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fix CRAN NOTE about files in temp directory #349

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Aug 21, 2021
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fix CRAN NOTE about files in temp directory #349

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3 changes: 2 additions & 1 deletion .ci/r_tests_windows.ps1
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ $env:_R_CHECK_EXAMPLE_TIMING_THRESHOLD_ = 30
# see: https://stackoverflow.com/a/63837547/8302386
$env:_R_CHECK_SYSTEM_CLOCK_ = 0

$R_VER = "4.1.0"
$R_VER = "4.1.1"
$ProgressPreference = "SilentlyContinue" # progress bar bug extremely slows down download speed
Invoke-WebRequest -Uri https://cloud.r-project.org/bin/windows/base/old/$R_VER/R-$R_VER-win.exe -OutFile R-win.exe -MaximumRetryCount 5
Start-Process -FilePath R-win.exe -NoNewWindow -Wait -ArgumentList "/VERYSILENT /DIR=$env:R_LIB_PATH\R /COMPONENTS=main,x64" ; Check-Output $?
Expand All @@ -50,6 +50,7 @@ Invoke-WebRequest -Uri https://sourceforge.net/projects/qpdf/files/qpdf/10.3.1/q
Copy-Item .\qpdf -Destination $env:R_LIB_PATH -Recurse

initexmf --set-config-value [MPM]AutoInstall=1
$env:MIKTEX_EXCEPTION_PATH = "$env:TEMP\miktex"
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This is to avoid the following new CRAN NOTE on Windows:

* checking for detritus in the temp directory ... NOTE
Found the following files/directories:
  'lastMiKTeXException'

Env variable was found in sources of MikTeX:
https://github.com/MiKTeX/miktex/blob/ab8ebca7c70fe8c9a1392dfb2393a0a7683e14cc/Libraries/MiKTeX/Core/Exceptions.cpp#L155-L183
https://github.com/MiKTeX/miktex/blob/ab8ebca7c70fe8c9a1392dfb2393a0a7683e14cc/Libraries/MiKTeX/Core/include/miktex/Core/Environment.h#L37

We cannot remove MikTeX temp files during running testthat because PDF generation happens later in CRAN checks after tests have been finished.
Ideally, this path should be controlled via TempDir config value, but it doesn't.
https://mirror.truenetwork.ru/CTAN/systems/win32/miktex/doc/miktex.pdf

initexmf --set-config-value [Core]TempDir="$env:TEMP\miktex"


cd "$env:GITHUB_WORKSPACE\R-package"
Add-Content .Renviron "R_LIBS=$env:R_LIB_PATH"
Expand Down
7 changes: 7 additions & 0 deletions R-package/tests/testthat/setup.R
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Expand Up @@ -41,3 +41,10 @@ y_MULTIclass = sample(1:5, 100, replace = TRUE)

set.seed(6)
W = runif(100)

# Temporary I/O structures

# default directory where the temporary 'rgf' files are saved
#------------------------------------------------------------

default_dir = file.path(dirname(tempdir()), 'rgf')
4 changes: 4 additions & 0 deletions R-package/tests/testthat/teardown.R
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@@ -0,0 +1,4 @@
context("teardown")

# remove temporary 'rgf' files
if (dir.exists(default_dir)) unlink(default_dir, recursive = TRUE, force = TRUE)
11 changes: 0 additions & 11 deletions R-package/tests/testthat/test-RGF_package.R
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Expand Up @@ -466,11 +466,6 @@ testthat::test_that("the 'cleanup' method (ESTIMATOR specific) works as expected
skip_test_if_no_python()
skip_test_if_no_module("rgf.sklearn")

#--------------------------------------------------------------------------------
# default directory where the temporary 'rgf' files are saved

default_dir = file.path(dirname(tempdir()), 'rgf')

#--------------------------------------------------------------------------------
# RGF

Expand Down Expand Up @@ -515,11 +510,6 @@ testthat::test_that("the 'cleanup' method (APPLIES TO ALL ESTIMATORS) works as e
skip_test_if_no_python()
skip_test_if_no_module("rgf.sklearn")

#--------------------------------------------------------------------------------
# default directory where the temporary 'rgf' files are saved

default_dir = file.path(dirname(tempdir()), 'rgf')

#--------------------------------------------------------------------------------
# RGF

Expand Down Expand Up @@ -549,4 +539,3 @@ testthat::test_that("the 'cleanup' method (APPLIES TO ALL ESTIMATORS) works as e
testthat::expect_true( init_exists_upd_rgf && (init_num_files_rgf > 0) && (init_num_files_fastrgf > init_num_files_rgf) &&
( init_num_files_rgf > length(lst_files_tmp) && init_num_files_fastrgf > length(lst_files_tmp_end_state) ) ) # normally, both initial and end state must have the same length [ length(lst_files_tmp) == length(lst_files_tmp_end_state) ]
})