"Issues detected" remains after issue is resolved

[keithnewman]

Issue description

When inteRgrate::check_all() detects an issue which is later resolved, the "Issues Detected" message will continue to be displayed on subsequent calls to check_all.

Steps to reproduce the issue

1. Start a new, empty R session.
2. Find an R package that currently passes inteRgrate::check_all()
3. Make a change that will cause the check_all tests to fail. For the example results below, I changed the NEWS.md file to have an incorrect format.
4. Run inteRgrate::check_all()
5. Revert the changes made to the code to get back to the package which previously passes inteRgrate::check_all()
6. Run inteRgrate::check_all(). Check through the results to confirm no errors other than the "Issues Detected" warning at the end.
7. Restart the R session (don't save anything in workspace)
8. Run inteRgrate::check_all()

What's the expected result?

• The "Issues Detected" message should not appear once the offending issue is resolved.

What's the actual result?

• The "Issues Detected" message continues to be displayed after the issue is fixed, until the session is restarted.

Additional details

An output that changes is under the "Creating a tag...create_tag()" section where the output from the passing version is

ℹ No tagging: doesn't seem to be a CI process

but after failing and reverting to the original method, this is stuck on

ℹ No tagging: fix checking errors

Despite no checking errors being shown.

Output from a working and passing package check:

Restarting R session...

> inteRgrate::check_all()

── inteRgrate version 1.0.22 ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

── Installing package ──

✔  checking for file ‘/tmp/RtmpMJTIaD/file8e3e5178dc1a/<package_name>/DESCRIPTION’
─  preparing ‘<package_name>’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘<package_name>_1.1.6.tar.gz’ (776ms)
   
Installing package into ‘/home/keith/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
* installing *source* package ‘<package_name>’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (<package_name>)
── R CMD build ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘.../DESCRIPTION’ ...
─  preparing ‘<package_name>’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘<package_name>_1.1.6.tar.gz’ (803ms)
   
── R CMD check ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
─  using log directory ‘/tmp/RtmpMJTIaD/file8e3e2b1b5db6/<package_name>.Rcheck’
─  using R version 4.2.0 (2022-04-22)
─  using platform: x86_64-pc-linux-gnu (64-bit)
─  using session charset: UTF-8
✔  checking for file ‘<package_name>/DESCRIPTION’ ...
─  checking extension type ... Package
─  this is package ‘<package_name>’ version ‘1.1.6’
─  package encoding: UTF-8
✔  checking package namespace information ...
✔  checking package dependencies (1.4s)
✔  checking if this is a source package ...
✔  checking if there is a namespace
✔  checking for executable files ...
✔  checking for hidden files and directories ...
✔  checking for portable file names
✔  checking for sufficient/correct file permissions
✔  checking whether package ‘<package_name>’ can be installed (808ms)
✔  checking installed package size ...
✔  checking package directory
✔  checking DESCRIPTION meta-information ...
✔  checking top-level files ...
✔  checking for left-over files
✔  checking index information
✔  checking package subdirectories ...
✔  checking R files for non-ASCII characters ...
✔  checking R files for syntax errors ...
✔  checking whether the package can be loaded ...
✔  checking whether the package can be loaded with stated dependencies ...
✔  checking whether the package can be unloaded cleanly ...
✔  checking whether the namespace can be loaded with stated dependencies ...
✔  checking whether the namespace can be unloaded cleanly ...
✔  checking loading without being on the library search path ...
✔  checking dependencies in R code ...
✔  checking S3 generic/method consistency (437ms)
✔  checking replacement functions ...
✔  checking foreign function calls ...
✔  checking R code for possible problems (571ms)
✔  checking Rd files ...
✔  checking Rd metadata ...
✔  checking Rd cross-references ...
✔  checking for missing documentation entries ...
✔  checking for code/documentation mismatches (461ms)
✔  checking Rd \usage sections (452ms)
✔  checking Rd contents ...
✔  checking for unstated dependencies in examples ...
✔  checking contents of ‘data’ directory (910ms)
✔  checking data for non-ASCII characters (949ms)
✔  checking data for ASCII and uncompressed saves ...
✔  checking examples (1.2s)
✔  checking PDF version of manual (579ms)
   
   
── Checking lint...check_lintr() 
....
✔ Lint looks good

── Checking namespace for imports()...check_namespace() 
✔ Imports look good - 0 found, 0 allowed

── Checking file extensions...check_r_filenames() 
ℹ 3 R files found
✔ Extensions look good
✔ Filenames look good

── Checking version...check_version() 
From gitlab.com:[redacted]/[redacted]/r/[redacted]-to-[redacted]
 * branch            main       -> FETCH_HEAD
   94b4bf7..417ff43  main       -> origin/main
✔ Your version is fine!

