[Bioc-devel] Vignette building timing out

Tue Sep 17 17:40:14 CEST 2024

I just tried building locally and killed it after 25 minutes so it is not limited to the builders.

I knitr::purl your Rmd vignettes to pull the R code and did system.time calls
> system.time(source("Diffusion-Map-recap.R", echo=FALSE))
   user  system elapsed
195.056   0.109 195.298
There were 50 or more warnings (use warnings() to see the first 50)
> system.time(source("Diffusion-Maps.R", echo=FALSE))
   user  system elapsed
198.771   0.064 198.970
There were 50 or more warnings (use warnings() to see the first 50)
> system.time(source("Global-Sigma.R", echo=FALSE))
   user  system elapsed
  1.369   0.035   1.435
> system.time(source("tidyverse.R", echo=FALSE))
   user  system elapsed
  0.580   0.013   0.741
> system.time(source("DPT.R", echo=FALSE))
   user  system elapsed
  1.191   0.046   1.286

Gene-Relevance appears to have issues
> system.time(source("Gene-Relevance.R", echo=FALSE))
> gms[-1] %>% map(~ .$ids[1:10]) %>% purrr::reduce(intersect) %>% c .... [TRUNCATED]
Error:
! [conflicted] intersect found in 3 packages.
Either pick the one you want with `::`:
� lubridate::intersect
� GenomicRanges::intersect
� base::intersect
Or declare a preference with `conflicts_prefer()`:
� `conflicts_prefer(lubridate::intersect)`
� `conflicts_prefer(GenomicRanges::intersect)`
� `conflicts_prefer(base::intersect)`
Run `rlang::last_trace()` to see where the error occurred.
Warning messages:
1: In DiffusionMap(allen_hvg, distance = ., knn_params = list(method = "covertree")) :
  You have 5000 genes. Consider passing e.g. n_pcs = 50 to speed up computation.
2: In DiffusionMap(allen_hvg, distance = ., knn_params = list(method = "covertree")) :
  You have 5000 genes. Consider passing e.g. n_pcs = 50 to speed up computation.
3: In DiffusionMap(allen_hvg, distance = ., knn_params = list(method = "covertree")) :
  You have 5000 genes. Consider passing e.g. n_pcs = 50 to speed up computation.
4: In grid.Call.graphics(C_points, x$x, x$y, x$pch, x$size) :
  semi-transparency is not supported on this device: reported only once per page
Timing stopped at: 169 1.436 170.6

Maybe since there is a conflict of the function that it is waiting for a response that it never receives?   You could try resolving this and see if that helps.

Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Philipp Angerer <phil.angerer using gmail.com>
Sent: Sunday, September 15, 2024 11:25 AM
To: Wolfgang Huber <wolfgang.huber using embl.org>
Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Vignette building timing out

Hi Wolfgang,

Yeah, that cell is now broken, but that doesn�t influence anything but that
cell�s output.
I still have nothing to go by to possibly fix this and am dependent on the
Bioconductor staff to help debug this.

Best, Phil

Am Do., 29. Aug. 2024 um 15:59 Uhr schrieb Wolfgang Huber <
wolfgang.huber using embl.org>:

> Hi Philipp
>
> Just a quick guess, since the error message mentions timing out: at least
> one of your vignettes loads data from the internet, have you checked
> whether that could be the culprit?
> Of couse that may be confounded if the Bioconductor build server sits in a
> different part of the internet than you locally.
>
> I noted in Gene-Relevance.Rmd that the last code chunk, the httr::GET('
> https://secure-web.cisco.com/1POgRrVvWFfc5hblaWMl95j2Rg8yHSX7DGPkyvm8k-_kebz7Qat0vDsWptJ2O0EFFFb9yMmllaXPRITBIqK8p5HDCl0Kp9efFF2VuDIvyqXblzppEFs_BMLDBlwqSeXe5KFuz22i3AVeKsREpTOAONozg09_V9tj2kzUWvJlC_85vDKO9dbNkO_bjI-SONnw9lJUTyhxys0N7vHIqTR9-ZLvGDF6RtL5kqznzeWjhkIKwp3NtnUWOCqs4HrWaqEHeATPDhUDiIpGx1q8XpZsjO-k31fvvDe4luGeIc14rfao3vtuEPgUX1lgy_4sn7KwB/https%3A%2F%2Fwww.uniprot.org%2Funiprot%2F�� query, returned an empty tibble.
>
>
> Thank you and kind regards
> Wolfgang
>
> ---
> Wolfgang Huber
> EMBL
> https://secure-web.cisco.com/1ex0p-HjtKpg4aVKZjmf0iiA1ZRWBeSqcbRDfbKJUE86-zioht3bRcj3O0zpnEut6upD3ezmugs-fj7ZFzwvVSAYouglB-q3XtRszl5BJ2iMw8tCq-cwUjF_1-HijTGonddGsxFTnweoF-zZOAKksa5W0dMoacdS097AVsl8RNk3xsyiWfoNzHnET7edY9__K1u7TWBLvW0QKfZLrddoYPJZ6Wmp5XRjkMFZrOjfiJxK15BAXhC7njd4iEjNLWEg9R99NsnC5XXd2ixxtwNCOf5OZdH1GDgoQlhhANb9IlDD6NoSWd74BujaHipjkhUFh/https%3A%2F%2Fwww.huber.embl.de%2F
> ORCID 0000-0002-0474-2218
>
>
>
>
>
>
>
> > On 28. Aug 2024, at 11:44, Philipp Angerer <phil.angerer using gmail.com>
> wrote:
> >
> > Hi,
> >
> > I'm getting e-mails that the builds for my package fail:
> >
> https://secure-web.cisco.com/1TLvhuWSVVY2Lx68AwNF2b3CNbbV2SuBf1rNlFz8m1n_tg6unhK8LaBsWAC9VPTXzbsjV6a6sqlAGOqlcq2bsVZmZClAPeZvBrxfdhy-WiRALN7FjJs_wyuTBiE2cKTOjfE23kfKq-ctIAsmtps_7NY0jl0GRFvmgkZNjERAys514cm_WqMvxkJjKKDFO_-YVWmwFcwojfNLY7y1Cs4I9RmBomUuI5dtmp5NMR09_-sUWeb3zuAh3-6wYzdb2OyjtJYAGsNQKT8JFRt6CnO8WKnrNt0qq_WtAxKU89Aj-UdBnjmwPtgNCTEgpSdLUuSQV/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.19%2Fbioc-LATEST%2Fdestiny%2Fnebbiolo1-buildsrc.html
> >
> > No clue why that suddenly happens, I can't reproduce it locally.
> >
> > The bioconductor team forced me to switch away from my vignette building
> > solution using Jupyter notebooks to knitr, so I have zero experience why
> > that might be acting up.
> >
> > How can I make that go away?
> > Best, Phil
> >
> > [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel using r-project.org mailing list
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