Re: [Bioc-devel] Request to Retire COHCAP Bioconductor Package

Buffalo, New York 14263 From: Bioc-devel on behalf of Charles Warden via Bioc-devel Sent: Monday, April 15, 2024 7:14 PM To: bioc-devel@r-project.org Cc: Xiwei Wu ; Yate-Ching Yuan Subject: [Bioc-devel] Request to Retire COHCAP Bioconductor Package Hi,

Re: [Bioc-devel] Request to Retire COHCAP Bioconductor Package

rk 14263 From: Bioc-devel on behalf of Charles Warden via Bioc-devel Sent: Monday, April 15, 2024 7:14 PM To: bioc-devel@r-project.org Cc: Xiwei Wu ; Yate-Ching Yuan Subject: [Bioc-devel] Request to Retire COHCAP Bioconductor Package Hi, I have greatly appreciated the assistance

[Bioc-devel] Request to Retire COHCAP Bioconductor Package

Hi, I have greatly appreciated the assistance provided by Bioconductor support over several years! However, my requested end date to work in the Integrative Genomics Core at City of Hope is 4/30/2024. Later this year, I will be starting a PhD program at UC-Riverside. When I was previously

Re: [Bioc-devel] Request to add maintainers for diffHic

8:31 AM To: bioc-devel Cc: Hannah Coughlan ; Gordon K Smyth Subject: [Bioc-devel] Request to add maintainers for diffHic Could Hannah and Gordon (in cc) be given push access to Bioc's diffHic repository? Note, this is in addition to my current push access, as I will be responsible for the large b

[Bioc-devel] Request to add maintainers for diffHic

Could Hannah and Gordon (in cc) be given push access to Bioc's diffHic repository? Note, this is in addition to my current push access, as I will be responsible for the large body of C++ code still in the package. Thanks, -A ___

Re: [Bioc-devel] Request for undeprecation for exomePeak2

Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of $Br2?L(B via Bioc-devel Sent: Friday, December 8, 2023 12:42 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Request for undep

[Bioc-devel] Request for undeprecation for exomePeak2

Dear Bioconductor Team， The build error of package exomePeak2 has now been fixed，I would like to request undeprecate the package on bioconductor. Best wishes， Zhen Wei Maintainer of exomePeak2 package ___ Bioc-devel@r-project.org mailing list

[Bioc-devel] Request for undeprecation for exomePeak2

Dear Bioconductor Team， The build error of package exomePeak2 has now been fixed，I would like to request undeprecate the package on bioconductor. Best wishes， Zhen Wei Maintainer of exomePeak2 package ___ Bioc-devel@r-project.org mailing list

Re: [Bioc-devel] Request to reverse package deprecation (and support pushing changes)

rk 14263 From: Bioc-devel on behalf of L Rutter Sent: Thursday, November 9, 2023 7:02 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] Request to reverse package deprecation (and support pushing changes) Good afternoon: I'm the maintainer for the Bioconductor package "bigPint&q

[Bioc-devel] Request to reverse package deprecation (and support pushing changes)

Good afternoon: I'm the maintainer for the Bioconductor package "bigPint", located here . I've recently tried to push changes I made to resolve ERRORS in my package by the command " git push upstream devel". However, this has

Re: [Bioc-devel] Request for undeprecation of motifbreakR

From: Bioc-devel on behalf of Coetzee, Simon via Bioc-devel Sent: Wednesday, June 28, 2023 1:05 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Request for undeprecation of motifbreakR Dear bioc-devel, I am sorry for not being responsive to the error messages related to the buildin

Re: [Bioc-devel] Request for undeprecation of motifbreakR

Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Coetzee, Simon via Bioc-devel Sent: Wednesday, June 28, 2023 1:05 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Request for undeprecation of motifbreakR Dear bioc-devel, I

[Bioc-devel] Request for undeprecation of motifbreakR

Dear bioc-devel, I am sorry for not being responsive to the error messages related to the building of motifbreakR. As you can likely see, I was responsive to errors earlier in the year, entering many changes to keep up to date with the changing conditions of the Bioc universe, and bugs that I

