[R/download_classes.R:32:1:](https://github.com/russHyde/miiq/blob/7351514f918f9d24bb9f98823f20d38a87e6b2fe/R/download_classes.R#L32) *style:* **functions should have cyclomatic complexity of less than 15, this has 27.**
```r
.check_marray_dl_config <- function(
^
```
[R/list_manipulation.R:24:1:](https://github.com/russHyde/miiq/blob/7351514f918f9d24bb9f98823f20d38a87e6b2fe/R/list_manipulation.R#L24) *style:* **functions should have cyclomatic complexity of less than 15, this has 18.**
```r
get_or_else <- function(
^
```
[R/microarray_classes.R:243:1:](https://github.com/russHyde/miiq/blob/7351514f918f9d24bb9f98823f20d38a87e6b2fe/R/microarray_classes.R#L243) *style:* **Variable and function name style should be snake_case or CamelCase.**
```r
gld_fnDefault_esetAnnotation <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/microarray_classes.R:286:1:](https://github.com/russHyde/miiq/blob/7351514f918f9d24bb9f98823f20d38a87e6b2fe/R/microarray_classes.R#L286) *style:* **Variable and function name style should be snake_case or CamelCase.**
```r
gld_fnDefault_transformAndProbeFilter <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/microarray_functions.R:323:37:](https://github.com/russHyde/miiq/blob/7351514f918f9d24bb9f98823f20d38a87e6b2fe/R/microarray_functions.R#L323) *style:* **Variable and function name style should be snake_case or CamelCase.**
```r
                                    entrezgene.db) {
                                    ^~~~~~~~~~~~~
```
[R/microarray_functions.R:437:30:](https://github.com/russHyde/miiq/blob/7351514f918f9d24bb9f98823f20d38a87e6b2fe/R/microarray_functions.R#L437) *style:* **Variable and function name style should be snake_case or CamelCase.**
```r
    Biobase::featureData(es)$entrez.id <- es_entrez_id
                             ^~~~~~~~~
```
[R/preprocess_functions.R:19:30:](https://github.com/russHyde/miiq/blob/7351514f918f9d24bb9f98823f20d38a87e6b2fe/R/preprocess_functions.R#L19) *style:* **Variable and function name style should be snake_case or CamelCase.**
```r
  Biobase::featureData(gset)$entrez.id <- split_and_join(
                             ^~~~~~~~~
```
[tests/testthat/test-filter_functions.R:4:16:](https://github.com/russHyde/miiq/blob/7351514f918f9d24bb9f98823f20d38a87e6b2fe/tests/testthat/test-filter_functions.R#L4) *warning:* **no visible global function definition for ‘random_eset’**
```r
  no_probes <- random_eset(n_probes = 0)
               ^~~~~~~~~~~
```
[tests/testthat/test-filter_functions.R:10:17:](https://github.com/russHyde/miiq/blob/7351514f918f9d24bb9f98823f20d38a87e6b2fe/tests/testthat/test-filter_functions.R#L10) *warning:* **no visible global function definition for ‘random_eset’**
```r
  no_samples <- random_eset(n_samples = 0)
                ^~~~~~~~~~~
```
[tests/testthat/test-filter_functions.R:16:12:](https://github.com/russHyde/miiq/blob/7351514f918f9d24bb9f98823f20d38a87e6b2fe/tests/testthat/test-filter_functions.R#L16) *warning:* **no visible global function definition for ‘random_eset’**
```r
  empty <- random_eset(n_probes = 0, n_samples = 0)
           ^~~~~~~~~~~
```
[tests/testthat/test-filter_functions.R:113:31:](https://github.com/russHyde/miiq/blob/7351514f918f9d24bb9f98823f20d38a87e6b2fe/tests/testthat/test-filter_functions.R#L113) *style:* **Variable and function name style should be snake_case or CamelCase.**
```r
  Biobase::fData(eset_entrez)$entrez.id <- c(NA, "", "12345", "12345///786")
                              ^~~~~~~~~
```


I don’t use jquery

Sent from my iPhone

> On Dec 17, 2019, at 4:57 PM, Yonatan <notifications@github.com> wrote:
>
> only bootstrap without jquery?
> I think it better to use react-strap: https://reactstrap.github.io/
> it is not a good practice to use both jquery and react in the same app
> Try to avoid including external js libs in that way (prefer to use npm and import)
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub, or unsubscribe.


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https://github.com/YaroST12/RAPHAEL_Kernel/commit/fceaba8687748aca42a529c4757d6c3aa43d1758
: )


[AppVeyor has built](https://ci.appveyor.com/project/cypress-io/cypress/builds/29600850/job/5d5kdqkkcd6d8b1i) the `win32 ia32` version of the Test Runner.

You can install this pre-release platform-specific build using instructions at [https://on.cypress.io/installing-cypress#Install-pre-release-version](https://on.cypress.io/installing-cypress#Install-pre-release-version).

You will need to use custom `CYPRESS_INSTALL_BINARY` url and install Cypress using an url instead of the version.

    set CYPRESS_INSTALL_BINARY=https://cdn.cypress.io/beta/binary/3.8.1/win32-ia32/appveyor-develop-05987c43726c05965d623e71eee9b857a98c86c6-29600850/cypress.zip
    npm install https://cdn.cypress.io/beta/binary/3.8.1/win32-ia32/appveyor-develop-05987c43726c05965d623e71eee9b857a98c86c6-29600850/cypress.zip


Deployment failed with the following error:

~~~
Your `package.json` file is missing a `build` property inside the `scripts` property.
~~~


- changed necessity to have image open for writing when commanding imported image to be open in another instance of RIDE (now image can be write-protected)
- fixed selection of all files after an image to import has instead been opened in another instance of RIDE


Veuillez passer par ce dossier


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This argument is superfluous since `-F` implies `POST`


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Calling convention and arguments are both different. The bytecode invokes go by calling it as a built-in function, with either 1 or 2 string arguments. Shimming everything to pass through c_goto would require knowing what is on the stack in advance.


это все плюсы, а минусы какие есть?


Glad you like the framework @AkhilMukkamala! I have been working on FoalTS for almost one year and half now and I'm going to keep going that way. I work very hard on it so that in the next few years it will become widely used in Node.JS ecosystem.

Regarding the roadmap, I prioritize issues and features every month or couple of months. At the beginning of January, version 1.4 will be released (see [features](https://github.com/FoalTS/foal/pull/592)). Then, in January and February, I'm planning to work on file uploads and downloads (with the support of local file system and AWS S3) and to work on simplify the session system (less code required, better readability).


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add space after `,`


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What do you mean bro?

