yonicd / covrpage Goto Github PK
View Code? Open in Web Editor NEWCreate a summary readme for the testthat subdirectory to communicate with potential users
Home Page: https://yonicd.github.io/covrpage/
License: Other
Create a summary readme for the testthat subdirectory to communicate with potential users
Home Page: https://yonicd.github.io/covrpage/
License: Other
Shouldn't use_covrpage
and use_covrpage_vignette
come first?
The vignette produced by covrpage
has a typo:
"contigency" should be "contingency"
in particular https://yonicd.github.io/covrpage/reference/sinfo.html is puzzling
I see the setwd
in the on.exit
, but it's not returning to the working directory on error for some reason. In particular, when building my root/README.md
fails.
covrpage
calls Pandoc to convert between formats. However, it seems to be tied to a narrow range of versions due to the options it uses.
1.19.2.4
it fails because pandoc: Unknown extension: gfm_auto_identifiers
3.1.6
it fails because Unknown option --atx-headers.
[WARNING] Deprecated: --atx-headers. Use --markdown-headings=atx instead.
[WARNING] Deprecated: markdown_github. Use gfm instead.
This looks like it's caused by pandoc arguments changing with every version. Could it be feasible to extract the pandoc version using e.g. pandoc --version| head -1| cut -d' ' -f2
and adapting the options according to that?
๐ any idea why I get https://travis-ci.org/maelle/trying.lockedata.starters/builds/480813189#L2111 ?
It's supposed to get installed before getting used cf https://github.com/maelle/trying.lockedata.starters/blob/master/tic.R
i.e.
person(given = "Locke Data",
role = "fnd",
comment = "https://itsalocke.com")
and maybe link its pkgdown
version from covrpage
report-as-vignette + report-as-README.
"This package extends the information that is communicated with the potential user with a cover page for the tests in the form of summary tables of results from covr and testthat." make the potential user understand how to use the information.
I am not sure how to use it: would you tell users to stay away from a version with failing tests for instance?
There's also an aspect covrpage
can't simplify, I think: you might have a failing test, and a corresponding issue in the issue tracker. In the covrpage
report, one would only see the failing test, no link to that existing issue.
an easy one :-)
I updated to R-devel (4.0
) and running the following command
covrpage::covrpage(
update_badge = TRUE,
vignette = TRUE,
preview = TRUE
)
is now giving me the following error:
Error in file(con, "r") : cannot open the connection
Here is the traceback:
24: file(con, "r")
23: readLines(file.path(lib, pkg_name, "R", pkg_name))
22: add_hooks(pkg$package, tmp_lib, fix_mcexit = should_enable_parallel_mcexit_fix(pkg))
21: covr::package_coverage()
20: covrpage::coverage_skip(test_path = "../tests/testthat", test_skip = test_skip)
19: eval(expr, envir, enclos)
18: eval(expr, envir, enclos)
17: withVisible(eval(expr, envir, enclos))
16: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
error = eHandler, message = mHandler)
15: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
enclos)), warning = wHandler, error = eHandler, message = mHandler))
14: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
13: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
debug = debug, last = i == length(out), use_try = stop_on_error !=
2L, keep_warning = keep_warning, keep_message = keep_message,
output_handler = output_handler, include_timing = include_timing)
12: evaluate::evaluate(...)
11: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),
keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&
options$include) 0L else 2L, output_handler = knit_handlers(options$render,
options))
10: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),
stop_on_error = if (options$error && options$include) 0L else 2L,
output_handler = knit_handlers(options$render, options)))
9: block_exec(params)
8: call_block(x)
7: process_group.block(group)
6: process_group(group)
5: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {
setwd(wd)
cat(res, sep = "\n", file = output %n% "")
message("Quitting from lines ", paste(current_lines(i),
collapse = "-"), " (", knit_concord$get("infile"),
") ")
})
4: process_file(text, output)
3: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
2: rmarkdown::render(input = "tests/_covrpage.Rmd", output_file = "README.md",
output_dir = "tests", output_format = "github_document",
output_options = list(toc = TRUE, toc_depth = 3))
1: covrpage::covrpage(update_badge = TRUE, vignette = TRUE, preview = TRUE)
Some other details that might be helpful:
> sessioninfo::session_info(include_base = TRUE)
- Session info ----------------------------------------------------------------------
setting value
version R Under development (unstable) (2020-02-28 r77874)
os Windows 10 x64
system x86_64, mingw32
ui RStudio
language (EN)
collate English_United States.1252
ctype English_United States.1252
tz Europe/Berlin
date 2020-03-0
Recently I submitted my package and got this comment from CRAN
maintainers and so I had to add skip_on_travis()
for a lot of tests to reduce the duration of running tests on CRAN
machines.