Re: [Bioc-devel] Request for advice on ANCOMBC package error messages in Linux platform

two builders. Best, Jim -Original Message- From: Bioc-devel On Behalf Of Huang Lin (Frederick) Sent: Tuesday, April 18, 2023 3:06 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] Request for advice on ANCOMBC package error messages in Linux platform

[Bioc-devel] Request for advice on ANCOMBC package error messages in Linux platform

Dear BioC team, I am the creator of the ANCOMBC package ( http://bioconductor.org/packages/release/bioc/html/ANCOMBC.html). Recently, I committed a bug-fixed change to the ANCOMBC package. Unfortunately, I received error messages for both Bioc 3.16 and 3.17. The error occurred ONLY on the

Re: [Bioc-devel] Request GWAS.BAYES to be un-deprecated

Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Jake Williams Sent: Wednesday, October 13, 2021 11:29 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Request GWAS.BAYES to be un-deprecated

[Bioc-devel] Request GWAS.BAYES to be un-deprecated

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

Re: [Bioc-devel] Request access to EGSEA123

oc-devel on behalf of monther.alhamdo...@csl.com.au Sent: Monday, December 7, 2020 5:30 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] Request access to EGSEA123 Hi there, I am one of the maintainers of EGSEA123 workflow package and it seems the package is failing due to an error that I need

[Bioc-devel] Request access to EGSEA123

Hi there, I am one of the maintainers of EGSEA123 workflow package and it seems the package is failing due to an error that I needs to fix. Can you please give me access to the package. This is my BiocCredentials email m.hamdo...@gmail.com Thanks, Monther

Re: [Bioc-devel] Request package deprecation

lf of Crispin > Miller > Sent: Thursday, August 27, 2020 5:27 AM > To: bioc-devel@r-project.org > Subject: [Bioc-devel] Request package deprecation > > Hi there, > I’ve moved email address since creation of this package but I would like > to request deprecation and End

Re: [Bioc-devel] Request package deprecation

rk 14263 From: Bioc-devel on behalf of Crispin Miller Sent: Thursday, August 27, 2020 5:27 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Request package deprecation Hi there, I�ve moved email address since creation of this package but I would like to

[Bioc-devel] Request package deprecation

Hi there, I’ve moved email address since creation of this package but I would like to request deprecation and End of Life for the package: simpleaffy It’s been superseded and is out of date. Best wishes, Crispin Miller [[alternative HTML version deleted]]

Re: [Bioc-devel] request

, Ashwath ; Bioc-devel@r-project.org Subject: Re: [Bioc-devel] request Please view the nightly build report http://bioconductor.org/checkResults/devel/bioc-LATEST/CSSQ/ compare the time that your package had a 'snapshot' taken for the build to start Snapshot Date: 2020-05-29 16:51:41 -0400 (Fri, 29

Re: [Bioc-devel] request

Please view the nightly build report http://bioconductor.org/checkResults/devel/bioc-LATEST/CSSQ/ compare the time that your package had a 'snapshot' taken for the build to start Snapshot Date: 2020-05-29 16:51:41 -0400 (Fri, 29 May 2020) and commit hash and date of the last commit included in

Re: [Bioc-devel] request

Hello all, I am the maintainer for CSSQ (https://bioconductor.org/packages/release/bioc/html/CSSQ.html). I had made some changes (Re authorship and email addresses) to the package last night. I made sure to push them to both the master and RELEASE_3_11 branches and confirmed the changes by

[Bioc-devel] request

Dear Biocondcutor admins: This is Zhen Yang from Fudan University, as the maintainer of the Bioconductor package of "FEM" (https://bioconductor.org/packages/release/bioc/html/FEM.html), I would like to make some update to this package. However, my last email (yangz...@picb.ac.cn) has been

Re: [Bioc-devel] Request to undeprecate MANOR

New York 14263 From: Bioc-devel on behalf of Pierre Neuvial Sent: Monday, April 6, 2020 4:58 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Request to undeprecate MANOR Hi, I have updated the Maintainer email address for the MANOR package, so the