Thanks,
Simon

Sent from Simon Hoang's iPhone

> On 17 Dec 2019, at 15:15, Scott Taylor <notifications@github.com> wrote:
>
>
> Shouldn't leave empty declarations 👀
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub, or unsubscribe.


[AppVeyor has built](https://ci.appveyor.com/project/cypress-io/cypress/builds/29600850/job/oa49s0l2lpv9axd1) the `win32 x64` version of the Test Runner.

You can install this pre-release platform-specific build using instructions at [https://on.cypress.io/installing-cypress#Install-pre-release-version](https://on.cypress.io/installing-cypress#Install-pre-release-version).

You will need to use custom `CYPRESS_INSTALL_BINARY` url and install Cypress using an url instead of the version.

    set CYPRESS_INSTALL_BINARY=https://cdn.cypress.io/beta/binary/3.8.1/win32-x64/appveyor-develop-05987c43726c05965d623e71eee9b857a98c86c6-29600850/cypress.zip
    npm install https://cdn.cypress.io/beta/binary/3.8.1/win32-x64/appveyor-develop-05987c43726c05965d623e71eee9b857a98c86c6-29600850/cypress.zip


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-82-usfs.pantheonsite.io/)

Created multidev environment [pr-82](https://dashboard.pantheon.io/sites/41bd818c-c95f-4bfb-ae68-63c3075be556#pr-82) for usfs.


[Circle has built](https://circleci.com/gh/cypress-io/cypress/217407) the `darwin x64` version of the Test Runner.

You can install this pre-release platform-specific build using instructions at [https://on.cypress.io/installing-cypress#Install-pre-release-version](https://on.cypress.io/installing-cypress#Install-pre-release-version).

You will need to use custom `CYPRESS_INSTALL_BINARY` url and install Cypress using an url instead of the version.

    export CYPRESS_INSTALL_BINARY=https://cdn.cypress.io/beta/binary/3.8.1/darwin-x64/circle-develop-05987c43726c05965d623e71eee9b857a98c86c6-217404/cypress.zip
    npm install https://cdn.cypress.io/beta/npm/3.8.1/circle-develop-05987c43726c05965d623e71eee9b857a98c86c6-217340/cypress.tgz


![](https://github.trello.services/images/mini-trello-icon.png) [Input Flexibility](https://trello.com/c/CupvNgb4/1-input-flexibility)


No need for a .test file if you use unitrun afaik


здесь нужно добавить else, иначе собака будет добавляться каждый раз.


![](https://github.trello.services/images/mini-trello-icon.png) [Add Text Color](https://trello.com/c/vWYANMGN/3-add-text-color)


We are not keeping this function, right?


I don’t really understand what it means


![](https://github.trello.services/images/mini-trello-icon.png) [Add Card Color](https://trello.com/c/tzoV8Gnq/4-add-card-color)


What's the default codec that `ffmpeg` will use for this endpoint? is it necessary to specify a `pcm` one?


![](https://github.trello.services/images/mini-trello-icon.png) [Hand Numbers when Splitting](https://trello.com/c/jIn99rGU/10-hand-numbers-when-splitting)


show


Aliasing failed with the following error:

~~~
Error! Instance verification timed out (5m)
~~~


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![](https://github.trello.services/images/mini-trello-icon.png) [Tune Scrolling Behav.](https://trello.com/c/ICXuNFip/5-tune-scrolling-behav)


Pushing names from the namelist to the stack is a common instruction in the bytecode.


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Thanks for your quick reply, I'll take a look at this later. When using "SEARCH" command in the aliyun (alibaba) enterprise mail "ALL" flag must be added, so I thought it's a message flag. And it also not support the charset flag. :(


![](https://github.trello.services/images/mini-trello-icon.png) [Change Input Behav.](https://trello.com/c/0nvIt3K7/7-change-input-behav)


![](https://github.trello.services/images/mini-trello-icon.png) [ASCII Art Intro](https://trello.com/c/R2fUl5U0/8-ascii-art-intro)


Deploy preview for _website_ ready!

Built with commit 07def0e63c80c74e01e298b941cfaeabfaf224d5

https://shopware-pwa-ctv0hx57v.now.sh


I am pretty sure those double-backslashes are supposed to be there


![](https://github.trello.services/images/mini-trello-icon.png) [Game Ending (Credits)](https://trello.com/c/H1Fp2cG8/11-game-ending-credits)


![](https://github.trello.services/images/mini-trello-icon.png) [Sound](https://trello.com/c/7m9X0kZl/12-sound)


находясь в foreach, мы не можем удалять элементы из списка, по которому проходимся, так как foreach предназначен только для чтения


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* https://exelm-git-master.honai.now.sh


I knowing that it is possible without this file, but I wanted to make another file for comments and add it here


on self.client where is the "client" variable created?


add 2 space indentation before `match`


Well done. I noticed it was missing. :)


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In this example, I don’t understand how to implement it.


Errors: 0, Warnings: 0

    Details: details


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* https://aremycolorsaccessible.sitaggart.now.sh
* https://aremycolorsaccessible-git-master.sitaggart.now.sh


Hi Ali,

Am fixing that now, but encountered another problem for Delhi - NA on all distance and duration e.g. participantM01745 / 1045. Could you look into that?

Thanks

Rob

________________________________
From: Ali Abbas <notifications@github.com>
Sent: 17 December 2019 13:49
To: ITHIM/ITHIM-R <ITHIM-R@noreply.github.com>
Cc: Johnson, Rob <rob.johnson@mrc-bsu.cam.ac.uk>; Mention <mention@noreply.github.com>
Subject: Re: [ITHIM/ITHIM-R] adding checking for NAs (4859a2e)

@robj411<https://github.com/robj411> Failing for Delhi. This assumes that trip_duration column exists. Is this a requirement now? My understanding either trip_duration or trip_distance is enough.

If you like, I can fix this in Delhi's dataset.

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub<https://github.com/ITHIM/ITHIM-R/commit/4859a2e52f5b4b06765dd2aed26a732375d9b571?email_source=notifications&email_token=AGB2LN3TMH5O2EYYIXDPT4TQZDKHZA5CNFSM4J33XUQ2YY3PNVWWK3TUL52HS4DFVVBW63LNNF2EG33NNVSW45FKMNXW23LFNZ2F62LEZYBCY2WD#commitcomment-36465347>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AGB2LNZQO4AOBXBC4YYOGOTQZDKHZANCNFSM4J33XUQQ>.


Please add a comment here. Something like
"`eval'` is an auxiliary function used by the `#eval` command implementation. We convert the `IO.Error` to a string to simplify its implementation in C++. We should remove `eval'` after we move to the new frontend implemented in Lean."


