Re: [Bioc-devel] Possible https://code.bioconductor.org SSL certificate issue

curl works for me now as well. Glad it's resolved! -Robert On Wed, Mar 6, 2024 at 11:13 AM Gábor Csárdi wrote: > Yes, it started failing about then, so I am pretty sure it is related. > > Thanks, Gabor > > On Wed, 6 Mar 2024 at 16:39, Mike Smith wrote: > > > Maintainer of the

Re: [Bioc-devel] Possible https://code.bioconductor.org SSL certificate issue

That does seem weird. curl does indeed complain, but both Edge and Firefox running on my Pop!OS 22.04 have no problems with the certificate. -Robert On Wed, Mar 6, 2024 at 3:41 AM Gábor Csárdi wrote: > I can't find any Linux distro that accepts that certificate. Even > Debian testing fails

Re: [Bioc-devel] Urgent minor deployment of a release?

on figshare, and none of the reviewers expressed any issues with it. Best of luck with the manuscript and package! -Robert -- Dr. Robert M Flight, PhD Bioinformatics Analyst Senior Puller of Rabbits from Hats Research Parasite Moseley Bioinformatics Lab Resource

Re: [Bioc-devel] Fwd: philr problems reported in the Multiple platform build/check report for BioC 3.17

Hi Justin, I pulled the Bioconductor devel docker image ( https://www.bioconductor.org/help/docker/#intro), fired it up, and installed your github version of philr. And run the vignette. And I can reproduce the error: > Error in philr.data.frame(otu.table, tree = tree, ...) : > > Zero values

Re: [Bioc-devel] EXTERNAL: R: release of new version of package

Jeroen, Yes, you will have to move up that version number. However, the way to do that is to git pull upstream master This will bring in the changes that have been made to version numbers by the Bioconductor team. If you don't do the pull first, you will likely get error messages and

Re: [Bioc-devel] Cytoscape installed on bioc builders?

image instead. Your only bet for testing Cytoscape functionality I believe is what you can do locally, either on your direct machine or via a virtual machine. Hope that helps, -Robert Robert M Flight, PhD Bioinformatics Research Associate Puller of Rabbits from Hats Research Parasite Resource Center

Re: [Bioc-devel] R-CMD-check fails on ubuntu-20.04 (release)

Hi Catherine, It looks like igraph is not installed, which RCy3 depends on. This seems odd, because my own package categoryCompare depends on RCy3 and igraph, and it is building fine in the Bioconductor release and dev. I would see if you can recreate this issue locally on the Ubuntu docker

Re: [Bioc-devel] "In Bioconductor since" date wrong

Yes, the badge appears to be correct, but value in the details is incorrect. Robert On Mon, Jul 29, 2019, 12:13 PM Shepherd, Lori wrote: > Just to verify - The badge at the top is correct but the information in > the details section at the bottom is showing the incorrect "in > Bioconductor

Re: [Bioc-devel] "In Bioconductor since" date wrong

Can confirm this is affecting other package pages too. See this on my own package as well. 3.8 shows 7 years, and then 3.9 and 3.10 show < 6 months. http://bioconductor.org/packages/3.10/bioc/html/categoryCompare.html Cheers, -Robert Robert M Flight, PhD Bioinformatics Research Associ

Re: [Bioc-devel] How can I print a message on console with library("myPackage")?

Instead of putting the message in the startup, perhaps make use of the BugReports field in the package DESCRIPTION, and maybe use a GitHub issues page with a good template This way you avoid annoying your users with startup messages, for something that should be accessible in the DESCRIPTION

Re: [Bioc-devel] Updating information on Bioconductor site

If the build report shows the right version, and the page doesn't appear to be updated (make sure you are checking development page), try a hard refresh on the page to make sure browser isn't using a cached version (I think it is Ctrl+shift+F5 on chrome). Robert On Sat, Sep 15, 2018, 1:05 PM

Re: [Bioc-devel] Updating information on Bioconductor site

John, I think that is all pulled directly from the corresponding sections in the DESCRIPTION file. So you would have to modify the DESCRIPTION, version bump, and push the changes up. After the next build, the changes should propagate to the website. Note that if you only do this on the master