[Bioc-devel] Request to undeprecate MANOR

Hi, I have updated the Maintainer email address for the MANOR package, so the package is not "Unresponsive/not-maintained" anymore. Also, I believe (*) I have fixed the build error that occurs for OS X on http://bioconductor.org/checkResults/release/bioc-LATEST/MANOR/ (a file encoding issue in

[Bioc-devel] Request to undeprecate MANOR

Hi, I have updated the Maintainer email address for the MANOR package, so the package is not "Unresponsive/not-maintained" anymore. Also, I believe (*) I have fixed the build error that occurs for OS X on http://bioconductor.org/checkResults/release/bioc-LATEST/MANOR/ (a file encoding issue in

[Bioc-devel] Request for activating Bioconductor repository account for Lumi and methyAnalysis package

Dear Bioconductor team, We are the maintainers of Bioconductor packages Lumi (https://bioconductor.org/packages/release/bioc/html/lumi.html) and methyAnalysis (https://bioconductor.org/packages/release/bioc/html/methyAnalysis.html). We were trying to obtain Bioconductor Git credentials by

Re: [Bioc-devel] Request R code this paper

l on behalf of Salwa > El-Aty > Sent: Tuesday, January 7, 2020 3:49 AM > To: Bioc-devel@r-project.org > Subject: [Bioc-devel] Request R code this paper > > Dear Sir > I want to help me about to send the R Codes of paper which title > "Generalized endpoint -inf

Re: [Bioc-devel] Request R code this paper

From: Bioc-devel on behalf of Salwa El-Aty Sent: Tuesday, January 7, 2020 3:49 AM To: Bioc-devel@r-project.org Subject: [Bioc-devel] Request R code this paper Dear Sir I want to help me about to send the R Codes of paper which title "Generalized endpoint -inflated binomial

[Bioc-devel] Request R code this paper

Dear Sir I want to help me about to send the R Codes of paper which title "Generalized endpoint -inflated binomial model" .COMPUTATION STATISTICS AND DATA ANALYSIS .89 , 2015 Best Regards Salwa. A.Mousa Sent from my Samsung device [[alternative HTML version deleted]]

[Bioc-devel] request R CODESof paper which title "Generalized endpoint -inflated binomial modole

Dear Sir I want to help me about to send the R Codes of paper which title "Generalized endpoint -inflated binomial model" .COMPUTATION STATISTICS AND DATA ANALYSIS .89 , 2015 Best Regards Salwa. A.Mousa [[alternative HTML version deleted]]

Re: [Bioc-devel] Request to un-deprecate a package

Hi, “biocLite" will stay deprecated for R version 3.5.2. Please note that the issue is not with “biocLite" but with “mmnet". “mmnet” has been deprecated for R-3.5.z and is defunct for R-3.6.z. There are other workaround solutions to this, where you may install the package from the tarball

Re: [Bioc-devel] Request upstream pull --force of sanitized master branch

Thanks for fixing this Nitesh and Sam! I wrote that R check and forgot that it depended on the Gencode url. I had to fix this too for recount https://github.com/leekgroup/recount/commit/056e81c326143e3748b452988ac15a6bed3b035e. Best, Leo On Mon, Nov 5, 2018 at 3:14 PM Turaga, Nitesh wrote: >

Re: [Bioc-devel] Request upstream pull --force of sanitized master branch

Hi Sam, I fixed the RELEASE_3_8 branch as well. There was a minor discrepancy in the commit history for RELEASE_3_8 though, (which I fixed in git.bioconductor.org/packages/bumphunter) so you should resync RELEASE_3_8 in rafalab/bumphunter. The commit history on rafalab/bumphunter:RELEASE_3_8

Re: [Bioc-devel] Request upstream pull --force of sanitized master branch

Hi Nitesh, I have fixed the commit history for rafalab/bumphunter RELEASE_3_8 branch, and request synchronization with Bioconductor RELEASE_3_8. We need this, because bumphunter is not building on RELEASE_3_8, due to an obsolete URL in one of the tests. thanks, - Sam On 11/5/18 7:56 AM,