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* https://lawra-website-git-master.21711933.now.sh


BREAKING_CHANGE: Para que funcione hay que migrar los nuevos 2 campos que hice en models

`python manage.py makemigrations`
`python manage.py migrate`

y luego hay que correr otra vez datos_iniciales para que levante las imagenes de unidad

`python manage.py datos_iniciales`


The following doc(s) have been deployed to the [addsearchm](https://addsearchm-static-docs.pantheonsite.io/docs) Multidev environment:
- [gatsby/src/layout/seo.js](https://github.com/pantheon-systems/documentation/commit/16d9b39c601a1b08d7cf9a305668adaaefad666f/gatsby/src/layout/seo.js)


Good catch, filed https://github.com/mozilla/release-notes/pull/10 to fix


> It is fascinating on so many levels how someone can keep being so persistent yet still utterly fail at having a discussion on a serious technical level. I have yet to see a single comment that didn't pull this persons statements into absolute absurdity. Curious what make someone become so incapable to function on a level that is even worth considering engaging with directly. I'm really only following this discussion still for the sociological aspects of it, my statements on the matter at hand are written above already, no need to repeat them.

Isn't it what do you (those who claim yourselves as "developers of dogecoin") respond to my questions? And I asked many of them. Now let's look at this

https://sochain.com/block/DOGETEST/2103767?__cf_chl_jschl_tk__=a20de44d7956617754ac9534de301cc2abe75883-1576596384-0-AZvXvzUqQ4hdxJTOz49NX_rrh0hei7iUw2TARXTg-C5PKJyCWtoK5gR8JMuLKaf1opqjGpsyuAInt3F6n4kyRqi9pRHY8Y_mnsJm6D8z-_l6eHG-neDH9irgZgx8D4YG3D4jR8UEO9O56rOa_xG2ICCXmy-j8fZJ_mbZrY8ZOBZLbOx7Lc73Qg4gRmc5erSIB3t06FhB25YFgf84pCgNj3PtFiIqiB0lok-0dWsrKMDJcH0_t8wPpieNKeIvmditdivZEMToeIA9EYGzTW-G7coRqKA0mQWzvskOLf4MCAVf

![Screenshot from 2019-12-17 18-11-54](https://user-images.githubusercontent.com/31012408/71009311-0fab8300-20fb-11ea-9f1f-4952bc7eb2bf.png)

Is this tx not relayed? Is it not mined?


Thank you for the feedback! I've removed the console logs and also
refactored the code to remove the ternary operator. I unintentionally left
the console logs in the code before submitting and will try to do better to
delete them before committing. Also, going forward, I won't use ternary
operators in complex code.

Regards.
Jon

Jon Grossman
jon@jonegrossman.com
www.jonegrossman.com

On Tue, Dec 17, 2019 at 8:05 AM Yonatan <notifications@github.com> wrote:

> please avoid using ? : statement in complex code, especially if you have
> html elements in one of the cases
> suggest to use {isSpinning && (...}) and {!isSpinning && (...)}
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <https://github.com/Itc-bootcamp-2019/micro-blogging-front-end-JonathanGrossman/commit/13567107ee157623e9e0d9dfd706d655459bb11f?email_source=notifications&email_token=AMLK7WPCJJ62FXF2YSVXUHLQZDMCNA5CNFSM4J336PA2YY3PNVWWK3TUL52HS4DFVVBW63LNNF2EG33NNVSW45FKMNXW23LFNZ2F62LEZYBCY26Q#commitcomment-36465616>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/AMLK7WJU63GWZDUAJRSE4BLQZDMCNANCNFSM4J336PAQ>
> .
>


Have you figured out the UTF8 issue?


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@kirainmoe

这里这个文件夹 `hasee-tongfang-macos/kexts/Alternative Kexts/Wireless/DW1560:DW1830/`

`DW1560:DW1830/` 中间有一个冒号。FAT 分区是不支持文件名带冒号的，所以这个文件夹会在复制进 EFI 分区的时候失败。虽然不会导致什么严重的后果，最多有人在看说明复制驱动的时候找不到驱动会有点迷惑。我也是终端里 cp 复制出错的时候才注意到的。

一个不算bug的bug，我就不开issue了，应该也能看到。😊


u needa update


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* https://chatkartweb-git-master.chatkart.now.sh


custom module names aren't known as compile-time, so if a user renamed "Freecam" to "Spectator", or something similar, the lookup map would surely map "Spectator" to the "Freecam" module, but the code still asks ModuleManager for "Freecam" regardless.


ok


Typo, actually should be in `options` objects


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Thus is the CSS submission.


> This is a mailbox flag, not a message flag.
>
> See https://godoc.org/github.com/emersion/go-imap-specialuse

https://github.com/dreamszl/go-imap/commit/f0a926f58725366ada0371f842f5f536f347ce71#diff-059dc0366ae402fcb2b70107da19b22dR337
And this is the reason I want to add this flag. Maybe a bad commit order.


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* https://mukemmel-blog-git-master.ja1.now.sh


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Same here


Deploy preview for _website_ ready!

Built with commit c60d8aaa5b38fe9a3d206b03a1c243fadc035f52

https://spartacus-5tfxr664x.now.sh


Thanks @nsoranzo. This was driving me a little crazy. Now I understand the syntax needed to pass this test.


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wertyman


The phTmlNfc_Shutdown() call stops TML specific thread which would otherwise continue running until you close/kill the application.


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Sorry for the noice but would it be possible to release this in a new version? It seems version 1.1.4 doesn't contain this update.


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Cambios en el modulo, relaciones, campos calculados, vistas


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good catch!


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The title won't show when `show_chase_reference` is false.


line 24 you mkdir /data/tmp but by line 42 you expose /app/data/TEMP
this is true of all the Dockerfiles


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needs changes in /etc/systemd/system/phoniebox-startup-sound-service

[Unit]
Description=Phoniebox Startup Sound
After=network.target

[Service]
WorkingDirectory=/home/pi/RPi-Jukebox-RFID
ExecStart=/home/pi/RPi-Jukebox-RFID/scripts/startup-service-script.sh

[Install]
WantedBy=multi-user.target


Deployment failed with the following error:

~~~
The property `env` is not allowed in now.json when using Now 2.0 – please remove it.
~~~


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Sorry, I had them the wrong way around. "rotation-degrees" is KEY_ROTATION, "rotation" is the undocumented one. Anyway, KEY_ROTATION was added in API 23, so I’m not sure how this would behave with minSdkVersion 18.


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sorry @ciber96  - my son was playing "his own server". Fixing


This is my home base where my projects come alive.


