocGeneric::order

Hi Michael, On 05/11/2017 03:27 PM, Michael Lawrence wrote: There is a bug in S4Vectors, but thanks to an R 3.4 bug in the methods package (recently fixed in devel), the bug is masked. So, we should fix S4Vectors. The problem is that order,Rle has a default for the 'method' argument that differs

Re: [Bioc-devel] Question about BiocGeneric::order

There is a bug in S4Vectors, but thanks to an R 3.4 bug in the methods package (recently fixed in devel), the bug is masked. So, we should fix S4Vectors. The problem is that order,Rle has a default for the 'method' argument that differs from that of the generic. Since R 3.3, base::order() is smart

Re: [Bioc-devel] Question about BiocGeneric::order

Thank you Hervé, I got that. Good to know that BioC 3.6 require R 3.4.0. Yours Sincerely, Jianhong Ou TEL: 508-856-5379 LRB 608 Bioinformatician of Bioinformatics core at Department of Molecular, Cell and Cancer Biology UMASS Medical School 364 Plantation Street Worcester, MA 01605 Confidenti

Re: [Bioc-devel] Question about BiocGeneric::order

Hi Jianhong, I can't reproduce this but I'm using R 3.4.0. You seem to be using Bioc devel (aka BioC 3.6) with 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

Re: [Bioc-devel] Question about R functions

And note the existence of the "Internal" keyword for documentation: http://www.hep.by/gnu/r-patched/r-exts/R-exts_50.html On Fri, Mar 31, 2017 at 5:35 AM, Wolfgang Huber wrote: > > Thanks Juan; the .point used to be a way to do this, but since the > introduction of namespaces to R, it is neith

Re: [Bioc-devel] Question about R functions

Thanks Juan; the .point used to be a way to do this, but since the introduction of namespaces to R, it is neither necessary nor sufficient for private functions. See e.g. .Hub in the AnnotationHub package, or the .Call function in base. See https://cran.r-project.org/doc/manuals/r-release/R

Re: [Bioc-devel] Question about R functions

HI Jing, You should export FA FB and FC, but don't export FD. If using roxygen2 for documentation you use "#' @export" on the ones to export, and just don't document FD and it won't be exported by default. Hope that helps, -Nathan On 03/30/2017 04:02 PM, Jing Wang wrote: Hi, I have

Re: [Bioc-devel] Question about R functions

Hi Wang You can create internal functions calling them as ".function", the point is necessary to declare an internal function. Additionally, you can put all your internal functions in the same R file and is not necessary create the documentation for this functions. Best regards. Juan D. Henao 2

Re: [Bioc-devel] Question on the build and biocheck of the package

On 03/16/2017 01:56 PM, Aayush Raman wrote: Hello Hervé Thanks for a quick reply. I have some more questions: 1. This the report of the build of package from Bioconductor: http://bioconductor.org/spb_reports/DASC_buildreport_20170306051600.html. Here, you will see *dependencies error* in the to

Re: [Bioc-devel] Question on the build and biocheck of the package

tics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Aayush Raman Sent: Thursday, March 16, 2017 1:56:15 PM To: Herv� Pag�s Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Question on the build and biocheck of the package He

Re: [Bioc-devel] Question on the build and biocheck of the package

Hello Hervé Thanks for a quick reply. I have some more questions: 1. This the report of the build of package from Bioconductor: http://bioconductor.org/spb_reports/DASC_buildreport_20170306051600.html. Here, you will see *dependencies error* in the tokay2 BUILD SRC output. Should I include these

Re: [Bioc-devel] Question on the build and biocheck of the package

Hi Ar, On 03/15/2017 12:57 AM, Aayush Raman wrote: Hello Everyone, I have developed a Bioconductor package and submit the issue to build and check. I have some questions regarding on the build and BioCheck of the package. Here are the questions: 1. It has passed the build and check on Mac OS a

Re: [Bioc-devel] question on package build

I can investigate this and see what was going on however, you deleted the first comment when submitting packages that included the link to your github repository. Until you add the section agreeing to the Bioconductor terms of package review and include the link to your github repository we can

Re: [Bioc-devel] question on bioconductor/package submission

On 03/05/2017 04:40 AM, 张腾 wrote: Hi I have developed a bioconductor package that has been built and checked without errors and warnings on all platforms. I have built a repository in Github and upload my package to my repository, then I submit an issue to Bioconductor website. The package has b

Re: [Bioc-devel] question on bioconductor/package citation

On Sat, Mar 4, 2017 at 6:13 AM, Dwivedi, Bhakti wrote: > Hi, > > > > I have a few general questions. With such a rigorous peer-review process > in place for new package submissions in Bioconductor, I was wondering if > there is a way to assess the package acceptance rate? > > > > The reason I ask

Re: [Bioc-devel] question on bioconductor/package citation

On 03/04/2017 09:13 AM, Dwivedi, Bhakti wrote: Hi, I have a few general questions. With such a rigorous peer-review process in place for new package submissions in Bioconductor, I was wondering if there is a way to assess the package acceptance rate? One could summarize the number times the

Re: [Bioc-devel] Question about status of new package submission

Dear Lori : Thanks for giving prompt help on this issue. Because of I forked old version of contribution repository, my package issued on wrong place. Now I update package submission issue to the suggested repository, it can be visible the issue list. Thank you very much. Best regards : Jurat O

Re: [Bioc-devel] Question about status of new package submission

Are you sure you submitted the package to the right location? Normally we see new packages as issues on https://github.com/Bioconductor/Contributions/issues once they are submitted. Please ensure you use this link to submit your package: https://github.com/Bioconductor/Contributions/issues/new

Re: [Bioc-devel] Question, R, get sequence genes

On 12/04/2016 11:34 PM, Keyvān Karami via Bioc-devel wrote: Hi My question is how i can get sequence some genes with " BSgenome.Btaurus.UCSC.bosTau8" i want to get sequence of a list of locations of genes like: chr25 3510245435102482 chr19 4403596944036049 chr18 10444115

Re: [Bioc-devel] Question about sumbition process and biocviews

On 11/12/2016 12:28 PM, Ioannis Vardaxis wrote: Hi, I don¹t get any error in R CMD build pkg at all, I only get a note in the BiocCheck that the macro '\insertRef¹ is unknown. However it is only a note, I have no errors nor warnings. Is it ok if I submit the package like that? I can¹t find any

Re: [Bioc-devel] Question about sumbition process and biocviews

Hi, I don¹t get any error in R CMD build pkg at all, I only get a note in the BiocCheck that the macro '\insertRef¹ is unknown. However it is only a note, I have no errors nor warnings. Is it ok if I submit the package like that? I can¹t find any solution. Output: > system("R CMD check --no-bu

Re: [Bioc-devel] Question about sumbition process and biocviews

Create a folder \inst and place the REFERENCES.bib in it. (see attached) Then in the R function add: #’ @references \insertRef{ENCODE_1}{PkgA}. You have to have the Rdpack installed. -- Ioannis Vardaxis Stipendiat IMF NTNU On 07/11/16 13:49, "Ioannis Vardaxis" wrote: > > > > > >On 07/11/1

Re: [Bioc-devel] Question about sumbition process and biocviews

On 11/08/2016 08:26 AM, Ioannis Vardaxis wrote: Create a folder \inst and place the REFERENCES.bib in it. (see attached) Then in the R function add: #’ @references \insertRef{ENCODE_1}{PkgA}. You have to have the Rdpack installed. when I do that (see https://github.com/mtmorgan/PkgA/tree/pars

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