Can't you rather provide a reduced test set of most important tests and
run less important ones only conditionally if some env var is set that
you only define on your machine?
But when I re-ran covrpage::covrpage()
, my code coverage dropped from 95%
to 80%
. Is there any way for covrpage
to also include skipped tests while computing code coverage?
the map_test and map_testthat functions are good developer utility functions to query a test file or the the testthat dir with needing to run the tests. It gives a quick full account of what is being tested in a package.
create new vignettes that explain how end users and other developers can benefit from using the package.
Pretty sure this is an issue about the Unicode handling in R (under windows). This is what the README
page looks like:
https://github.com/IndrajeetPatil/ggstatsplot/tree/master/tests
Hi @yonicd !
Thanks for this package, this does exactly what I was looking for.
I'm having trouble getting this to run on the greta dev branch - here
I get the following error as it is knitting the document when running covrpage::covrpage()
|............................ | 45%
label: unnamed-chunk-4 (with options)
List of 1
$ include: logi FALSE
Quitting from lines 64-65 (_covrpage.Rmd)
Error: Failure in `/private/var/folders/9c/k3wqmhhx4qsb3fd66n4prhlw0000gq/T/Rtmp1uZo28/R_LIBS10d117a5e4050/greta/greta-tests/testthat.Rout.fail`
In addition: Warning messages:
1: In for (filter in .globals$class_filters) classes <- filter(classes) :
closing unused connection 6 (<-localhost:11582)
2: In for (filter in .globals$class_filters) classes <- filter(classes) :
closing unused connection 5 (<-localhost:11582)
3: closing unused connection 7 (<-localhost:11582)
4: closing unused connection 6 (<-localhost:11582)
I'm fairly sure this is to do with the fact that greta is big and complex, but just wanted to flag it here in case it is
have dummy packages that can be used in examples and vignettes to show how the outputs to such outcomes should be used and interpreted.
grouping of functions in the references for pkgdown
Function | Description | Group |
---|---|---|
coverage_skip() | Run covr with failing tests | Testing Utility |
covr_log() | Log of code coverage | Postprocess |
covr_summary() | Summary outputs for covr object | Output Manipulation |
covrpage() | Render covrpage | Invoking |
covrpage_ci() | covrpage for travis | Invoking |
covrpage_log() | Log of covrpage outputs | Postprocess |
make_badge() | Create covrpage Badge | Setup |
map_test() | Map a single test file | Testing Utility |
map_testthat() | Hierarchy structure of testthat tests | Testing Utility |
%>% | Re-export magrittr pipe operators | General Utility |
sinfo() | importFrom utils sessionInfo packageVersion | General Utility |
tencrypt() | Encrypt Travis environment variables | Setup |
testthat_summary() | Summary outputs for testthat object | Output Manipulation |
use_covrpage() | Add covrpage to Travis CI for a git directory | Setup |
use_covrpage_vignette() | Create a vignette for covrpage | Setup |
If I am not mistaken, currently if any of the test fails, the existing README.md
document is not updated, right?
I am wondering if it will be possible for covrpage::covrpage()
to generate this document even when tests fail and add the count of failed tests in the failed
column of the respective table.
For example, two of my tests fail for function lm_effsize_ci
:
Quitting from lines 57-62 (_covrpage.Rmd)
Error: Failure in `C:/Users/inp099/AppData/Local/Temp/RtmpGwN3eM/R_LIBS2c5862e6c43/ggstatsplot/ggstatsplot-tests/testthat.Rout.fail`
h grouping and labeling, which is not allowed.-- 1. Failure: lm_effsize_ci works (@test_lm_effsize_ci.R#59) ----------------------------------------------------------------
df2$conf.low[2] not equal to 0.09086971.