Hi! This is the friendly automated conda-forge-webservice.

I updated the Github team because of this commit.

- @demartinofra was added to conda-forge. Welcome to conda-forge!
  Go to https://github.com/orgs/conda-forge/invitation see your invitation.

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Không push file này lên.


il [ctIdentificativoUnivoco](https://github.com/italia/pagopa-specifichepagamenti-schemi/blob/384dacb671a19d4684d1acb663784341cf30bce3/nodo/PagInf_RPT_RT_6_2_0.xsd#L374) e' riferito da [identificativoUnivocoAttestante](https://github.com/italia/pagopa-specifichepagamenti-schemi/blob/384dacb671a19d4684d1acb663784341cf30bce3/nodo/PagInf_RPT_RT_6_2_0.xsd#L596), che e' un PSP, in cui sono possibili ABI e BIC da 8 e quindi la limitazione ad una stringa tra 11 e 16 direi che non e' corretta


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コミットログの URL の末尾 8888 でなく 888 です。


this doesn't seem to work.
i am not seeing the prime icon on lobbies.
can other people see it but not exactly me?


Use `./scummvm --start-movie=HandV workshop` for that


Tried deploying on Heroku, but I got too confused. Maybe later, when I'm not so pressed for time.


Is this best-practice? `latest` maps to `16.04` and not `18.04` atm.


fixed #1


@JuliaRegistrator register


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Registration pull request created: [JuliaRegistries/General/6842](https://github.com/JuliaRegistries/General/pull/6842)

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if [Julia TagBot](https://github.com/apps/julia-tagbot) is installed, or can be done manually through the github interface, or via:
```
git tag -a v0.1.5 -m "<description of version>" e43f33d6958ef1ddd234e44c521e7e793b069369
git push origin v0.1.5
```


@chad-iris whats your take on this, was removing units on this intended or an uninteded side effect


Could we then call those with `cb_` prefix?


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* https://nuro-sh-git-master.nuro.now.sh


Deployment failed with the following error:

~~~
Could not find a secret by name "mystik-mongodb-uri"
~~~


File was downloaded as part of Introduction to TensorFlow for Artificial Intelligence, Machine Learning, and Deep Learning Week 1 from https://colab.sandbox.google.com/github/lmoroney/dlaicourse/blob/master/Course%201%20-%20Part%202%20-%20Lesson%202%20-%20Notebook.ipynb


The changes in this commit is now applied on the DEV version of the bot


@JuliaRegistrator register()


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Registration pull request created: [JuliaRegistries/General/6843](https://github.com/JuliaRegistries/General/pull/6843)

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if [Julia TagBot](https://github.com/apps/julia-tagbot) is installed, or can be done manually through the github interface, or via:
```
git tag -a v0.6.2 -m "<description of version>" 0d7d06c413409ecacbadaba000e903eeaaec21c5
git push origin v0.6.2
```


@Utumno Added some more docstrings and a fixup, this is also rebased on latest nightly so you can feel free to just set your HEAD to this and skip the conflict resolution :P


Har kanske känt mig lite väl ensam på det repot. Haha!

On Tue, Dec 17, 2019, 15:23 Mattias Nordqvist <notifications@github.com>
wrote:

> poop? 💩
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
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>


You always create this vec, you should let the caller allocate and pass a mut ref to it. The only concern of this fn is to wait and fetch the events.


Wow so many fixes thanks. I think I can actually make a new pre-release on the main bot


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registration page in login page


Hi! This is the friendly automated conda-forge-webservice.

I updated the Github team because of this commit.

- @timkpaine was added to this feedstock maintenance team.

You should get push access to this feedstock and CI services.

Feel free to join the community [chat room](https://gitter.im/conda-forge/conda-forge.github.io).

NOTE: Please make sure to not push to the repository directly.
      Use branches in your fork for any changes and send a PR.
      More details [here](https://conda-forge.org/docs/maintainer/updating_pkgs.html#forking-and-pull-requests)


well the entire bot-say thing is now deprecated


I do not like mixing the concept of Pollable with Epoll. The Pollable concerns are just being a fd wrapper. The Epoll concern is to wrap the epoll fd and also provide wrappers that work on that fd and an API for users to call.


So instead of fixing it
I will remove it


Now maintains correct _heading_ when strafing. Still working on accuracy.


this definition has more parameters in it.


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Not sure I understand why an individual numerator or denominator would want have units? They are coefficients of polynomials, and so should be unitless, right? Maybe I am not understanding your concern?


Then could you please add above comment explaining all different parameters, and then I will adapt my code to this one?


But only the Spark boxes access this area?
There is no other system in memory for the other boxes. Only the Spark boxes have been real multiboots for ages and use them.
From this point of view, the renaming is confusing


🔥 Device tests completed (Failed) on TvOS on [Azure DevOps](https://dev.azure.com/devdiv/DevDiv/_build/index?buildId=3328253)(TvOS): [Html Report](http://xamarin-storage/jenkins/xamarin-macios/pull-request/0a5a8f3c1e56307421703b5258c6ee5f18dab4ef/3328253/device-tests/jenkins-results/tests/index.html) 🔥

🔥 Tests failed catastrophically on TvOS  (no summary found)


🔥 Device tests completed (Failed) on iOS32b on [Azure DevOps](https://dev.azure.com/devdiv/DevDiv/_build/index?buildId=3328252)(iOS32b): [Html Report](http://xamarin-storage/jenkins/xamarin-macios/pull-request/0a5a8f3c1e56307421703b5258c6ee5f18dab4ef/3328252/device-tests/jenkins-results/tests/index.html) 🔥

🔥 Tests failed catastrophically on iOS32b  (no summary found)


🔥 Device tests completed (Failed) on iOS on [Azure DevOps](https://dev.azure.com/devdiv/DevDiv/_build/index?buildId=3328251)(iOS): [Html Report](http://xamarin-storage/jenkins/xamarin-macios/pull-request/0a5a8f3c1e56307421703b5258c6ee5f18dab4ef/3328251/device-tests/jenkins-results/tests/index.html) 🔥

🔥 Tests failed catastrophically on iOS  (no summary found)


