Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

fix some errors in R-package after upgrade to 1.0.7 #342

Merged
merged 7 commits into from
Mar 21, 2021

Conversation

StrikerRUS
Copy link
Member

@StrikerRUS StrikerRUS commented Mar 21, 2021

  • After the recent refactoring of Python finding routine reticulate fails to find Python from conda environment.
     echo "Sys.setenv(RETICULATE_PYTHON = '$CONDA_PREFIX/bin/python')" >> .Rprofile
    
    similarly to the same command on Windows fixes this.
    Add-Content .Rprofile "Sys.setenv(RETICULATE_PYTHON = '$([RegEx]::Escape($env:CONDA_PREFIX))/python.exe')"
  • roxygen2 starting from 7.1.0 version starts to produce references to new() and clone() methods. They are broken for some reason:
    LaTeX errors found:
    ! Undefined control sequence.
    l.152 \hypertarget
                      {method-new}{}
    The control sequence at the end of the top line
    of your error message was never \def'ed. If you have
    ! Undefined control sequence.
    l.231 \hypertarget
                      {method-clone}{}
    
    Here is the corresponding PR: Fix internal R6 links in LaTeX / PDF r-lib/roxygen2#1007. As a workaround I recreated Rd files with the roxygen2 7.0.2 which doesn't generate that links. Later I believe we will be able to make some refactoring of docs and make RGF package compatible with roxygen2 7.1.x. Also I saw a lot of warnings during roxygen2::roxygenise() which is not good and indicates that we should refactor docs ideally.

Copy link
Collaborator

@mlampros mlampros left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thank you. I got the warnings for updating the documentation based on the new version of roxygen but I didn't give too much attention because it's not required for submitting successfully the package to CRAN.

@mlampros mlampros merged commit 2651369 into R-package-update-cran Mar 21, 2021
@StrikerRUS StrikerRUS deleted the dev branch March 21, 2021 12:15
StrikerRUS added a commit that referenced this pull request Mar 22, 2021
* update to CRAN version 1.0.7

* added the _R_CHECK_EXAMPLE_TIMING_THRESHOLD_ environment variable

* added the _R_CHECK_SYSTEM_CLOCK_ environment variable

* modified the r_tests.sh

* modified the r_tests.sh

* modified the r_tests.sh

* fix some errors in R-package after upgrade to 1.0.7 (#342)

* fixes

* test

* test

* fixes

* fixes

* fixes

* fixes

* fix compatibility with roxygen2 > 7.0 (#343)

* Update .ci/r_tests_windows.ps1

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* Update .ci/r_tests_windows.ps1

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* Update R-package/tests/testthat/helper-skip.R

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Development

Successfully merging this pull request may close these issues.

2 participants