Re: [Bioc-devel] Request upstream pull --force of sanitized master branch

Hi Sam, I have updated your “master” branch on git.bioconductor.com to reflect what you have on GitHub, at https://github.com/rafalab/bumphunter. You will not get the duplicate commit error when you push to the master branch anymore. However, RELEASE_3_8 still has duplicate commits in the

[Bioc-devel] Request upstream pull --force of sanitized master branch

Dear Bioconductor, I believe I have removed all duplicate commits from the bumphunter package. The main branch in rafalab/bumphunter incorporates the new commit history. It passes 'library(devtools); build("."); install(); check("."); BiocCheck(".")' I am contacting you in accordance with

[Bioc-devel] Request the change of the email of the maintainer

Hello, I am writing to request to change the maintainer email of phosphonormalizer package. The information needed is included below: Current maintainer email: sohrab.saraei at utu.fi New maintainer email: sohrab.saraei at helsinki.fi Kind regards, Sohrab Saraei

Re: [Bioc-devel] Request the change of the email of the maintainer

Hi Sohrab, If you still have access to the old email you can change this yourself. Activate your account here with the old email: https://git.bioconductor.org/BiocCredentials Once activated you can login. Then got to --> user profile --> update email. If you don't have access to

Re: [Bioc-devel] Request for comment metagenomeFeatures package

Thanks, Martin. I agree using AnnotationHub to manage the db resources is a better option than how it is currently setup. A pull request would be much appreciated. On Tue, Aug 4, 2015 at 3:14 PM Vincent Carey st...@channing.harvard.edu wrote: On Tue, Aug 4, 2015 at 3:00 PM, Martin Morgan

[Bioc-devel] Request for comment metagenomeFeatures package

We are starting to work on an infrastructure for annotation of 16S metagenomic sequencing datasets and would like your comments and/or contributions. Below are links to two github repositories: metagenomeFeatures and greengenes13.5MgDb. The metagenomeFeatures package contains two classes; mgDb,

Re: [Bioc-devel] Request for comment metagenomeFeatures package

very interesting development, we have several folks who will take a look. FYI %vjcair R CMD INSTALL greeng*b Bioconductor version 3.2 (BiocInstaller 1.19.9), ?biocLite for help Loading required package: digest Loading required package: tools Loading required package: utils Loading required

Re: [Bioc-devel] Request for comment metagenomeFeatures package

On 08/04/2015 06:43 AM, Nathan Olson wrote: We are starting to work on an infrastructure for annotation of 16S metagenomic sequencing datasets and would like your comments and/or contributions. Below are links to two github repositories: metagenomeFeatures and greengenes13.5MgDb. The

Re: [Bioc-devel] Request for comment metagenomeFeatures package

On Tue, Aug 4, 2015 at 3:00 PM, Martin Morgan mtmor...@fredhutch.org wrote: On 08/04/2015 06:43 AM, Nathan Olson wrote: We are starting to work on an infrastructure for annotation of 16S metagenomic sequencing datasets and would like your comments and/or contributions. Below are links to

Re: [Bioc-devel] request for more notices about build issues

- Original Message - From: Michael Love michaelisaiahl...@gmail.com To: bioc-devel@r-project.org Sent: Wednesday, April 8, 2015 11:03:02 AM Subject: [Bioc-devel] request for more notices about build issues dear core Bioc-ers, It would be nice to have more devel mailing list

Re: [Bioc-devel] request for more notices about build issues

works for me. Thanks Dan. On Tue, Apr 14, 2015 at 2:34 PM, Dan Tenenbaum dtene...@fredhutch.org wrote: - Original Message - From: Michael Love michaelisaiahl...@gmail.com To: bioc-devel@r-project.org Sent: Wednesday, April 8, 2015 11:03:02 AM Subject: [Bioc-devel] request for more

Re: [Bioc-devel] request for more notices about build issues

Is this a use case for a graphical build report that displays the build status on a graph/DAG? http://www.bioconductor.org/packages/release/bioc/vignettes/pkgDepTools/inst/doc/pkgDepTools.pdf pkgDepTools, combined with a computable build report (a downloadable version of the current build