Re: [Bioc-devel] Replacement for CytoscapeWindowClass from devel RCy3

> setNodeShapeMapping(‘shape’, nodeShapes, mapping.type= ‘p’, default.shape= > 'ellipse') > > > Ok. Hope that helps! > - Alex > > On Mar 30, 2018, at 4:54 PM, Robert M. Flight <rfligh...@gmail.com> wrote: > > OK, I'll have to try out some of the examples and see if i

[Bioc-devel] Replacement for CytoscapeWindowClass from devel RCy3

e checked via method signatures. Thanks, -Robert Robert M Flight, PhD Bioinformatics Research Associate Puller of Rabbits from Hats Research Parasite Resource Center for Stable Isotope Resolved Metabolomics Manager, Systems Biology and Omics Integration Journal Club Markey Cancer Center CC4

Re: [Bioc-devel] not all bioc packages visible on github?

Paul, My understanding was that the Bioconductor github repos were going to die, and it was up to the maintainer where the source was, and a public source need not be available. I asked about this previously, and there was too much confusion between the official Bioconductor repos and developers

Re: [Bioc-devel] Do we have an unpacked archive for BioC, so that we can URL link to individual files ?

Right, in all this, I was forgetting the vast amount of confusion with the Bioc GitHub mirror. I apologise. Looking forward to having the web interface available. Robert On Mon, Nov 20, 2017, 17:08 Martin Morgan <martin.mor...@roswellpark.org> wrote: > On 11/20/2017 04:58 PM, Robert

Re: [Bioc-devel] Do we have an unpacked archive for BioC, so that we can URL link to individual files ?

The other thing Steffen could do is keep personal clones of those packages on GitHub, but that's probably not ideal. -Robert On Mon, Nov 20, 2017 at 4:58 PM Robert M. Flight <rfligh...@gmail.com> wrote: > So, what if there was a MetaBioconductor site and repo similar to the > Meta

Re: [Bioc-devel] Do we have an unpacked archive for BioC, so that we can URL link to individual files ?

% of work would be done for them). Just a thought. -Robert Robert M Flight, PhD Bioinformatics Research Associate Puller of Rabbits from Hats Research Parasite Resource Center for Stable Isotope Resolved Metabolomics Manager, Systems Biology and Omics Integration Journal Club Markey Cancer Center CC434

Re: [Bioc-devel] Bioconductor-mirror permanently removed August 25th

I agree with Jim. It has been very useful to have the Bioconductor GitHub mirror to examine code, and the CRAN mirror as well. A post-hook to push there would be very useful. -Robert On Wed, Sep 6, 2017 at 11:07 AM Jim Hester wrote: > This mirror could be relatively

Re: [Bioc-devel] Package not being built on Windows or Mac

> > Cheers, > H. > > > > > Dan > > > > > > - Original Message - > >> From: "James W. MacDonald" <jmac...@uw.edu> > >> To: "Robert M. Flight"

[Bioc-devel] Package not being built on Windows or Mac

that would be the case. Regards, Robert Robert M Flight, PhD Bioinformatics Research Associate Puller of Rabbits from Hats Resource Center for Stable Isotope Resolved Metabolomics Manager, Systems Biology and Omics Integration Journal Club Markey Cancer Center CC434 Roach Building University o

Re: [Bioc-devel] Package reference manuals in html

Yes, this seems like a time where using a non-standard site directory on Github is useful, or as Sean said, using a separate branch to serve the html content. -Robert On Fri, Dec 23, 2016 at 12:19 PM Sean Davis wrote: > Github allows you to set the branch for the docs

Re: [Bioc-devel] package review help

Regarding Cytoscape, at least, I know RCytoscape and categoryCompare use active Cytoscape sessions during vignette builds, but the build maintainers need to know about it. I also don't know if the review builds would have access to that. Robert On Fri, Sep 30, 2016, 9:53 PM Vincent Carey

Re: [Bioc-devel] downloads number status shields for packages

Those numbers are used to calculate the percentile download stat that is already on a given bioconductor package landing page. See http://bioconductor.org/packages/release/bioc/html/RTCGA.html I believe this was the way the Bioc admins went instead of just raw downloads. -Robert On Wed, May 4,

Re: [Bioc-devel] namespace question

In the cases of having conflicting names, is it not appropriate then to use the "package::function" form for calling a particular function? On Wed, Mar 30, 2016 at 11:14 PM Michael Lawrence wrote: > I can't find the hash function in IRanges. Are you sure it has one? >

