[Bioc-devel] issue to open a file from UCSC

Hi, I have an error in the package compilation because of issues accessing a file from UCSC. Are you aware of such type of issue? What do I need to do? Quitting from lines 337-345 [cometwebPlot] (coMET.Rnw) Error: processing vignette 'coMET.Rnw' failed with diagnostics: error in evaluating the

Re: [Bioc-devel] Failed to obtain 'hguid' cookie

Center for Science and Medicine 1470 Madison Ave, 6th Floor New York, NY 10029 tel: 1- 212-824-9253 Email: tiphaine.mar...@mssm.edu<mailto:tiphaine.mar...@mssm.edu> From: Herv� Pag�s Sent: Friday, October 20, 2023 12:18 PM To: Martin, Tiphaine ; bioc-d

[Bioc-devel] Failed to obtain 'hguid' cookie

Hi, I have my package that failed to build its vignette because of failing to obtain 'hguid' cookie. Could you please tell me how I can solve this? thanks, Tiphaine Tiphaine Martin Assistant Professor Department of Oncological

[Bioc-devel] FW: coMET problems reported in the Multiple platform build/check report for BioC 3.13

Hi, I have a question. I receive an error message for my COMET package, but when I click on the link. I do not find the error. Could you advise me what I need to do ? Thanks Tiphaine -Original Message- From: bbs-nore...@bioconductor.org Sent: Friday, June 25, 2021 3:15 PM To: Martin

Re: [Bioc-devel] Last day to make commit before the RELEASE_3_13

for Science and Medicine 1470 Madison Ave, 6th Floor New York, NY 10029 tel: 1- 212-824-9253 Email: tiphaine.mar...@mssm.edu<mailto:tiphaine.mar...@mssm.edu> From: Kern, Lori Sent: Tuesday, May 18, 2021 10:44 AM To: Martin, Tiphaine ; bioc-devel@r-project.org S

Re: [Bioc-devel] Last day to make commit before the RELEASE_3_13

Hi, I submitted my update of my package to master Sunday (1.23.1). I did not see a new update in build/check report (http://bioconductor.org/checkResults/devel/bioc-LATEST/coMET/) Did I miss something when I submit it? Thanks, Tiphaine -Original Message- From: Bioc-devel On Behalf Of

Re: [Bioc-devel] issue with ssh public key

Hi, This was my previous email. Please could you put my new email tiphaine.mar...@mssm.edu<mailto:tiphaine.mar...@mssm.edu> Could you remind me how I can change later if need it. Thanks, Tiphaine From: Nitesh Turaga Sent: Monday, May 3, 2021 9:07 AM To: Martin, Tiphaine ; bioc-d

[Bioc-devel] issue with ssh public key

Hi, I try to submit update of my package comet I do not remember about my ssh public key I have this error message and I request it tiphaine.mar...@mssm.edu is not associated with a maintainer of a Bioconductor package. Could you help me please? Thanks, Tiphaine

Re: [Bioc-devel] failling to build vignette

and Medicine 1470 Madison Ave, 6th Floor New York, NY 10029 tel: 1- 212-824-8403 Email: tiphaine.mar...@mssm.edu From: Shepherd, Lori Sent: Monday, December 17, 2018 2:41:59 PM To: Martin, Tiphaine; bioc-devel@r-project.org Subject: Re: failling to build vignette

[Bioc-devel] failling to build vignette

Hi, I need to advise to build my vignette. It seems that my vignette could not build under Bioconductor 3.9. I try to find where it fails, but I don't find the bug. I updated my vignette last February to work with new version of BiocStyle and it did well for Bioconductor 3.8, but it seems

Re: [Bioc-devel] incompatibility between logo for build et the version and success of compilation

Great, thanks Lori. From: Shepherd, Lori <lori.sheph...@roswellpark.org> Sent: 18 April 2018 17:46:24 To: Martin, Tiphaine; bioc-devel@r-project.org Subject: Re: incompatibility between logo for build et the version and success of compilation This page

[Bioc-devel] incompatibility between logo for build et the version and success of compilation

Hi, I updated the dev version of my package, http://bioconductor.org/packages/3.7/bioc/html/coMET.html if I am looking the webpage, it seems that my build fails and I can install only the version 11.3. however, if i am looking at the different compilations, everything is ok for the version

Re: [Bioc-devel] Questions about tokay2 and import 'grDevices::windows' versus 'IRanges::windows'

thanks, I am going to do that. Best, Tiphaine From: Martin Morgan <martin.mor...@roswellpark.org> Sent: 01 March 2018 20:56:10 To: Martin, Tiphaine; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Questions about tokay2 and import 'grDevices::w

[Bioc-devel] Questions about tokay2 and import 'grDevices::windows' versus 'IRanges::windows'

hi, I have a warning under windows (tokay2) for my devel version of my package (coMET). I am not sure how to answer it: * checking whether package 'coMET' can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import 'grDevices::windows' by

