[Bioc-devel] extraChIPs build error on kunpeng2

[Martin Grigorov]

Hi,

On Tue, Oct 10, 2023 at 10:30 AM Stevie Pederson <
stephen.pederson.au using gmail.com> wrote:

> Hi,
>
> I've got a build error on kunpeng2 which has me a bit stuck, with the build
> report available here:
>
> https://bioconductor.org/checkResults/3.18/bioc-LATEST/extraChIPs/kunpeng2-checksrc.html


I see no ERRORs for this package on any of the build runners!


>
> I'm
> struggling to understand where it's coming from as it doesn't seem related
> to the package itself. I think the key section is this one:
>
> * checking examples ... ERROR
> Running examples in ‘extraChIPs-Ex.R’ failed
> The error occurred in:
>
> R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
> Copyright (C) 2023 The R Foundation for Statistical Computing
> Platform: aarch64-unknown-linux-gnu (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
>   Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
> > pkgname <- "extraChIPs"
> > source(file.path(R.home("share"), "R", "examples-header.R"))
> > options(warn = 1)
> > base::assign(".ExTimings", "extraChIPs-Ex.timings", pos = 'CheckExEnv')
> > base::cat("name\tuser\tsystem\telapsed\n", file=base::get(".ExTimings",
> pos = 'CheckExEnv'))
> > base::assign(".format_ptime",
> + function(x) {
> +   if(!is.na(x[4L])) x[1L] <- x[1L] + x[4L]
> +   if(!is.na(x[5L])) x[2L] <- x[2L] + x[5L]
> +   options(OutDec = '.')
> +   format(x[1L:3L], digits = 7L)
> + },
> + pos = 'CheckExEnv')
> >
> > ### * </HEADER>
>
> I also tried setting up the docker locally using the instructions here:
> https://blog.bioconductor.org/posts/2023-06-09-debug-linux-arm64-on-docker/
> .
> After adding a step to install all of my package dependencies, I can't
> reproduce the error on my local ARM64 image. However, I do get the
> following, quite different error:
>
> * checking PDF version of manual without index ... ERROR
> Re-running with no redirection of stdout/stderr.
> Hmm ... looks like a package
> Converting parsed Rd's to LaTeX ....
> Creating pdf output from LaTeX ...
> Warning in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,
>  :
>   texi2dvi script/program not available, using emulation
> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  :
>   pdflatex is not available
> Warning in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,
>  :
>   texi2dvi script/program not available, using emulation
> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  :
>   pdflatex is not available
> Error in running tools::texi2pdf()
>
> Is anyone able to shed some insights as to what may be up? The key part of
> the kunpeng2 error doesn't resemble any of my code, and I'm guessing the
> docker image doesn't have pdflatex. Maybe?
>

You can install pdflatex with: apt install texlive-latex-extra
It installs many dependencies. I guess this is the reason why it is not
pre-installed on ghcr.io/bioconductor/bioconductor:devel-r-latest



>
> Thanks in advance,
>
> Stevie
>
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