Skip to content

Latest commit

 

History

History
262 lines (160 loc) · 7.26 KB

cran-comments.md

File metadata and controls

262 lines (160 loc) · 7.26 KB
Raw

Update logs (for R-cran only)

2024-11-01

Version 1.2.0 (current)

To address the CRAN issues (2024-11-05)

\dontrun{} should only be used if the example really cannot be executed (e.g. because of missing additional software, missing API keys, ...) by the user. That's why wrapping examples in \dontrun{} adds the comment ("# Not run:") as a warning for the user. Does not seem necessary. Please replace \dontrun with \donttest.
Please unwrap the examples if they are executable in < 5 sec, or replace dontrun{} with \donttest{}.
-> create_group.Rd; freesurfer_brain.Rd; geom_freemesh.Rd

Thanks, currently there are three \dontrun{} because these examples do require users to

  • download additional data and software that are not licensed under, nor built into this package.
  • run the code in interactive sessions

I have also tried my best to provide toy-examples if possible. This package originally has lots of dontruns and I have converted most of them to donttest back in version 0.1.2 (see comments down below). I believe these three dontrun cases have been left since then.

Please make sure that you do not change the user's options, par or working directory. If you really have to do so within functions, please ensure with an *immediate* call of on.exit() that the settings are reset when the function is exited.
e.g.:
...
oldpar <- par(no.readonly = TRUE) # code line i
on.exit(par(oldpar)) # code line i + 1
...
par(mfrow=c(2,2)) # somewhere after
...
e.g.: ->  R/class_electrode_proto.R; R/ext_media.R; R/plot_volume-slices.R
If you're not familiar with the function, please check ?on.exit. This function makes it possible to restore options before exiting a function even if the function breaks. Therefore it needs to be called immediately after the option change within a function.

Thanks, I have added on.exit to all functions that change options and par.

Just in case you miss it, there are multiple lines changing par in the function plot_slices (R/plot_volume-slices.R), and I make sure the par remain unchanged via the following two lines at the very beginning.

oldpar <- graphics::par(no.readonly = TRUE)
on.exit({ graphics::par(oldpar) })

To address the previous CRAN issues (2024-11-01)

URL: https://cran.r-project.org/web/packages/threeBrain/index.html

Package ‘threeBrain’ was removed from the CRAN repository.

...

Archived on 2024-02-18 as requires archived package 'ravetools'. , Also, claims to be the copyright holder of the work of other authors and contributors.

...

Package ravetools has been updated and on CRAN now. The dependency is cleared.

This package (threeBrain) is developed out of fun and used in my thesis and later projects. I am the solo developer in this project (wrote 99.99% code). Other contributors are explicitly claimed in the DESCRIPTION.

There is one external JavaScript library three-brain-js. The code is located at inst/threeBrainJS. I am also the main maintainer and contributor of that project. The distribution included is a compiled bundle that is released under MPL-2.0 as a whole. As required, the license file has been included when npm compiles the bundles, see inst/threeBrainJS/dist. There might some other external programs, but they can't claim the authorship of the release bundle. Their corresponding license files are included too.

Self check: 0 errors | 0 warnings | 1 note

❯ checking installed package size ... NOTE
    installed size is  7.3Mb
    sub-directories of 1Mb or more:
      R              2.0Mb
      threeBrainJS   2.9Mb

I (tried, but) can't reduce the size anymore from JavaScript engine and package functions.

2024-02-06

Version 1.0.2 (passed)

2023-07-03

Version 1.0.1 (passed)

2023-06-03

Version 1.0.0 (passed)

2023-01-31

Version 0.2.9 (passed)

2022-10-15

Version 0.2.7 (passed)

2022-08-24

Version 0.2.6 (passed)

2022-05-29

Version 0.2.5 (passed)

2021-12-02

Version 0.2.4 (passed)

2021-10-13

Version 0.2.3 (passed)

2021-08-02

Version 0.2.2 (passed)

Skipped a version

2021-07-18

Version 0.2.0 (passed)

2021-01-09

Version 0.1.9 (passed)

2020-06-23

Version 0.1.8 (passed)

2020-05-12

Version 0.1.7 (passed)

2020-05-12

Version 0.1.6 (passed)

2020-03-12

Version 0.1.6 (passed)

2020-01-20

Version 0.1.5 (passed)

2019-10-18

Version 0.1.4 (passed)

2019-09-10

Version 0.1.3 (passed)

2019-06-27

Version 0.1.2 (passed)

2019-06-10

Version 0.1.2

Rejected in manual screening

Reason:

Thanks, please replace \dontrun{} by \donttest{} or unwap the examples 
if they can be executed in less than 5 sec per Rd-file.

You have examples for unexported functions which cannot run in this way.
Please either add threeBrain::: to the function calls in the examples, 
omit these examples or export these functions.

Please fix and resubmit.

Solution:

  • exported internal functions needed by examples
  • changed dontrun to donttest

2019-06-09

Version 0.1.2

Update JavaScript library, added scatter plot methods. Removed files in inst/ that trigger warnings (like installed.packages).

Rejected in pre-test

Reason:

Package has a VignetteBuilder field but no prebuilt vignette index.

Solution:

I removed old vignette causing this note. Removed VignetteBuilder field in DESCRIPTION.

2019-03-08

Version 0.1.0

  • Passed cran check but rejected from manual checks

Rejected by Swetlana Herbrandt.

Reason:

Thanks, please do not use installed.packages(). See help page of 
installed.packages():
"This can be slow when thousands of packages are installed, so do not 
use this to find out if a named package is installed (use system.file or 
find.package) nor to find out if a package is usable (call require and 
check the return value) nor to find details of a small number of 
packages (use packageDescription). It needs to read several files per 
installed package, which will be slow on Windows and on some 
network-mounted file systems."


Please do not change waning options (options(warn=-1)) in your functions.

Please add examples in your Rd-files.

Please fix and resubmit.

Check:

  1. There's a file AFNIio.R in inst/ folder that triggers these warnings. threeBrain doesn't need this file to function properly. However, it's not recommended to change the script due to compatibility issues.
  2. Also this file has lots of syntax mistakes. I plan to write my own afni readers in the later versions

Solution:

  • AFNIio.R has been removed.
  • Examples added to S3 functions create_group, geom_freemesh and geom_sphere. At current stage, not many geometry types are supported. Plan to add plane and particle system later on in the next big version, but these geometries are totally enough for iEEG/ECoG analysis.

2019-03-07

Version 0.1.0

  • Self check has one note: Possibly mis-spelled words in DESCRIPTION
  • Passed cran check but rejected by manual checks

Rejected by Uwe Ligges.

Reason:

 The Description field should not start with the package name,
     'This package' or similar.

Please also single quote software names such as 'FreeSurfer'.

Solution:

Re-wrote DESCRIPTION, added single quotes to software names