[Bioc-devel] Update in BioMart/ENSEMBL alters coMET

Hi, Could you inform me which modification you did in biomaRt ? or in ENSEMBL ? Indeed, I have my R package (coMET) use biomaRt to access to data. From the last update in BiomaRt (12/14/2017), I have a new error message. Do you change the name of database associated with ENSEMBL ? This is

[Bioc-devel] Push to both Bioconductor and GitHub for coMET package

Hi, I tried to push my update to GitHub and Bioconductor. I succeed to create my fork in my GitHub Id following this page (Pull upstream changes). I then updated and pushed on GitHub my update, but I cannot for bioconductor when I follow recommandation on this page (Sync an existing GitHub

[Bioc-devel] FW: Push to both Bioconductor and GitHub for coMET package

Hi, I tried to push my update to GitHub and Bioconductor. I succeed to create my fork in my GitHub Id following this page (Pull upstream changes). I then updated and pushed on GitHub my update, but I cannot for bioconductor when I follow recommandation on this page (Sync an existing GitHub

[Bioc-devel] Push to both Bioconductor and GitHub for coMET package

Hi, I tried to push my update to GitHub and Bioconductor. I succeed to create my fork in my GitHub Id following this page (http://bioconductor.org/developers/how-to/git/pull-upstream-changes/). I then updated and pushed on GitHub my update, but I cannot for bioconductor when I follow

[Bioc-devel] Cannot update the release in svn

Hi, I cleaned my gitHub repository to have now the repository coMET in my gitHub as the fork of coMET from bioconductor. I followed the directive from http://bioconductor.org/developers/how-to/git-mirrors/ as I need to correct bug in the current release but when I try to run 1. git svn

Re: [Bioc-devel] BioC 3.1 branch created

? * I had a GitHub repository bridged to the 3.0 release branch. Is it ok to use the same GitHub repository, and use SVN wins during the bridge creation? That should update GitHub with the new release code, right? Many thanks, Kevin On 17 April 2015 at 11:43, Martin, Tiphaine tiphaine.mar

Re: [Bioc-devel] BioC 3.1 branch created

Hi Dan, When I try to access on my package, I have ³Internal Server Error². Maybe I make a mistake somewhere. https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/ coMET https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/coMET Regards, Tiphaine On 17/04/2015

Re: [Bioc-devel] Warning message: multiple methods tables found for ‘score’

I will commit my fix to coMET and cross fingers that the error doesn't appear in the build system Tiphaine From: Hervé Pagès hpa...@fredhutch.org Sent: 10 April 2015 20:30 To: Michael Lawrence; Martin, Tiphaine Cc: bioc-devel Subject: Re: [Bioc-devel

[Bioc-devel] New package: coMET

only for human genome). It is possible also to extract the correlations between omic features with their pvalues. Please let me know of any issues you encounter. Thanks, Tiphaine Martin Tiphaine Martin I PhD Student I TwinsUK Department of Twin Research, Kings College London, St

Re: [Bioc-devel] Bioconductor 3.1 release schedule now available

-to/version-numbering/ Dan Best, Kasper On Mon, Mar 16, 2015 at 9:29 PM, Martin, Tiphaine tiphaine.mar...@kcl.ac.uk wrote: Dear Dan, I have 2 naive questions. I would like to know whether we (developers of a R package currently only in the development version of Bioconductor

Re: [Bioc-devel] Bioconductor 3.1 release schedule now available

Dear Dan, I have 2 naive questions. I would like to know whether we (developers of a R package currently only in the development version of Bioconductor) need to say that we would like to have our packages accessible in the next version of Bioconductor or it is automatic for any packages

[Bioc-devel] Change of schema of ENSEMBL biomart

Hi Everybody, Yesterday, I observed that ENSEMBL changed a little their schema of the dataset hsapiens_gene_ensembl. In my case, some of my functions were impacted by the change from external_gene_id to external_gene_name. Maybe there are other change in this dataset or other datasets.

Re: [Bioc-devel] runnable examples for internal function ?

Yep you guess well about my colleagues :) sorry. Thank you for your advices. Tiphaine From: Hervé Pagès hpa...@fhcrc.org Sent: 16 October 2014 19:43 To: Martin, Tiphaine; Michael Lawrence; Dan Tenenbaum Cc: bioc-devel@r-project.org Subject: Re: [Bioc

[Bioc-devel] runnable examples for internal function ?

Hi, I would like to know if I need to add a runnable example for each function that has keyword either internal or not. I ask that because with BiocCheck, version 1.0.2, I had a message for function with keyword internal such as Checking exported objects have runnable examples... *

[Bioc-devel] Non-ASCII in datase from Biomart EMBL via Gviz package

Hi, I need to create dataset BiomartGeneRegionTrack via Gviz package to run examples in my packages. But when I run R CMD check coMET, i have warning message for the checking : checking data for non-ASCII characters ... WARNING Warning: found non-ASCII strings '[alpha cell,acidophil