── Checking .gitignore...check_gitignore() 
✔ .gitignore looks good

── Checking tidy descriptions...check_tidy_descriptions() 
✔ Setting active project to '/home/keith/[redacted]/[redacted]-intro/r_pkgs/<package_name>'
✔ Your description is tidy!

── Checking file permissions...check_file_permissions() 
✔ File modes looks good

── Checking line breaks...check_line_breaks() 
✔ Line breaks look good

── Creating a tag...create_tag() 
ℹ No tagging: doesn't seem to be a CI process

── Checking NEWS.md...check_news() 
✔ Your NEWS.md has the correct format

── Checking Rproj...check_rproj() 
ℹ Reading <package_name>.Rproj
✔ Rproj looks good!

After modifying the NEWS file to have an incorrect header:

> inteRgrate::check_all()

── inteRgrate version 1.0.22 ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

── Installing package ──

✔  checking for file ‘/tmp/RtmpMJTIaD/file8e3e5f8a2d15/<package_name>/DESCRIPTION’ ...
─  preparing ‘<package_name>’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘<package_name>_1.1.6.tar.gz’ (830ms)
   
Installing package into ‘/home/keith/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
* installing *source* package ‘<package_name>’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (<package_name>)
── R CMD build ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘.../DESCRIPTION’ ...
─  preparing ‘<package_name>’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘<package_name>_1.1.6.tar.gz’ (826ms)
   
── R CMD check ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
─  using log directory ‘/tmp/RtmpMJTIaD/file8e3e57f67323/<package_name>.Rcheck’
─  using R version 4.2.0 (2022-04-22)
─  using platform: x86_64-pc-linux-gnu (64-bit)
─  using session charset: UTF-8
✔  checking for file ‘<package_name>/DESCRIPTION’ ...
─  checking extension type ... Package
─  this is package ‘<package_name>’ version ‘1.1.6’
─  package encoding: UTF-8
✔  checking package namespace information ...
✔  checking package dependencies (3.2s)
✔  checking if this is a source package ...
✔  checking if there is a namespace
✔  checking for executable files ...
✔  checking for hidden files and directories ...
✔  checking for portable file names
✔  checking for sufficient/correct file permissions
✔  checking whether package ‘<package_name>’ can be installed (775ms)
✔  checking installed package size ...
✔  checking package directory
✔  checking DESCRIPTION meta-information ...
✔  checking top-level files ...
✔  checking for left-over files
✔  checking index information
✔  checking package subdirectories ...
✔  checking R files for non-ASCII characters ...
✔  checking R files for syntax errors ...
✔  checking whether the package can be loaded ...
✔  checking whether the package can be loaded with stated dependencies ...
✔  checking whether the package can be unloaded cleanly ...
✔  checking whether the namespace can be loaded with stated dependencies ...
✔  checking whether the namespace can be unloaded cleanly ...
✔  checking loading without being on the library search path ...
✔  checking dependencies in R code ...
✔  checking S3 generic/method consistency (393ms)
✔  checking replacement functions ...
✔  checking foreign function calls ...
✔  checking R code for possible problems (562ms)
✔  checking Rd files ...
✔  checking Rd metadata ...
✔  checking Rd cross-references ...
✔  checking for missing documentation entries ...
✔  checking for code/documentation mismatches (457ms)
✔  checking Rd \usage sections (454ms)
✔  checking Rd contents ...
✔  checking for unstated dependencies in examples ...
✔  checking contents of ‘data’ directory (887ms)
✔  checking data for non-ASCII characters (927ms)
✔  checking data for ASCII and uncompressed saves ...
✔  checking examples (1.2s)
✔  checking PDF version of manual (574ms)
   
   
── Checking lint...check_lintr() 
....
✔ Lint looks good

── Checking namespace for imports()...check_namespace() 
✔ Imports look good - 0 found, 0 allowed

── Checking file extensions...check_r_filenames() 
ℹ 3 R files found
✔ Extensions look good
✔ Filenames look good

── Checking version...check_version() 
From gitlab.com:[redacted]/[redacted]/r/[redacted]-to-[redacted]
 * branch            main       -> FETCH_HEAD
✖ Please update the package version

── Checking .gitignore...check_gitignore() 
✔ .gitignore looks good

── Checking tidy descriptions...check_tidy_descriptions() 
✔ Your description is tidy!

