Re: [Bioc-devel] Possible https://code.bioconductor.org SSL certificate issue
My strong suspicion is this is because curl does not support AIA via openSSL on Linux. But browsers will use AIA (hence the reports of Firefox, etc working). Here's an old GitHub issue referencing the problem though it's not the most recent writing on the topic. https://github.com/curl/curl/issues/2793 If this is the case, the root cause is that somewhere in the cert chain is incomplete, which AIA can rescue. You could inspect the cert chain will openSSL. I'm away from a terminal or I'd give it a peek. Hope this helps, - Spencer On Wed, Mar 6, 2024, 3:00 AM Gábor Csárdi wrote: > Anyone know where to report issues with code.bioconductor.org? > > This is what I see from a vanilla Ubuntu 22.04 (and also from Fedora > 40/41, etc.): > > root@6bff5eca88b0:~# curl https://code.bioconductor.org/ > curl: (60) SSL certificate problem: unable to get local issuer certificate > More details here: https://curl.se/docs/sslcerts.html > > curl failed to verify the legitimacy of the server and therefore could not > establish a secure connection to it. To learn more about this situation and > how to fix it, please visit the web page mentioned above. > > Gabor > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] bpparam Non-deterministic Default
This GitHub issue, although lengthy, discusses some of the technical difficulties associated with pulling from the random stream. I've linked to a comment from Martin that discusses this in particular, but there's other good stuff in the rest of the issue. https://github.com/Bioconductor/BiocParallel/pull/140#issuecomment-921627153 -Spencer On Fri, Nov 26, 2021, 10:41 PM Ellis Patrick wrote: > Hi All, > > Sorry I'm not an advanced user. What is the disadvantage of pulling the > default from .Random.seed? As a non-advanced user it took me way too long > to figure out that set.seed() doesn't work. > > Thanks, > Ellis > > -Original Message- > From: Bioc-devel On Behalf Of Spencer > Nystrom > Sent: Saturday, 27 November 2021 2:15 PM > To: Dario Strbenac > Cc: bioc-devel@r-project.org > Subject: Re: [Bioc-devel] bpparam Non-deterministic Default > > I agree with Martin. I think it is worse for beginners to falsely believe > their results are deterministic when they are not. This sounds like a > problem that should be solved with documentation and maybe even examples of > setting the RNG seed manually. > > I also worry about advanced users and pollution of RNG seed global state > by having packages assign their own seed. Just sounds like a mess for > little gain. > > -Spencer > > > On Fri, Nov 26, 2021, 7:00 PM Dario Strbenac via Bioc-devel < > bioc-devel@r-project.org> wrote: > > > Hello, > > > > Might it instead made possible to set an RNGseed value by specifying > > one to bpparam but still get the automated back-end selection, so that > > it could easily be set to a particular value in an R package? > > > > -- > > Dario Strbenac > > University of Sydney > > Camperdown NSW 2050 > > Australia > > > > ___ > > Bioc-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel. > > ethz.ch > > > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] bpparam Non-deterministic Default
I agree with Martin. I think it is worse for beginners to falsely believe their results are deterministic when they are not. This sounds like a problem that should be solved with documentation and maybe even examples of setting the RNG seed manually. I also worry about advanced users and pollution of RNG seed global state by having packages assign their own seed. Just sounds like a mess for little gain. -Spencer On Fri, Nov 26, 2021, 7:00 PM Dario Strbenac via Bioc-devel < bioc-devel@r-project.org> wrote: > Hello, > > Might it instead made possible to set an RNGseed value by specifying one > to bpparam but still get the automated back-end selection, so that it could > easily be set to a particular value in an R package? > > -- > Dario Strbenac > University of Sydney > Camperdown NSW 2050 > Australia > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] External dependencies and reproducibility in all platforms
Hi Fabricio,
For another bit of practical advice (in particular, guarding against
missing dependencies on user machines), you may also find it helpful to
export a few `x_is_installed()` functions that return TRUE/FALSE if a
dependency is missing. You can use them in your functions to throw
informative errors, and they can be used in examples by wrapping the
example in an `if` block to only run if the tool is detected without
throwing the missing error. Same with vignettes, etc. These could also be
used by your users to troubleshoot detection of the tool. Ideally, like
Hervé mentioned, you have some testing on a system with your deps
installed, or you'll get a false sense of success testing on a machine with
lots of skips.
I hate to use this as a chance to plug some of my own work, but this is
rather relevant, I wrote a package on CRAN that can help with some of this
path resolution/checking that I used to solve this problem for another bioc
package. You can check out the manual here:
https://snystrom.github.io/cmdfun/ to see if it may be useful, but if you
have things solved with basilisk it's probably unneeded.
