New test failures with R 3.6

[jimhester]

It looks like there are a number of tests failures exposed by R 3.6, we should get these fixed.

[dschlaep]

#377 is likely one of them (it has R-devel in the title, but that version is by now R v3.6)

[russHyde]

Had a look at this under R 3.6.1 (with current lintr master, xml2=1.2.2, rcpp=1.0.2, libxml=2.9.9)

Here master is b5dff71

# In lintr dir on branch matching master
Rscript -e "devtools::load_all(); testthat::test_dir('tests/testthat', reporter = 'summary')" > test_failures.txt

The first 10 failing tests were in these files:

absolute_path_linter: ...................................................
assignment_linter: ....1
clear_cache: ...
load_cache: ...
save_cache: ...........
cache_file: ..
retrieve_file: ..
cache_lint: ..
retrieve_lint: ........
has_lint: ...
find_new_line: .........
lint with cache: ............
checkstyle_output: .
closed_curly_linter: ............
commas_linter: ..............
commented_code_linter: ............2
comments: ...
defaults: ...........................
deprecated: ..........
equals_na_linter: ...3
error: ....
parse_exclusions: .......
normalize_exclusions: ................
exclude: 4
expect_lint: .5..67
extraction_operator_linter: .......................
function_left_parentheses_linter: .......................
get_source_expression: ...............
implicit_integer_linter: .......................
infix_spaces_linter: ...........8
knitr_formats: 9abcde...

Here's an example failure:

── 1. Error: returns the correct linting (@test-assignment_linter.R#12)  ───────
Opening and ending tag mismatch: expr line 8 and equal_assign [76]
1: expect_lint("blah=1", rex("Use <-, not =, for assignment."), assignment_linter) at tests/testthat/test-assignment_linter.R:12
2: lint(file, ...) at /home/ah327h/progs/pull_requests/lintr/R/expect_lint.R:45
3: get_source_expressions(filename) at /home/ah327h/progs/pull_requests/lintr/R/lint.R:36
4: lapply(top_level_expressions(parsed_content), function(loc) {
       line_nums <- parsed_content$line1[loc]:parsed_content$line2[loc]
       expr_lines <- source_file$lines[line_nums]
       names(expr_lines) <- line_nums
       content <- get_content(expr_lines, parsed_content[loc, ])
       id <- as.character(parsed_content$id[loc])
       edges <- component_edges(tree, id)
       pc <- parsed_content[c(loc, edges), ]
       list(filename = filename, line = parsed_content[loc, "line1"], column = parsed_content[loc, 
           "col1"], lines = expr_lines, parsed_content = pc, xml_parsed_content = xml2::read_xml(xmlparsedata::xml_parse_data(pc)), 
           content = content, find_line = find_line_fun(content), find_column = find_column_fun(content))
   }) at /home/ah327h/progs/pull_requests/lintr/R/get_source_expressions.R:83
5: FUN(X[[i]], ...)
6: xml2::read_xml(xmlparsedata::xml_parse_data(pc)) at /home/ah327h/progs/pull_requests/lintr/R/get_source_expressions.R:92
7: read_xml.character(xmlparsedata::xml_parse_data(pc))
8: read_xml.raw(charToRaw(enc2utf8(x)), "UTF-8", ..., as_html = as_html, options = options)
9: doc_parse_raw(x, encoding = encoding, base_url = base_url, as_html = as_html, options = options)

All the other test-failures that came up in those first 10 tests died with the same lines:

6: xml2::read_xml(xmlparsedata::xml_parse_data(pc)) at /home/ah327h/progs/pull_requests/lintr/R/get_source_expressions.R:92
7: read_xml.character(xmlparsedata::xml_parse_data(pc))
8: read_xml.raw(charToRaw(enc2utf8(x)), "UTF-8", ..., as_html = as_html, options = options)
9: doc_parse_raw(x, encoding = encoding, base_url = base_url, as_html = as_html, options = options)

So. In my R 3.6.1 env I tried running the same tests after downgrading xml2 and Rcpp to match the versions I had in an R 3.5.1 env where all the lintr tests pass (Rcpp=1.0.1, xml2=1.2.0; the R 3.5.1 env also has libxml2=2.9.9, so matches my R 3.6.1 env for that at least). The same test failures were thrown.