    :x: Test Failed: va/tests/accessibility

composer va:test:accessibility

```
audited 183 packages in 1.169s
found 2 low severity vulnerabilities
  run `npm audit fix` to fix them, or `npm audit` for details

> axe_tests@1.0.0 test /var/aegir/projects/cms/pr696
> node ./tests/accessibility/aXeAccessibilityCheck.js

!!!  NUMBER OF NEW VIOLATIONS on http://pr696.ci.cms.va.gov 0
!!!  NUMBER OF NEW VIOLATIONS on http://pr696.ci.cms.va.gov/sections  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr696.ci.cms.va.gov/node/add/page  = 1
[ { id: 'duplicate-id',
    impact: 'minor',
    tags: [ 'cat.parsing', 'wcag2a', 'wcag411' ],
    description: 'Ensures every id attribute value is unique',
    help: 'id attribute value must be unique',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/duplicate-id?application=webdriverjs',
    nodes: [ [Object], [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://pr696.ci.cms.va.gov/node/add/landing_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr696.ci.cms.va.gov/node/add/documentation_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr696.ci.cms.va.gov/node/add/event  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr696.ci.cms.va.gov/node/add/health_care_local_facility  = 1
[ { id: 'label',
    impact: 'critical',
    tags:
     [ 'cat.forms',
       'wcag2a',
       'wcag332',
       'wcag131',
       'section508',
       'section508.22.n' ],
    description: 'Ensures every form element has a label',
    help: 'Form elements must have labels',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/label?application=webdriverjs',
    nodes:
     [ [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://pr696.ci.cms.va.gov/node/add/health_care_region_detail_page  = 1
[ { id: 'duplicate-id',
    impact: 'minor',
    tags: [ 'cat.parsing', 'wcag2a', 'wcag411' ],
    description: 'Ensures every id attribute value is unique',
    help: 'id attribute value must be unique',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/duplicate-id?application=webdriverjs',
    nodes: [ [Object], [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://pr696.ci.cms.va.gov/node/add/health_care_region_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr696.ci.cms.va.gov/node/add/office  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr696.ci.cms.va.gov/node/add/outreach_asset  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr696.ci.cms.va.gov/node/add/person_profile  = 1
[ { id: 'duplicate-id-aria',
    impact: 'critical',
    tags: [ 'cat.parsing', 'wcag2a', 'wcag411' ],
    description:
     'Ensures every id attribute value used in ARIA and in labels is unique',
    help: 'IDs used in ARIA and labels must be unique',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/duplicate-id-aria?application=webdriverjs',
    nodes: [ [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://pr696.ci.cms.va.gov/node/add/press_release  = 1
[ { id: 'aria-allowed-attr',
    impact: 'critical',
    tags: [ 'cat.aria', 'wcag2a', 'wcag412' ],
    description: 'Ensures ARIA attributes are allowed for an element\'s role',
    help: 'Elements must only use allowed ARIA attributes',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/aria-allowed-attr?application=webdriverjs',
    nodes: [ [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://pr696.ci.cms.va.gov/node/add/regional_health_care_service_des  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr696.ci.cms.va.gov/node/add/news_story  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr696.ci.cms.va.gov/node/add/support_service  = 0
[]
!!!  VIOLATION TYPES FOUND: 5 PROCESS EXITED WITH CODE 1  !!!
> npm install --only=production
> npm test
Tue, 17 Dec 2019 16:00:15 GMT axe-webdriverjs deprecated Error must be handled as the first argument of axe.analyze. See: #83 at tests/accessibility/aXeAccessibilityCheck.js:44:14
Tue, 17 Dec 2019 16:00:18 GMT axe-webdriverjs deprecated Error must be handled as the first argument of axe.analyze. See: #83 at tests/accessibility/aXeAccessibilityCheck.js:56:42
Failed to inject axe-core into one of the iframes!
Failed to inject axe-core into one of the iframes!
npm ERR! Test failed.  See above for more details.
Script npm test handling the va:test:accessibility event returned with error code 1
```

- **On:** devshop.cms.va.gov
- **In:** 01:13


I just made it enable for our tests, it won't harm as if you don't add "mount-sh4" to your "MACHINE_ESSENTIAL_EXTRA_RDEPENDS" there will be no change.


Successfully deployed to following URLs:

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* https://metechi-landing-git-master.metechi.now.sh


@alexmucde Kindly review this patch. Thank you!


Deployment failed with the following error:

~~~
Your `package.json` file is missing a `build` property inside the `scripts` property.
~~~