1/1 mismatches
[1] 0.0762 - 0.0909 == -0.0147
-- 2. Failure: lm_effsize_ci works (@test_lm_effsize_ci.R#60) ----------------------------------------------------------------
df2$conf.high[2] not equal to 0.3558572.
1/1 mismatches
[1] 0.39 - 0.356 == 0.0339
== testthat results ==========================================================================================================
OK: 52 SKIPPED: 1 FAILED: 2
1. Failure: lm_effsize_ci works (@test_lm_effsize_ci.R#59)
2. Failure: lm_effsize_ci works (@test_lm_effsize_ci.R#60)
Error: testthat unit tests failed
Execution halted
But since the doucment is not updated, the table still reads like the following:
just curious
Hi,
I tried to use covrpage()
on several of my packages and it always ends up failing with the same message:
Quitting from lines 64-65 (_covrpage.Rmd)
Error in set_makevars(new, path, makevars_file, assignment = assignment) :
Multiple results for CXXFLAGS found, something is wrong.FALSE
Am I missing something or is it broken?
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For some reason, the main function is not working for me. Not sure why.
library(ggstatsplot)
covrpage::covrpage(update_badge = FALSE,
vignette = FALSE,
preview = TRUE)
#>Error in check_for_pkgs(path) :
The following packages must be installed: BayesFactor(>=0.9.12-4.2),boot(>=1.3-20),broom(>=0.5.1),broom.mixed(>=0.2.3),cowplot(>=0.9.4),crayon(>=1.3.4),dplyr(>=0.7.8),effsize(>=0.7.4),exact2x2(>=1.6.3),ggcorrplot(>=0.1.2),ggExtra(>=0.8),ggplot2(>=3.1.0),ggrepel(>=0.8.0),ggsignif(>=0.4.0),glue(>=1.3.0),groupedstats(>=0.0.5),jmv(>=0.9.6),magrittr(>=1.5),metafor(>=2.0-0),paletteer(>=0.2.0),psych(>=1.8.12),purrr(>=0.3.0),purrrlyr(>=0.0.3),rlang(>=0.3.1),scales(>=1.0.0),sjstats(>=0.17.3),tibble(>=2.0.1),tidyr(>=0.8.2)
Here is the traceback
> traceback()
3: stop(sprintf("The following packages must be installed: %s",
paste0(ret, collapse = ",")))
2: check_for_pkgs(path)
1: covrpage::covrpage(update_badge = FALSE, vignette = FALSE, preview = TRUE)
Created on 2019-02-10 by the reprex package (v0.2.1)
As you can see in the session information, I have all the needed packages installed-
devtools::session_info()
#> - Session info ----------------------------------------------------------
#> setting value
#> version R Under development (unstable) (2018-11-30 r75724)
#> os Windows 10 x64
#> system x86_64, mingw32
#> ui RTerm
#> language (EN)
#> collate English_United States.1252
#> ctype English_United States.1252
#> tz America/New_York
#> date 2019-02-10
#>
#> - Packages --------------------------------------------------------------
#> package * version date lib
#> assertthat 0.2.0 2017-04-11 [1]
#> backports 1.1.3 2018-12-14 [1]
#> BayesFactor 0.9.12-4.2 2018-05-19 [1]
#> bayesplot 1.6.0 2018-08-02 [1]
#> boot 1.3-20 2017-08-06 [2]
#> broom 0.5.1.9000 2019-01-20 [1]
#> broom.mixed 0.2.3.9000 2019-01-23 [1]
#> callr 3.1.1 2018-12-21 [1]
#> cli 1.0.1.9000 2019-01-20 [1]
#> cluster 2.0.7-1 2018-04-13 [2]
#> coda 0.19-2 2018-10-08 [1]
#> codetools 0.2-16 2018-12-24 [1]
#> coin 1.2-2 2017-11-28 [1]
#> colorspace 1.4-0 2019-01-13 [1]
#> covr 3.2.1 2018-10-18 [1]
#> covrpage 0.0.70 2019-02-11 [1]
#> cowplot 0.9.4 2019-01-08 [1]
#> crayon 1.3.4 2017-09-16 [1]
#> curl 3.3 2019-01-10 [1]
#> data.table 1.12.0 2019-01-13 [1]
#> DEoptimR 1.0-8 2016-11-19 [1]
#> desc 1.2.0 2019-01-21 [1]
#> devtools 2.0.1.9000 2019-01-29 [1]
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#> dplyr 0.8.0 2019-02-06 [1]
#> effsize 0.7.4 2018-12-21 [1]
#> emmeans 1.3.2 2019-01-22 [1]
#> estimability 1.3 2018-02-11 [1]
#> evaluate 0.12 2018-10-09 [1]