Will investigate further

[russHyde]

My debugging example looks like this:

expect_lint("blah=1", rex("Use <-, not =, for assignment."), assignment_linter)
Error in doc_parse_raw(x, encoding = encoding, base_url = base_url, as_html = as_html,  : 
  Opening and ending tag mismatch: expr line 8 and equal_assign [76]

This throws the doc_parse_raw error above

xml2:::read_xml.character calls xml2:::read_xml.raw calls xml2:::doc_parse_raw

With this example, and debug(xml2:::read_xml.character):

> debug(xml2:::read_xml.character)
> expect_lint("blah=1", rex("Use <-, not =, for assignment."), assignment_linter)
debugging in: read_xml.character(my_xml)
debug: {
    if (length(x) == 0) {
        stop("Document is empty", call. = FALSE)
    }
    options <- parse_options(options, xml_parse_options())
    if (grepl("<|>", x)) {
        read_xml.raw(charToRaw(enc2utf8(x)), "UTF-8", ..., as_html = as_html, 
            options = options)
    }
    else {
        con <- path_to_connection(x)
        if (inherits(con, "connection")) {
            read_xml.connection(con, encoding = encoding, ..., 
                as_html = as_html, base_url = x, options = options)
        }
        else {
            doc <- doc_parse_file(con, encoding = encoding, as_html = as_html, 
                options = options)
            xml_document(doc)
        }
    }
}
Browse[2]> ls()
[1] "as_html"  "encoding" "options"  "x"
Browse[2]> cat(x, file = "")
<?xml version="1.0" encoding="UTF-8"standalone="yes" ?>
<exprlist>
<equal_assign line1="1" col1="1" line2="1" col2="6" start="8" end="13">
<expr line1="1" col1="1" line2="1" col2="4" start="8" end="11">
<SYMBOL line1="1" col1="1" line2="1" col2="4" start="8" end="11">blah</SYMBOL>
</expr>
<EQ_ASSIGN line1="1" col1="5" line2="1" col2="5" start="12" end="12">=</EQ_ASSIGN>
<expr line1="1" col1="6" line2="1" col2="6" start="13" end="13">
<NUM_CONST line1="1" col1="6" line2="1" col2="6" start="13" end="13">1</NUM_CONST>
</equal_assign>
</expr>
</exprlist>

So for some reason, the xml corresponding to the lint-example looks like

<equal_assign   ...> <expr[1] ...> ... </expr[1]> ... <expr[2] ...> ... </equal_assign> </expr[2]>

[russHyde]

In the R=3.6.1 env that I'm using I have xmlparsedata=1.0.2 (the same as in my R 3.5.1 env).

I suspect there's a problem with how xmlparsedata::xml_parse_data is converting data frames into xml trees (though I don't know why it's a R 3.6 specific thing)

[jimhester]

The R parser changed in regards to = and <- assignment in R 3.6 in the tokens it returns for = expressions, so that is the likely reason for the change.

[russHyde]

Thanks, I hadn't heard about that; I wonder why that would lead to the xml tree getting borked either side of the equal_assign in the above though. Will experiment further in xmlparsedata

[russHyde]

FYI I've ran all these tests using an updated xmlparsedata (following changes r-lib/xmlparsedata#6 to deal with the new equal_assign token in R-3.6's getParseData()) and using the current lintr master and they all pass locally in R-3.6.

[jimhester]

Great! @russHyde could you add Remotes: r-lib/xmlparsedata to the DESCRIPTION file, so we can use this version on the CI servers?

[russHyde]

No problem. Would that ensure that the updated version of xmlparsedata would be used whenever people use the github-version of lintr to test their packages on CI?