[R/calc_rel_contr_node_time.R:61:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/calc_rel_contr_node_time.R#L61) *style:* **Lines should not be more than 80 characters.**
```r
                                   ((1 - s) * (    num_nodes + num_hidden_nodes))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_rel_contr_node_time.R:61:48:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/calc_rel_contr_node_time.R#L61) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                                   ((1 - s) * (    num_nodes + num_hidden_nodes))
                                               ^
```
[R/calc_rel_contr_node_time.R:63:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/calc_rel_contr_node_time.R#L63) *style:* **Lines should not be more than 80 characters.**
```r
                                   ((1 - s) * (2 * num_nodes + num_hidden_nodes))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_rel_contr_node_time.R:75:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/calc_rel_contr_node_time.R#L75) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calc_expected_hidden_nodes_per_branch <- function(bl, lambda, mu) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_rel_contr_node_time.R:125:3:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/calc_rel_contr_node_time.R#L125) *style:* **Variable and function names should not be longer than 30 characters.**
```r
  calc_expected_hidden_nodes_per_dt <- function(t, lambda, mu) {
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_summary_statistics.R:64:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/calc_summary_statistics.R#L64) *style:* **Lines should not be more than 80 characters.**
```r
    # this is rather inefficient off course, RPANDA can do all pairwise comparisons?
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_summary_statistics.R:65:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/calc_summary_statistics.R#L65) *style:* **Lines should not be more than 80 characters.**
```r
    local_jsd <- tryCatch(RPANDA::JSDtree(list(true_tree, trees[[i]]), meth = "standard")[1,2],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_summary_statistics.R:65:93:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/calc_summary_statistics.R#L65) *style:* **Commas should always have a space after.**
```r
    local_jsd <- tryCatch(RPANDA::JSDtree(list(true_tree, trees[[i]]), meth = "standard")[1,2],
                                                                                ^
```
[R/calc_summary_statistics.R:79:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/calc_summary_statistics.R#L79) *style:* **Lines should not be more than 80 characters.**
```r
                                 "mean_branch_length", "nLTT", "jsd", "topo_dist")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/count_hidden.R:7:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/count_hidden.R#L7) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
reduce_tree <- function(tree) {
^
```
[R/create_equal_alignment.R:4:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/create_equal_alignment.R#L4) *style:* **Lines should not be more than 80 characters.**
```r
#' @param node_model model used to generate substitutions on the nodes (linked or unlinked)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_equal_alignment.R:14:23:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/create_equal_alignment.R#L14) *warning:* **no visible global function definition for ‘count_hidden’**
```r
  num_hidden_nodes <- count_hidden(input_tree)
                      ^~~~~~~~~~~~
```
[R/infer_phylogeny.R:8:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/infer_phylogeny.R#L8) *style:* **Lines should not be more than 80 characters.**
```r
#' @param sub_rate substitution rate used to generate the original alignment (if available), default is 1
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/infer_phylogeny.R:32:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/infer_phylogeny.R#L32) *style:* **Lines should not be more than 80 characters.**
```r
          clock_rate_param = beautier::create_clock_rate_param(value = sub_rate),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_independent.R:1:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_independent.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' simulate a sequence assuming node substitutions are shared among the offspring
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_independent.R:13:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_independent.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
sim_dual_independent <- function(phy,
^
```
[R/sim_dual_independent.R:14:34:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_independent.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                                 Q1 = NULL,
                                 ^~
```
[R/sim_dual_independent.R:15:34:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_independent.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                                 Q2 = NULL,
                                 ^~
```
[R/sim_dual_independent.R:37:20:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_independent.R#L37) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q1)) Q1 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_independent.R:38:20:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_independent.R#L38) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q2)) Q2 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_independent.R:41:22:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_independent.R#L41) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q1)) Q1 <- Q1[lower.tri(Q1)]
                     ^~
```
[R/sim_dual_independent.R:42:22:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_independent.R#L42) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q2)) Q2 <- Q2[lower.tri(Q2)]
                     ^~
```
[R/sim_dual_independent.R:69:7:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_independent.R#L69) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(number > length(phy$tip.label)) return(TRUE)
      ^
```
[R/sim_dual_independent.R:70:7:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_independent.R#L70) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(number <= length(phy_no_extinct$tip.label)) return(TRUE)
      ^
```
[R/sim_dual_independent.R:79:5:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_independent.R#L79) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)
    ^
```
[R/sim_dual_independent.R:80:6:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_independent.R#L80) *style:* **Commented code should be removed.**
```r
   # P <- nodeSub::slow_matrix(eig_q2, node_time, rate2)
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_independent.R:92:5:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_independent.R#L92) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(tl[i], eig_q1, rate1)
    ^
```
[R/sim_dual_independent.R:93:6:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_independent.R#L93) *style:* **Commented code should be removed.**
```r
    #P <- nodeSub::slow_matrix(eig_q1, tl[i], rate1)
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_independent.R:105:7:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_independent.R#L105) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(check_to_extinct_tip(to)) {
      ^
```
[R/sim_dual_independent.R:114:42:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_independent.R#L114) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_dual_independent.R:117:34:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_independent.R#L117) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  alignment_phydat <- phyDat.DNA( as.data.frame(res, stringsAsFactors = FALSE))
                                 ^
```
[R/sim_dual_linked.R:35:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_linked.R#L35) *style:* **functions should have cyclomatic complexity of less than 15, this has 17.**
```r
make_transition_matrix <- function(mut_double) {
^
```
[R/sim_dual_linked.R:111:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_linked.R#L111) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
sim_dual_linked <- function(phy,
^
```
[R/sim_dual_linked.R:112:29:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_linked.R#L112) *style:* **Variable and function name style should be snake_case.**
```r
                            Q = NULL,
                            ^
```
[R/sim_dual_linked.R:132:19:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_linked.R#L132) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q)) Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                  ^
```
[R/sim_dual_linked.R:135:21:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_linked.R#L135) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[R/sim_dual_linked.R:171:7:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_linked.R#L171) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(number > length(phy$tip.label)) return(TRUE)
      ^
```
[R/sim_dual_linked.R:172:7:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_linked.R#L172) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(number <= length(phy_no_extinct$tip.label)) return(TRUE)
      ^
```
[R/sim_dual_linked.R:191:6:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_linked.R#L191) *style:* **Commented code should be removed.**
```r
   # total_node_subs <- total_node_subs + node_subs_1 + node_subs_2
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_linked.R:196:7:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_linked.R#L196) *style:* **Variable and function name style should be snake_case.**
```r
      P <- get_p_matrix(branch_length, eig_q, rate)
      ^
```
[R/sim_dual_linked.R:210:9:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_linked.R#L210) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(check_to_extinct_tip(offspring[i])) {
        ^
```
[R/sim_dual_linked.R:220:42:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_linked.R#L220) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_dual_parent.R:1:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_parent.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' simulate a sequence assuming node substitutions are shared among the offspring
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_parent.R:13:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_parent.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 18.**
```r
sim_dual_parent <- function(phy,
^
```
[R/sim_dual_parent.R:14:27:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_parent.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                          Q1 = NULL,
                          ^~
```
[R/sim_dual_parent.R:15:27:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_parent.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                          Q2 = NULL,
                          ^~
```