#> exact2x2 1.6.3 2018-07-27 [1]
#> exactci 1.3-3 2017-10-02 [1]
#> fit.models 0.5-14 2017-04-06 [1]
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#> foreign 0.8-71 2018-07-20 [2]
#> fs 1.2.6 2018-08-23 [1]
#> generics 0.0.2 2019-01-20 [1]
#> ggcorrplot 0.1.2.9000 2018-12-17 [1]
#> ggExtra 0.8 2019-02-10 [1]
#> ggplot2 3.1.0.9000 2019-02-06 [1]
#> ggrepel 0.8.0 2018-05-09 [1]
#> ggridges 0.5.1 2018-09-27 [1]
#> ggsignif 0.4.0 2017-08-03 [1]
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#> whisker 0.3-2 2013-04-28 [1]
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Some ideas
Have one called "Getting started"
Have an articles TOC under site/articles
Since downloading the latest commits in pkgdown
and covrpage
, I can no longer get the covrpage
vignette article to build.
This is the error-
|- Building articles ------------------------------------------------------------
Reading 'vignettes/tests_and_coverage.Rmd'
simpleError in x[["class"]]: subscript out of bounds>
Error in x[["class"]] : subscript out of bounds
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I haven't worked out yet whether it's a problem in covrpage
/pkgdown
/pandoc
so recording this here. ๐ผ
In https://yonicd.github.io/covrpage/articles/tests_and_coverage.html on Firefox "Session Info" is clickable but looks like this i.e. without the arrow on the left.
add to use_covrpage and option to build a tic.R file and a travis.yml that has tic
dependency.
If you run travis::use_tic()
the setup would then be to have the pkgdown website built on Travis and deployed to a gh-pages branch.
It'd probably mess up with the current Travis covrpage report setup, but worth exploring for #28 maybe.
If not all dependencies of a package are installed (e.g. the package hasn't been built/installed yet) then rmarkdown::render
fails. Perhaps wrap in a try
-like context or confirm that the package being checked is itself installed.
I'm not sure I'd understand what it means if I didn't know the function. I don't have a good suggestion at the moment.
I am creating the vignette tests_and_coverage.Rmd
using covrpage::use_covrpage_vignette()
. After this, when I build the vignette for the package website using pkgdown::build_article("tests_and_coverage")
, I get the following warning:
Warning in if (!is.na(existing)) { :
the condition has length > 1 and only the first element will be used
The vignette html is rendered properly by pkgdown
, so not sure why the warning
.
This issue is related to issue #3 where we were testing the skip branch: There are some differences between local testing, the continous integration report, the coverage reported by covrpage on my machine and your report.
covrpage report:
ci (travis) : no errors + no fails
local (devtools::test
): no errors + no fails + 1 skip
local (devtools::check
): no errors + no fails
The last build badge URL is broken:
https://github.com/yonicd/covrpage/tree/vignette/tests/README.md
It opened file:///C:/Users/Maelle/Documents/ropensci/codemetar/tests/README.html
whereas it should file:///C:/Users/Maelle/Documents/ropensci/codemetar/tests/README.md because the html didn't exist.
I was trying the package in another package where I still have some failing test (work in progress..). Could it be possible to generate the page even if a test failed?
I think it uses test_check
(in case of using testthat), which has the argument of stop_on_failure
set to TRUE by default. Changing stop_on_failure
to FALSE would solve the issue, but maybe there is a reason behind this.
Here's the Weekly Digest for yonicd/covrpage:
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