[Bioc-devel] extraChIPs build error on kunpeng2

[Stevie Pederson]

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'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?

Thanks in advance,

Stevie

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