[Bioc-devel] request for more notices about build issues

dear core Bioc-ers, It would be nice to have more devel mailing list notices about large scale build issues, just to keep developers in the loop. (e.g. I often get a number of emails when GenomicRanges is down, asking why I'm breaking someone's downstream package). Or if you don't want to push

Re: [Bioc-devel] request to create BSgenome Bos_taurus_UMD3.1.1

So I went ahead and did BSgenome.Btaurus.UCSC.bosTau8. It should become available via biocLite() in the next couple of hours (in BioC devel only). H. On 03/26/2015 12:54 AM, Hervé Pagès wrote: Hi Byungkuk, On 03/25/2015 10:17 PM, Byungkuk Min wrote: Dear Dr.Pages, I've been trying to build

[Bioc-devel] Request for Comments on The NIH Software Discovery Index--a system for linking software, publications and users in the research community

On behalf of a number of software developers, end-users, publishers associated with the scientific analysis community, we would like to invite all of you to review a document generated as a result of a NIH BD2K supported meeting that focused on the opportunities and challenges of developing a

Re: [Bioc-devel] request: high-level seqlevel utilities

Hi, With the convenience that seqnamesStyles offers now, having to specify the chromosome name notation manually would feel like a step back. In terms of subsetting genomic ranges, I normally think of four major groups of interest: - Toplevel/standard: 1,..22,X,Y,MT - Autosomes: 1,..,22 -

Re: [Bioc-devel] request: high-level seqlevel utilities

Hi Michael, We decided to come up with one function called keepStandardChromosomes() which is a wrapper for both the functions suggested by you (i.e., keepPrimaryChromosomes() and keepAutosomes() ) Here is an example: library(AnnotationDbi) library(GenomicRanges) txdb -

Re: [Bioc-devel] request: high-level seqlevel utilities

I guess you mean dropSeqlevels, not keepSeqlevels? That should work. But your function needs some tweaking, I think. The function should just take the seqnameStyle from the object. There's no need to require the user to specify it, and then check for consistency. I would like to be able to just

Re: [Bioc-devel] request: high-level seqlevel utilities

Michael, Since there is no universal seqnameStyle defined for various objects and they do not internally store the seqnameStyle and species information, we decided to ask the user for all 3 arguments. Marc is aware of these issues and my code. Regarding the dependency of GenomicRanges on

Re: [Bioc-devel] request: high-level seqlevel utilities

Hi Sonali, Thank you for this much requested addition to the GenomicRanges API! I would like to second Michael Lawrence's assertion that keepAutosomes() is more straightforward and harder to misunderstand or misuse than a special case of keep/dropSeqlevels. (If the author of a function has

Re: [Bioc-devel] request: high-level seqlevel utilities

Is this being taken into consideration by anyone? Will it be worked on? Thanks, Michael On Thu, Dec 12, 2013 at 1:36 PM, Michael Lawrence micha...@gene.com wrote: We've found that analysts often need to restrict seqlevels to certain pre-defined sets of chromsomes. Given the variability

Re: [Bioc-devel] request: high-level seqlevel utilities

Hi Michael, I would second your request. In a package I'll submitting soon, I have a work-around for this by defining a set of functions like 'hsAutosomes', 'hsAllosomes' etc. that return the respective set of human chromosome names. Perhaps on could incorporate this in the 'seqinfo'

Re: [Bioc-devel] request: high-level seqlevel utilities

Hi Michael, That is an extremely interesting question. We have a couple of ideas and are beginning to work on it. We hope to come up with something soon. Thanks, Sonali. On 12/16/2013 6:14 AM, Michael Lawrence wrote: should be stored with the Seqinfo. It could be imputed (along with the

Re: [Bioc-devel] request: high-level seqlevel utilities

Awesome, thanks, Sonali. And welcome to the team. Michael On Mon, Dec 16, 2013 at 10:38 AM, Arora, Sonali sar...@fhcrc.org wrote: Hi Michael, That is an extremely interesting question. We have a couple of ideas and are beginning to work on it. We hope to come up with something soon.

