Package ‘XML’ is not available when running with R version 3.6.3

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1

Hi, I’m trying to get Travis setup for my R package. I’m new with Travis might be something very simple! My .travis.yml is very basic:

language: R
r: oldrel
cache: packages

Am trying to get it working with the old release of R (3.6.3) but the latest version of the XML package (which is a dependency) needs R>4.0. As a result I get the following error:

*     DONE (sctransform)
Installing 105 packages: xfun, rlang, base64enc, digest, stringi, magrittr, glue, markdown, highr, stringr, tinytex, mime, jsonlite, evaluate, htmltools, yaml, knitr, rmarkdown, gtable, Rcpp, plyr, listenv, globals, future, iterators, colorspace, utf8, assertthat, vctrs, pkgconfig, pillar, lifecycle, fansi, ellipsis, crayon, cli, tibble, rematch, ps, processx, backports, prettyunits, callr, rstudioapi, rprojroot, pkgbuild, desc, praise, pkgload, viridisLite, RColorBrewer, R6, munsell, labeling, farver, testthat, withr, scales, isoband, sys, askpass, bit, plogr, BH, memoise, bit64, openssl, generics, blob, tidyselect, purrr, httr, curl, rappdirs, DBI, RSQLite, dplyr, dbplyr, hms, S4Vectors, IRanges, Biobase, BiocGenerics, BiocManager, bookdown, RcppEigen, gridExtra, reshape2, ggplot2, future.apply, foreach, abind, progress, cellranger, BiocFileCache, AnnotationDbi, XML, BiocStyle, RNOmni, ggdendro, HGNChelper, readxl, cowplot, limma, biomaRt
Installing packages into ‘/home/travis/R/Library’
(as ‘lib’ is unspecified)
Error: (converted from warning) package ‘XML’ is not available (for R version 3.6.3)
Execution halted
The command "Rscript -e 'deps <- remotes::dev_package_deps(dependencies = NA);remotes::install_deps(dependencies = TRUE);if (!all(deps$package %in% installed.packages())) { message("missing: ", paste(setdiff(deps$package, installed.packages()), collapse=", ")); q(status = 1, save = "no")}'" failed and exited with 1 during .
Your build has been stopped.

Here is the build report

Could it be because the package which has XML as a dependency is installed from github?

Any suggestions on how to get this working would be very much welcomed!

2

You can find old version in here

3

The package you’re installing from Github doesn’t directly require XML.

Try to run package installation with verbose output by overriding the default install command with

install:
- Rscript --verbose -e 'deps <- remotes::dev_package_deps(dependencies = NA);remotes::install_deps(dependencies = TRUE);if (!all(deps$package %in% installed.packages())) { message("missing: ", paste(setdiff(deps$package, installed.packages()), collapse=", ")); q(status = 1, save = "no")}'

and see if it shows which dependency requires that high version of XML. You may need to require an earlier version of that dependency, or an earlier version of some higher-level dependency.