[R/sim_dual_parent.R:29:20:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_parent.R#L29) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q1)) Q1 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_parent.R:30:20:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_parent.R#L30) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q2)) Q2 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_parent.R:33:22:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_parent.R#L33) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q1)) Q1 <- Q1[lower.tri(Q1)]
                     ^~
```
[R/sim_dual_parent.R:34:22:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_parent.R#L34) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q2)) Q2 <- Q2[lower.tri(Q2)]
                     ^~
```
[R/sim_dual_parent.R:64:5:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_parent.R#L64) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)
    ^
```
[R/sim_dual_parent.R:86:7:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_parent.R#L86) *style:* **Variable and function name style should be snake_case.**
```r
      P <- get_p_matrix(branch_length, eig_q1, rate1)
      ^
```
[R/sim_dual_parent.R:105:42:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_dual_parent.R#L105) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_linked.R:12:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_linked.R#L12) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
sim_linked <- function(phy,
^
```
[R/sim_linked.R:13:24:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_linked.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
                       Q = NULL,
                       ^
```
[R/sim_linked.R:33:19:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_linked.R#L33) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q)) Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                  ^
```
[R/sim_linked.R:36:21:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_linked.R#L36) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[R/sim_linked.R:88:7:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_linked.R#L88) *style:* **Variable and function name style should be snake_case.**
```r
      P <- get_p_matrix(branch_length, eig_q, rate)
      ^
```
[R/sim_linked.R:108:42:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_linked.R#L108) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_normal.R:31:24:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_normal.R#L31) *style:* **Variable and function name style should be snake_case.**
```r
                       Q = NULL,
                       ^
```
[R/sim_normal.R:43:5:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_normal.R#L43) *style:* **Variable and function name style should be snake_case.**
```r
    Q <- rep(1, lbf * (lbf - 1) / 2)
    ^
```
[R/sim_normal.R:45:21:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_normal.R#L45) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[R/sim_normal.R:67:5:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_normal.R#L67) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(tl[i], eig, rate)
    ^
```
[R/sim_normal.R:81:40:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_normal.R#L81) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(x$tip.label, as.character( (k + 1):num_nodes))
                                       ^
```
[R/sim_unlinked_tree.R:10:5:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L10) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(class(phy) != "phylo") {
    ^
```
[R/sim_unlinked_tree.R:34:51:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L34) *style:* **Put spaces around all infix operators.**
```r
      to_add <- c(start_node, end_node, t0, t1, t0-t1)
                                                 ~^~
```
[R/sim_unlinked_tree.R:40:3:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L40) *style:* **Variable and function names should not be longer than 30 characters.**
```r
  calc_expected_hidden_nodes_per_dt <- function(t, lambda, mu) {
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:50:35:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L50) *style:* **Commas should always have a space after.**
```r
                  apply(branches[,c(3,4)], 1,
                                  ^
```
[R/sim_unlinked_tree.R:50:39:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L50) *style:* **Commas should always have a space after.**
```r
                  apply(branches[,c(3,4)], 1,
                                      ^
```
[R/sim_unlinked_tree.R:52:36:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L52) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                        lambda, mu) )
                                   ^
```
[R/sim_unlinked_tree.R:63:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L63) *style:* **Lines should not be more than 80 characters.**
```r
#' simulate a sequence assuming node substitutions are shared among the offspring
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:77:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L77) *style:* **functions should have cyclomatic complexity of less than 15, this has 43.**
```r
sim_unlinked_tree <- function(phy,
^
```
[R/sim_unlinked_tree.R:78:31:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L78) *style:* **Variable and function name style should be snake_case.**
```r
                              Q1 = NULL,
                              ^~
```
[R/sim_unlinked_tree.R:79:31:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L79) *style:* **Variable and function name style should be snake_case.**
```r
                              Q2 = NULL,
                              ^~
```
[R/sim_unlinked_tree.R:104:10:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L104) *style:* **Only use double-quotes.**
```r
    stop('lambda and mu have to be provided')
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:113:20:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L113) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q1)) Q1 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_unlinked_tree.R:114:20:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L114) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q2)) Q2 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_unlinked_tree.R:117:22:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L117) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q1)) Q1 <- Q1[lower.tri(Q1)]
                     ^~
```
[R/sim_unlinked_tree.R:118:22:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L118) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q2)) Q2 <- Q2[lower.tri(Q2)]
                     ^~
```
[R/sim_unlinked_tree.R:131:51:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L131) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  hidden_nodes <- add_hidden_nodes(phy, lambda, mu )
                                                  ^
```
[R/sim_unlinked_tree.R:146:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L146) *style:* **Lines should not be more than 80 characters.**
```r
  P_n <- nodeSub::slow_matrix(eig_q2, node_time, rate2)    #get_p_matrix(node_time, eig_q2, rate2)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:146:3:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L146) *style:* **Variable and function name style should be snake_case.**
```r
  P_n <- nodeSub::slow_matrix(eig_q2, node_time, rate2)    #get_p_matrix(node_time, eig_q2, rate2)
  ^~~
```
[R/sim_unlinked_tree.R:146:61:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L146) *style:* **Commented code should be removed.**
```r
  P_n <- nodeSub::slow_matrix(eig_q2, node_time, rate2)    #get_p_matrix(node_time, eig_q2, rate2)
                                                            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:151:7:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L151) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(number > length(phy$tip.label)) return(TRUE)
      ^
```
[R/sim_unlinked_tree.R:152:7:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L152) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(number <= length(phy_no_extinct$tip.label)) return(TRUE)
      ^
```
[R/sim_unlinked_tree.R:181:9:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L181) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( obs_hidden_nodes[i] > 0) {
        ^
```
[R/sim_unlinked_tree.R:186:10:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L186) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      for(j in 1:obs_hidden_nodes[i]) {
         ^
```
[R/sim_unlinked_tree.R:188:14:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L188) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        while(focal_t + dt >= total_bl) {
             ^
```
[R/sim_unlinked_tree.R:198:8:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L198) *style:* **Commented code should be removed.**
```r
      #P_b <- get_p_matrix(bl[1], eig_q1, rate1)
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:199:7:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L199) *style:* **Variable and function name style should be snake_case.**
```r
      P_b <-  nodeSub::slow_matrix(eig_q1, bl[1], rate1)
      ^~~
```
[R/sim_unlinked_tree.R:214:10:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L214) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      for(h in 1:obs_hidden_nodes[i]) {
         ^
```
[R/sim_unlinked_tree.R:227:10:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L227) *style:* **Commented code should be removed.**
```r
        #P_b <- get_p_matrix(bl[1], eig_q1, rate1)
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:228:9:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L228) *style:* **Variable and function name style should be snake_case.**
```r
        P_b <-  nodeSub::slow_matrix(eig_q1, bl[1], rate1)
        ^~~
```
[R/sim_unlinked_tree.R:247:8:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L247) *style:* **Commented code should be removed.**
```r
      #P <- get_p_matrix(tl[i], eig_q1, rate1)
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:248:7:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L248) *style:* **Variable and function name style should be snake_case.**
```r
      P <-  nodeSub::slow_matrix(eig_q1, tl[i], rate1)
      ^
```
[R/sim_unlinked_tree.R:263:7:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L263) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(check_to_extinct_tip(to)) {
      ^
```
[R/sim_unlinked_tree.R:270:42:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L270) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_unlinked_tree.R:273:34:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L273) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  alignment_phydat <- phyDat.DNA( as.data.frame(res, stringsAsFactors = FALSE))
                                 ^
```
[R/sim_unlinked_tree.R:282:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L282) *style:* **Lines should not be more than 80 characters.**
```r
#' simulate a sequence assuming node substitutions are shared among the offspring
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:301:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L301) *style:* **functions should have cyclomatic complexity of less than 15, this has 19.**
