percent_coverage is broken or inadequately documented

[jpritikin]

Following up on #374 and my call for community help, I did a bit more research. On my local machine, I ran:

library(devtools)
devtools::install_github("jpritikin/covr")  # based on 1.2.0-520-ge344676
library(covr)
library(roxygen2)
library(withr)

options(covr.gcov = "gcov-9")

withr::with_envvar(c(MAKE="make -j4"), {
  withr::with_makevars(getOption("covr.flags"), assignment = "+=", {
    utils::install.packages(
      ".", repos = NULL, type = "source",
      INSTALL_opts = c("--example",  "--install-tests", "--with-keep.source",
                       "--with-keep.parse.data", "--no-multiarch")
    )
  })
})
roxygenize('.', roclets=c('rd'))
c1 <- covr::package_coverage(type=c("tests","examples"), quiet=TRUE, pre_clean=FALSE)
pl <- covr:::per_line(c1)
s1 <- (t(sapply(pl, function(x) c(total=length(x$coverage),
                                 possible=sum(!is.na(x$coverage)),
                                 covered=sum(!is.na(x$coverage) & x$coverage > 0)))))
s1 <- as.data.frame(s1)
s1$pending = s1$possible - s1$covered
t1 <- colSums(s1[,2:4])
t1['covered'] / t1['possible']

From this last division, I obtained 0.4412056 which is very close to a recent commit on codecov. This number looks good. However, when I do,

percent_coverage(c1, by="line")
percent_coverage(c1, by="expression")

then I get numbers that don't make sense. I get 56.75 (by line) and 57.3 (by expression). I guess I could forget about percent_coverage and just use covr:::per_line. However, this API is not exported. Please suggest how I might proceed.

Thank you

[jimhester]

Could you exhibit the issues on a simpler package? I cannot observe the issue unless I can install the package locally, and I do not have the time to deal with installation issues trying to get OpenMX installed on my machine.

[jpritikin]

How about I save the output of covr::package_coverage (c1 above) as an rda and attach it somewhere? The question is why covr:::per_line and percent_coverage process the same information differently, yes?

[jpritikin]

Can you download from here?

[jpritikin]

Please confirm that you have everything you need to debug this issue.