── Checking file permissions...check_file_permissions() 
✔ File modes looks good

── Checking line breaks...check_line_breaks() 
✔ Line breaks look good

── Creating a tag...create_tag() 
ℹ No tagging: fix checking errors

── Checking NEWS.md...check_news() 
✖ Top line of NEWS.md not have correct format. It should be
# <package_name> 1.1.6 _2022-06-27_

── Checking Rproj...check_rproj() 
ℹ Reading <package_name>.Rproj
✔ Rproj looks good!
✖ Issues Detected
Error in inteRgrate::check_all() : Please fix

After reverting the code back to working order, but in the same R session as the last check:

> inteRgrate::check_all()

── inteRgrate version 1.0.22 ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────

── Installing package ──

✔  checking for file ‘/tmp/RtmpMJTIaD/file8e3e40410a30/<package_name>/DESCRIPTION’ ...
─  preparing ‘<package_name>’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘<package_name>_1.1.6.tar.gz’ (790ms)
   
Installing package into ‘/home/keith/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
* installing *source* package ‘<package_name>’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (<package_name>)
── R CMD build ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘.../DESCRIPTION’ ...
─  preparing ‘<package_name>’:
✔  checking DESCRIPTION meta-information ...
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘<package_name>_1.1.6.tar.gz’ (787ms)
   
── R CMD check ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
─  using log directory ‘/tmp/RtmpMJTIaD/file8e3e16ead3f0/<package_name>.Rcheck’
─  using R version 4.2.0 (2022-04-22)
─  using platform: x86_64-pc-linux-gnu (64-bit)
─  using session charset: UTF-8
✔  checking for file ‘<package_name>/DESCRIPTION’ ...
─  checking extension type ... Package
─  this is package ‘<package_name>’ version ‘1.1.6’
─  package encoding: UTF-8
✔  checking package namespace information ...
✔  checking package dependencies (1.4s)
✔  checking if this is a source package ...
✔  checking if there is a namespace
✔  checking for executable files ...
✔  checking for hidden files and directories ...
✔  checking for portable file names
✔  checking for sufficient/correct file permissions
✔  checking whether package ‘<package_name>’ can be installed (776ms)
✔  checking installed package size ...
✔  checking package directory
✔  checking DESCRIPTION meta-information ...
✔  checking top-level files
✔  checking for left-over files
✔  checking index information
✔  checking package subdirectories ...
✔  checking R files for non-ASCII characters ...
✔  checking R files for syntax errors ...
✔  checking whether the package can be loaded ...
✔  checking whether the package can be loaded with stated dependencies ...
✔  checking whether the package can be unloaded cleanly ...
✔  checking whether the namespace can be loaded with stated dependencies ...
✔  checking whether the namespace can be unloaded cleanly ...
✔  checking loading without being on the library search path ...
✔  checking dependencies in R code ...
✔  checking S3 generic/method consistency (398ms)
✔  checking replacement functions ...
✔  checking foreign function calls ...
✔  checking R code for possible problems (553ms)
✔  checking Rd files ...
✔  checking Rd metadata ...
✔  checking Rd cross-references ...
✔  checking for missing documentation entries ...
✔  checking for code/documentation mismatches (447ms)
✔  checking Rd \usage sections (450ms)
✔  checking Rd contents ...
✔  checking for unstated dependencies in examples ...
✔  checking contents of ‘data’ directory (872ms)
✔  checking data for non-ASCII characters (927ms)
✔  checking data for ASCII and uncompressed saves ...
✔  checking examples (1.2s)
✔  checking PDF version of manual (553ms)
   
   
── Checking lint...check_lintr() 
....
✔ Lint looks good

── Checking namespace for imports()...check_namespace() 
✔ Imports look good - 0 found, 0 allowed

── Checking file extensions...check_r_filenames() 
ℹ 3 R files found
✔ Extensions look good
✔ Filenames look good

── Checking version...check_version() 
From gitlab.com:[redacted]/[redacted]/r/[redacted]-to-[redacted]
 * branch            main       -> FETCH_HEAD
✔ Your version is fine!

── Checking .gitignore...check_gitignore() 
✔ .gitignore looks good

── Checking tidy descriptions...check_tidy_descriptions() 
✔ Your description is tidy!

── Checking file permissions...check_file_permissions() 
✔ File modes looks good

── Checking line breaks...check_line_breaks() 
✔ Line breaks look good

── Creating a tag...create_tag() 
ℹ No tagging: fix checking errors

── Checking NEWS.md...check_news() 
✔ Your NEWS.md has the correct format

── Checking Rproj...check_rproj() 
ℹ Reading <package_name>.Rproj
✔ Rproj looks good!
✖ Issues Detected
Error in inteRgrate::check_all() : Please fix