[Bioc-devel] Reducing number of dependencies

Dear Bioc gurus, I am trying to reduce the number of dependencies in my package. One of the suggestions is: Importing from so many packages makes the package vulnerable to any of > them becoming unavailable. Move as many as possible to Suggests and > use conditionally. In a script I woul

Re: [Bioc-devel] Best practice use pkgdown, docker with Bioconductor

Hi there, What about including the "_pkgdown.yml" file in the ".Rbuildignore" file? Would this somehow help "avoiding any issues with these external configurations and Bioconductor"? Thanks David On Tue, Apr 6, 2021 at 5:05 AM Andris Jankevics wrote: > Haven't used this, but I think you could

Re: [Bioc-devel] Unable to install bioconductor package in bioconductor docker

> but I didn't explore the answers there... > > Hope that helps; for what it's worth, the relevant part of the error > message you post is I think > > g++: fatal error: Killed signal terminated program cc1plus > compilation terminated. > > Martin > > On 1/17

[Bioc-devel] Unable to install bioconductor package in bioconductor docker

Dear bio I am trying to install the bioconductor package "mzR" in the following bioconductor docker containers without success: bioconductor/bioconductor_docker:RELEASE_3_12 bioconductor/bioconductor_docker:RELEASE_3_11 bioconductor/bioconductor_docker:devel (and also tried, tidyverse:3.6.1) Nit

Re: [Bioc-devel] Fwd: BioC 3.12 coming soon, package a4 and a4Base need your attention!

cies, which is a lot and means that > changes in any of those could break your package -- it sounds like a quite > fragile situation. > > Martin > > > > On 10/22/20, 2:13 AM, "Bioc-devel on behalf of David Jimenez-Morales" < > bioc-devel-boun...@r-

Re: [Bioc-devel] Fwd: BioC 3.12 coming soon, package a4 and a4Base need your attention!

Dear bioc team, I am getting the following warning that I do not understand and cannot reproduce locally (and my search online didn't help): * checking whether package ‘artMS’ can be installed ... WARNING Found the following signific

Re: [Bioc-devel] Error when pushing to RELEASE_3_11

Ok, I tried one more thing: I disabled the two-factor authentication and then I could push successfully. Now, the question is... How is this possible? Thanks, David On Thu, May 21, 2020 at 10:54 AM David Jimenez-Morales wrote: > Correct, git push upstream RELEASE_3_11 worked this t

Re: [Bioc-devel] Error when pushing to RELEASE_3_11

log in github again, and the user and password worked perfectly. So I am not sure why this is failing now. Any suggestions? THANKS! David On Thu, May 21, 2020 at 10:40 AM Nitesh Turaga wrote: > Hi, > > Just try again, you shouldn’t see this issue. > > Nitesh > > On Ma

[Bioc-devel] Error when pushing to RELEASE_3_11

Hello everybody, I am getting the following error when pushing upstream to the RELEASE branch: --> git push upstream RELEASE_3_11 Enumerating objects: 23, done. Counting objects: 100% (23/23), done. Delta compression using up to 8 threads Compressing objects: 100% (12/12), done. Writing objects:

Re: [Bioc-devel] Bioconductor 3.11 is Released!

Congratulations to the entire Bioconductor team for another successful release! I have one question. I cannot find the package artMS in the News . Is there anything wrong with the art

Re: [Bioc-devel] Latest commit didn't update package

Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > > > From: David Jimenez-Morales > Sen

Re: [Bioc-devel] Latest commit didn't update package

ffalo, New York 14263 > ------ > *From:* Bioc-devel on behalf of David > Jimenez-Morales > *Sent:* Monday, February 10, 2020 10:17 AM > *To:* bioc-devel > *Subject:* [Bioc-devel] Latest commit didn't update package > > Dear all, > > the latest

[Bioc-devel] Latest commit didn't update package

Dear all, the latest commit of the artMS package didn't update the package on release (it should be now 1.4.3). However, it worked on development (now version 1.5.3). I checked the git log and many other packages with commits after mine went through. >From the log: artMS https://bioconductor.or

[Bioc-devel] How to suppress startup messages

Hi there, Loading the bioconductor package artMS gets the following startup message: library(artMS) Package PerformanceAnalytics (1.5.2) loaded. Copyright (c) 2004-2018 Peter Carl and Brian G. Peterson, GPL-2 | GPL-3https://github.com/braverock/PerformanceAnalytics I know that the user has the o

Re: [Bioc-devel] Several vignettes with links between them

EE/inst/doc/basic.html > > > Best, > Kevin > > On Wed, Nov 14, 2018 at 6:13 AM David Jimenez-Morales < > biodavi...@gmail.com> wrote: > >> Dear all, >> >> I am working on creating several vignettes for my recently released >> package >> (artM

[Bioc-devel] Several vignettes with links between them

Dear all, I am working on creating several vignettes for my recently released package (artMS), instead of having only a long one (as suggested by the bioc reviewer). Two questions: - Is there a way to link vignettes between themselves? For example, if I have 3 new vignettes, let’s say vign