[Bioc-devel] request: high-level seqlevel utilities

We've found that analysts often need to restrict seqlevels to certain pre-defined sets of chromsomes. Given the variability across organisms, it would be nice to have an abstraction. We often see this in code: keepSeqlevels(seqinfo, as.character(1:22) keepSeqlevels(seqinfo, c(1:22, X, Y))

Re: [Bioc-devel] request: timings

On Sat, Mar 16, 2013 at 9:21 PM, Kasper Daniel Hansen kasperdanielhan...@gmail.com wrote: Is it possible to get _R_CHECK_TIMINGS_=0 set in the build system when R CMD check is being run? Not super important, but convenient and it should be easy to add. Done. This will be effective in

[Bioc-devel] request: timings

Is it possible to get _R_CHECK_TIMINGS_=0 set in the build system when R CMD check is being run? Not super important, but convenient and it should be easy to add. Kasper ___ Bioc-devel@r-project.org mailing list

Re: [Bioc-devel] Request to add 'normalize' to BiocGenerics

Hi Laurent, Robert, and others, On 02/20/2013 01:33 PM, Laurent Gautier wrote: On 2013-02-20 22:02, Hervé Pagès wrote: Hi Robert, Nice to hear from you! I'm just a little bit worried that if we put normalize() in BiocGenerics without at the same time have a take it or leave it policy, then

Re: [Bioc-devel] Request to add 'normalize' to BiocGenerics

Hi Herve I have absolutely no objections against 'normalize' in BiocGenerics, I think it is a good idea. However, the concept of a 'universal namespace' and that no package can mask symbols defined in other packages I find objectionable. There is no 'redefining' of functions as you suggest

Re: [Bioc-devel] Request to add 'normalize' to BiocGenerics

Is this not just an indication that normalize is now a poor choice of a function name? LEo On 20 Feb 2013, at 16:14, Wolfgang Huber wrote: Hi is it clear that all these different functions (methods) share similar semantics and enough (conceptually) of their interface? Wouldn't the

Re: [Bioc-devel] Request to add 'normalize' to BiocGenerics

Dear all, Looking at the alphabetical list of functions/methods in BioGenerics I have the feeling that all functions are really generic, i.e. general, with the exception of function 'annotation' which in my opinion should be part of BioBase as method for one or more of the BioBase classes.

Re: [Bioc-devel] Request to add 'normalize' to BiocGenerics

Hi Robert, Nice to hear from you! I'm just a little bit worried that if we put normalize() in BiocGenerics without at the same time have a take it or leave it policy, then most of the authors of the 10 packages are likely going to ignore that there is now a new normalize() in BiocGenerics. They

Re: [Bioc-devel] Request to add 'normalize' to BiocGenerics

On 02/20/2013 01:02 PM, Hervé Pagès wrote: ... Furthermore, the good citizens that modify their package to use the normalize() in BiocGenerics will be in a situation worth than before because, from an end user point of view, their normalize() function (which is now a method attached to

Re: [Bioc-devel] Request to add 'normalize' to BiocGenerics

On 2013-02-20 22:02, Hervé Pagès wrote: Hi Robert, Nice to hear from you! I'm just a little bit worried that if we put normalize() in BiocGenerics without at the same time have a take it or leave it policy, then most of the authors of the 10 packages are likely going to ignore that there is

Re: [Bioc-devel] Request to add 'normalize' to BiocGenerics

Hi Laurent, and maintainers of packages with a normalize() function, On 02/15/2013 04:28 AM, Laurent Gatto wrote: A quick (and incomplete) manual search using http://search.bioconductor.jp/ suggest the following usage of normalize: As a function: xps::normalize codelink::normalize

Re: [Bioc-devel] Request to add 'normalize' to BiocGenerics

Hi, I have no objection and I am willing to support this generic in the package codelink. I agree that it is better to wait for the next release cycle so that we maintainers have enough time to make the changes. Thank you, Diego On Wed, Feb 20, 2013 at 7:44 AM, Hervé Pagès hpa...@fhcrc.org