```r
create_equal_alignment_tree <- function(input_tree,
^
```
[R/sim_unlinked_tree.R:303:41:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L303) *style:* **Variable and function name style should be snake_case.**
```r
                                        Q1 = NULL,
                                        ^~
```
[R/sim_unlinked_tree.R:304:41:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L304) *style:* **Variable and function name style should be snake_case.**
```r
                                        Q2 = NULL,
                                        ^~
```
[R/sim_unlinked_tree.R:318:5:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L318) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(is.null(focal_alignment)) {
    ^
```
[R/sim_unlinked_tree.R:320:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L320) *style:* **Lines should not be more than 80 characters.**
```r
    focal_alignment <- nodeSub::sim_normal(input_tree, l = l, Q = Q1, bf = bf, rootseq = rootseq, rate = rate1)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:325:5:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L325) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(is.null(fraction) && is.null(node_time)) {
    ^
```
[R/sim_unlinked_tree.R:328:5:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L328) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(is.null(node_time)) {
    ^
```
[R/sim_unlinked_tree.R:329:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L329) *style:* **Lines should not be more than 80 characters.**
```r
    node_time <- nodeSub::calc_required_node_time(input_tree, s = fraction, model = model)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:331:5:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L331) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(is.null(fraction)) {
    ^
```
[R/sim_unlinked_tree.R:332:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L332) *style:* **Lines should not be more than 80 characters.**
```r
    fraction <- nodeSub::calc_fraction(input_tree, node_time = node_time, model = model)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:342:7:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L342) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(reconstruct_hidden_nodes) {
      ^
```
[R/sim_unlinked_tree.R:343:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L343) *style:* **Lines should not be more than 80 characters.**
```r
      if(model == "unlinked") proposed_alignment <- nodeSub::sim_unlinked_tree(input_tree,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:343:9:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L343) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(model == "unlinked") proposed_alignment <- nodeSub::sim_unlinked_tree(input_tree,
        ^
```
[R/sim_unlinked_tree.R:351:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L351) *style:* **Lines should not be more than 80 characters.**
```r
      if(model == "linked") stop("hidden nodes in linked model not implemented yet")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:351:9:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L351) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(model == "linked") stop("hidden nodes in linked model not implemented yet")
        ^
```
[R/sim_unlinked_tree.R:353:9:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L353) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(model == "unlinked") {
        ^
```
[R/sim_unlinked_tree.R:361:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L361) *style:* **Lines should not be more than 80 characters.**
```r
                                                            node_time = node_time)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:363:9:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L363) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(model == "linked") {
        ^
```
[R/sim_unlinked_tree.R:367:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L367) *style:* **Lines should not be more than 80 characters.**
```r
                                                       node_mut_rate_double = focal_rate ^ 2,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:382:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked_tree.R#L382) *style:* **Lines should not be more than 80 characters.**
```r
  proposed_alignment <- propose_alignments(buffer = c(), focal_rate = adjusted_rate)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked.R:1:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' simulate a sequence assuming node substitutions are shared among the offspring
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked.R:13:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 18.**
```r
sim_unlinked <- function(phy,
^
```
[R/sim_unlinked.R:14:26:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                         Q1 = NULL,
                         ^~
```
[R/sim_unlinked.R:15:26:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                         Q2 = NULL,
                         ^~
```
[R/sim_unlinked.R:37:20:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked.R#L37) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q1)) Q1 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_unlinked.R:38:20:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked.R#L38) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q2)) Q2 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_unlinked.R:41:22:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked.R#L41) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q1)) Q1 <- Q1[lower.tri(Q1)]
                     ^~
```
[R/sim_unlinked.R:42:22:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked.R#L42) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q2)) Q2 <- Q2[lower.tri(Q2)]
                     ^~
```
[R/sim_unlinked.R:71:5:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked.R#L71) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)
    ^
```
[R/sim_unlinked.R:84:5:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked.R#L84) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(tl[i], eig_q1, rate1)
    ^
```
[R/sim_unlinked.R:104:42:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked.R#L104) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_unlinked.R:107:34:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/sim_unlinked.R#L107) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  alignment_phydat <- phyDat.DNA( as.data.frame(res, stringsAsFactors = FALSE))
                                 ^
```
[R/util.R:2:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/util.R#L2) *style:* **Variable and function name style should be snake_case.**
```r
fast.table <- function(data) {
^~~~~~~~~~
```
[R/util.R:20:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/util.R#L20) *style:* **Variable and function name style should be snake_case.**
```r
phyDat.DNA <- function(data) {
^~~~~~~~~~
```
[R/util.R:35:3:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/util.R#L35) *style:* **Variable and function name style should be snake_case.**
```r
  AC <- matrix(c(c(1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 1, 1, 1),
  ^~
```
[R/util.R:108:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/util.R#L108) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
slow_matrix <- function(eig, branch_length, rate) {
^
```
[R/util.R:116:3:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/R/util.R#L116) *style:* **Variable and function name style should be snake_case.**
```r
  P <- matrix(NA, nrow = dim_size, ncol = dim_size)
  ^
```
[tests/testthat/test-dual_independent.R:10:3:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/tests/testthat/test-dual_independent.R#L10) *style:* **Variable and function name style should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-dual_parent.R:9:3:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/tests/testthat/test-dual_parent.R#L9) *style:* **Variable and function name style should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-dual-linked.R:9:3:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/tests/testthat/test-dual-linked.R#L9) *style:* **Variable and function name style should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-relative_node_time.R:22:1:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/tests/testthat/test-relative_node_time.R#L22) *style:* **Lines should not be more than 80 characters.**
```r
  obs_fraction <- ali$total_node_substitutions / (ali$total_node_substitutions + ali$total_branch_substitutions)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-sim_normal.R:20:3:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/tests/testthat/test-sim_normal.R#L20) *style:* **Variable and function name style should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-substitution.R:10:3:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/tests/testthat/test-substitution.R#L10) *style:* **Variable and function name style should be snake_case.**
```r
  Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
  ^
```
[tests/testthat/test-substitution.R:13:21:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/tests/testthat/test-substitution.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[tests/testthat/test-substitution.R:29:5:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/tests/testthat/test-substitution.R#L29) *style:* **Variable and function name style should be snake_case.**
```r
    P <- nodeSub::slow_matrix(eig = eig_q,
    ^
```
[tests/testthat/test-substitution.R:84:3:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/tests/testthat/test-substitution.R#L84) *style:* **Variable and function name style should be snake_case.**
```r
  Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
  ^
```
[tests/testthat/test-substitution.R:87:21:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/tests/testthat/test-substitution.R#L87) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[tests/testthat/test-substitution.R:94:3:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/tests/testthat/test-substitution.R#L94) *style:* **Variable and function name style should be snake_case.**
```r
  P1 <- nodeSub::slow_matrix(eig = eig_q,
  ^~
```
[tests/testthat/test-substitution.R:98:3:](https://github.com/thijsjanzen/nodeSub/blob/04033763e8f4a074a97f03f108a98e22ca2e1186/tests/testthat/test-substitution.R#L98) *style:* **Variable and function name style should be snake_case.**
```r
  P2 <- get_p_matrix(branch_length, eig_q, rate)
  ^~
```


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Instead of adding 2 such conditions, I think you should add a new abstract method to this code fix provider, with C# and VB overrides handling parent or grandparent appropriately. @CyrusNajmabadi what do you think?


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reveert


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If the above is release-specific why is this not?


BIM BIM gooooooo


bitflags! made this line look better, didn't it ? :)


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