Cheers,
-Spencer
On Mon, Aug 23, 2021 at 8:52 PM Fabricio de Almeida <
fabricio_almeidasi...@hotmail.com> wrote:
> Thank you very much, Hervé. That was very helpful!
>
> Best,
>
>
> =
>
>
> Fabrício de Almeida Silva
>
> Undergraduate degree in Biological Sciences (UENF)
>
> MSc. candidate in Plant Biotechnology (PGBV/UENF - RJ/Brazil)
>
> Laboratório de Química e Função de Proteínas e Peptídeos (LQFPP/CBB/UENF -
> RJ/Brazil)
>
> Personal website: https://almeidasilvaf.github.io
>
>
> De: Hervé Pagès
> Enviado: segunda-feira, 23 de agosto de 2021 19:49
> Para: Fabricio de Almeida ;
> bioc-devel@r-project.org
> Assunto: Re: [Bioc-devel] External dependencies and reproducibility in all
> platforms
>
> On 23/08/2021 17:05, Fabricio de Almeida wrote:
> > Thank you for the suggestions, Hervé.
> >
> > Indeed, the best thing to do is to document everything. I was
> > considering using {basilisk} or {herper} to keep a conda environment for
> > functions that depend on external software, but I think they are made
> > for Python code only via reticulate.
> >
> > Is there a fast way to see all software installed in the Bioc build
> system?
>
> No, but this should not matter. What you state in SystemRequirements
> doesn't depend on what's already installed on our build machines.
> Developers are often too focused on our build system. What about the end
> user machine? Ultimately this is where your software will get installed
> and used, and we don't know what's on their machine either. So you want
> to make sure that your SystemRequirements field + INSTALL file contain
> all the information that the end users will need in order to install and
> use your package. If the process is well documented for the end user,
> then it's well documented for us when we need to take care of the build
> machines.
>
> To improve user-friendliness your code should display a useful error
> message if a system command that your code depends on (e.g. salmon) is
> not found in the PATH.
>
> Hope this helps,
>
> H.
>
> >
> >
> > Best,
> >
> > /=/
> >
> > /
> > /
> >
> > /Fabrício de Almeida Silva/
> >
> > /Undergraduate degree in Biological Sciences (UENF)/
> >
> > /MSc. candidate in Plant Biotechnology (PGBV/UENF - RJ/Brazil)/
> >
> > /Laboratório de Química e Função de Proteínas e Peptídeos
> > (LQFPP/CBB/UENF - RJ/Brazil)/
> >
> > /Personal website: /https://almeidasilvaf.github.io
> >
> >
> >
> > *De:* Hervé Pagès
> > *Enviado:* segunda-feira, 23 de agosto de 2021 18:53
> > *Para:* Fabricio de Almeida ;
> > bioc-devel@r-project.org
> > *Assunto:* Re: [Bioc-devel] External dependencies and reproducibility in
> > all platforms
> > On 23/08/2021 16:35, Fabricio de Almeida wrote:
> >> Hi, Hervé.
> >>
> >>
> >> Thank you for making this clear to me. I will try to think of an optimal
> >> solution for this. The issue here is that my package works as the
> >> pipeline itself, similarly to how ORFik works.
> >>
> >> Out of curiosity, I just checked how ORFik and KnowSeq handle this
> >> situation:
> >>
> >> * for STAR, for instance, ORFik simply comments the function that runs
> >> STAR in @examples
> >> (https://github.com/Roleren/ORFik/blob/master/R/STAR.R
> >> > >). Quite a
> >> hacky solution to avoid the overuse of \donttest{}.
> >> * KnowSeq includes a function to download all external software
> >> (
> https://github.com/CasedUgr/KnowSeq/blob/75d5d9f526f5b4ac561455a46884fe0a1860ffa0/R/sraToFastq.R
> >> <
> https://github.com/CasedUgr/KnowSeq/blob/75d5d9f526f5b4ac561455a46884fe0a1860ffa0/R/sraToFastq.R
> > <
> https://github.com/Cas
[Bioc-devel] BFG repo cleanup for package under review
Sorry to ping about this twice, but my guess is this got buried over the long weekend. I need some help getting a cleaned up repo force pushed to the bioconductor repository ( g...@git.bioconductor.org:packages/memes ). This is for a package under review here: https://github.com/Bioconductor/Contributions/issues/1997. Thanks, -Spencer [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Force push after BFG cleanup for `memes` package submission
Hi, I just cleaned up my git history using bfg for a package I have under review (`memes`: https://github.com/Bioconductor/Contributions/issues/1997). If I could get some help pushing the cleaned up repo to the spb I'd appreciate it. Thanks, -Spencer [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
