Hi, On Tue, Oct 10, 2023 at 10:30 AM Stevie Pederson < stephen.pederson...@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 > > [[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
