HISKP-LQCD / hadron

R package implementing analysis tools for lattice QCD
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Installation from source fails on Ubuntu 22.04 #308

Closed kostrzewa closed 2 years ago

kostrzewa commented 2 years ago

Just to warn others: Installation from source is currently not possible on Ubuntu 22.04.

R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

The issue arises when roxygen2 attempts to generate the documentation and the exports:

 $ ./document 
autoreconf: export WARNINGS=
autoreconf: Entering directory '.'
autoreconf: configure.ac: not using Gettext
autoreconf: running: aclocal --force 
autoreconf: configure.ac: tracing
autoreconf: configure.ac: not using Libtool
autoreconf: configure.ac: not using Intltool
autoreconf: configure.ac: not using Gtkdoc
autoreconf: running: /usr/bin/autoconf --force
autoreconf: configure.ac: not using Autoheader
autoreconf: configure.ac: not using Automake
autoreconf: Leaving directory '.'
ℹ Updating hadron documentation
ℹ Loading hadron
Error: invalid version specification ‘0.68’
Execution halted

Scouring various forums has not brought any enlightenment (yet), why and where this version 0.68 comes up and why this errors out.

The traceback is also not very insightful, at least not for me:

> devtools::document()
ℹ Updating hadron documentation
ℹ Loading hadron
Error: invalid version specification ‘0.68’
> traceback()
20: stop(gettextf("invalid version specification %s", paste(sQuote(unique(x[!ok])), 
        collapse = ", ")), call. = FALSE, domain = NA)
19: .make_numeric_version(x, strict, .standard_regexps()$valid_R_system_version, 
        c("R_system_version", "package_version"))
18: R_system_version(paste(x[c("major", "minor")], collapse = "."))
17: package_version(list(major = 0, minor = VTE_VERSION))
16: ansi_has_hyperlink_support()
15: cli::style_hyperlink(paste0(basename(file), ":", line), paste0("file://", 
        file), params = c(line = line, col = 1))
14: paste0("[", cli::style_hyperlink(paste0(basename(file), ":", 
        line), paste0("file://", file), params = c(line = line, col = 1)), 
        "]")
13: link_to(tag$file, tag$line)
12: paste0(link_to(tag$file, tag$line), " @", tag$tag, " ", if (is.null(tag$raw)) ("(automatically generated) "), 
        message[[1]])
11: warn_roxy_tag(x, "must be a single paragraph")
10: roxy_tag_parse.roxy_tag_title(tokens[[i]])
9: roxy_tag_parse(tokens[[i]])
8: parse_tags(tokens)
7: .f(call = .l[[1L]][[i]], srcref = .l[[2L]][[i]], tokens = .l[[3L]][[i]], 
       ...)
6: purrr::pmap(list(call = as.list(parsed)[has_tokens], srcref = refs[has_tokens], 
       tokens = tokens[has_tokens]), block_create)
5: FUN(X[[i]], ...)
4: lapply(files, tokenize_file)
3: parse_package(base_path, env = NULL)
2: roxygen2::roxygenise(pkg$path, roclets)
1: devtools::document()
urbach commented 2 years ago

Hmm, I don't have a problem with linux mint (I think latest version) and

R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"

Just to warn others: Installation from source is currently not possible on Ubuntu 22.04.

R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

The issue arises when roxygen2 attempts to generate the documentation and the exports:

 $ ./document 
autoreconf: export WARNINGS=
autoreconf: Entering directory '.'
autoreconf: configure.ac: not using Gettext
autoreconf: running: aclocal --force 
autoreconf: configure.ac: tracing
autoreconf: configure.ac: not using Libtool
autoreconf: configure.ac: not using Intltool
autoreconf: configure.ac: not using Gtkdoc
autoreconf: running: /usr/bin/autoconf --force
autoreconf: configure.ac: not using Autoheader
autoreconf: configure.ac: not using Automake
autoreconf: Leaving directory '.'
ℹ Updating hadron documentation
ℹ Loading hadron
Error: invalid version specification ‘0.68’
Execution halted

Scouring various forums has not brought any enlightenment (yet), why and where this version 0.68 comes up and why this errors out.

The traceback is also not very insightful, at least not for me:

> devtools::document()
ℹ Updating hadron documentation
ℹ Loading hadron
Error: invalid version specification ‘0.68’
> traceback()
20: stop(gettextf("invalid version specification %s", paste(sQuote(unique(x[!ok])), 
        collapse = ", ")), call. = FALSE, domain = NA)
19: .make_numeric_version(x, strict, .standard_regexps()$valid_R_system_version, 
        c("R_system_version", "package_version"))
18: R_system_version(paste(x[c("major", "minor")], collapse = "."))
17: package_version(list(major = 0, minor = VTE_VERSION))
16: ansi_has_hyperlink_support()
15: cli::style_hyperlink(paste0(basename(file), ":", line), paste0("file://", 
        file), params = c(line = line, col = 1))
14: paste0("[", cli::style_hyperlink(paste0(basename(file), ":", 
        line), paste0("file://", file), params = c(line = line, col = 1)), 
        "]")
13: link_to(tag$file, tag$line)
12: paste0(link_to(tag$file, tag$line), " @", tag$tag, " ", if (is.null(tag$raw)) ("(automatically generated) "), 
        message[[1]])
11: warn_roxy_tag(x, "must be a single paragraph")
10: roxy_tag_parse.roxy_tag_title(tokens[[i]])
9: roxy_tag_parse(tokens[[i]])
8: parse_tags(tokens)
7: .f(call = .l[[1L]][[i]], srcref = .l[[2L]][[i]], tokens = .l[[3L]][[i]], 
       ...)
6: purrr::pmap(list(call = as.list(parsed)[has_tokens], srcref = refs[has_tokens], 
       tokens = tokens[has_tokens]), block_create)
5: FUN(X[[i]], ...)
4: lapply(files, tokenize_file)
3: parse_package(base_path, env = NULL)
2: roxygen2::roxygenise(pkg$path, roclets)
1: devtools::document()

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kostrzewa commented 2 years ago

Hmm, I don't have a problem with linux mint (I think latest version) and R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"

Does this include installation from source? Things work fine with the package, but I need stuff from the tseries branch which I haven't gotten around to getting ready for merge / release yet.

urbach commented 2 years ago

Hmm, I don't have a problem with linux mint (I think latest version) and R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"

Does this include installation from source? Things work fine with the package, but I need stuff from the tseries branch which I haven't gotten around to getting ready for merge / release yet.

I just did './document' in my source version...

kostrzewa commented 2 years ago

Asked the roxygen2 authors for support: https://github.com/r-lib/roxygen2/issues/1369

kostrzewa commented 2 years ago

This is caused by https://github.com/r-lib/cli/issues/441, which has been fixed in very recent versions of r-lib/cli. As a workaround one can do devtools::install_github('r-lib/cli') to install the head commit directly from github.