Re: [Bioc-devel] License question for experimental data package

g/wiki/CC0) for a data package, as the data is already publicly available, you have just packaged it together into a useful set. My 2 cents. -Robert Robert M Flight, PhD Bioinformatics Research Associate Resource Center for Stable Isotope Resolved Metabolomics Manager, Systems Biology and Omics I

Re: [Bioc-devel] Bioc twitter bot is on repeat

___ > From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Robert > M. Flight [rfligh...@gmail.com] > Sent: Tuesday, November 24, 2015 6:39 PM > To: Jim Hester; Michael Love > Cc: bioc-devel@r-project.org > Subject: Re: [Bioc-devel] Bioc twitter bot is

Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors

with double commits I believe. On Fri, Jun 19, 2015 at 10:23 AM, Robert M. Flight rfligh...@gmail.com wrote: So this seems to work quite nicely. But in my own testing of committing with my categoryCompare package, there is one interesting issue of Github complaining about how many commits ahead

Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors

as we roll out this functionality. Jim On Wed, Jun 17, 2015 at 9:06 AM, Robert M. Flight rfligh...@gmail.com wrote: Why not write your own *readme.md* file for the package and put the link there? There is nothing stopping the maintainer from having a README file in the package. Although

Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors

Why not write your own *readme.md* file for the package and put the link there? There is nothing stopping the maintainer from having a README file in the package. Although it does not show up on the Bioconductor page, it shows up nicely on Github: My package:

Re: [Bioc-devel] Bioconductor Git/GitHub Mirrors

Correct link is http://bioconductor.org/developers/how-to/git-mirrors/ On Tue, Jun 16, 2015 at 3:00 PM Dan Tenenbaum dtene...@fredhutch.org wrote: Dear Bioconductors, We're pleased to announce the availability of Bioconductor Git Mirrors. These are read-only GitHub repositories (available

Re: [Bioc-devel] Gene annotation: TxDb vs ENSEMBL/NCBI inconsistency

Ludwig, If you do this search on the UCSC genome browser (which this annotation package is built from), you will see that the longest variant is what is shown

Re: [Bioc-devel] best way to transition users to new version of package

of the new package in the deprecated version. I also agree it would be important to provide a vignette providing a guide to the new functionality compared to the old. -Robert On Thu, May 28, 2015, 10:46 AM Martin Morgan mtmor...@fredhutch.org wrote: On 05/28/2015 06:32 AM, Robert M. Flight wrote

Re: [Bioc-devel] best way to transition users to new version of package

the hood, with warning that they will be deprecated in next version. I'd appreciate feedback on what the best approach would be in this case. Cheers, -Robert Robert M Flight, PhD Bioinformatics Research Associate Resource Center for Stable Isotope Resolved Metabolomics

[Bioc-devel] best way to transition users to new version of package

appreciate feedback on what the best approach would be in this case. Cheers, -Robert Robert M Flight, PhD Bioinformatics Research Associate Resource Center for Stable Isotope Resolved Metabolomics Markey Cancer Center University of Kentucky Lexington, KY Twitter: @rmflight Web: rmflight.github.io EM

Re: [Bioc-devel] Bug tracker for Bioconductor?

of a github repo, or any other bug tracker that the developer wants to use. My 2 cents. -Robert Robert M Flight, PhD Bioinformatics PostDoctoral Scholar Twitter: @rmflight https://twitter.com/rmflight Web: rmflight.github.io The most exciting phrase to hear in science, the one that heralds new

Re: [Bioc-devel] git-svn bridge: Track devel and release in different branches of same repo

so infrequently that it seems more of a pain than anything, and have been planning to implement something along the lines of what Ilari describes so that release can be updated if necessary. Cheers, -Robert Robert M Flight, PhD Bioinformatics PostDoctoral Scholar Resource Center for Stable

Re: [Bioc-devel] package download statistics

Sweet Dan, that is good to know. I realize of course you would only have stats for the Bioconductor.org server. That is still pretty useful. -Robert On Fri, Apr 19, 2013 at 1:42 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: On Fri, Apr 19, 2013 at 8:51 AM, Robert M. Flight rfligh...@gmail.com