[Circle has built](https://circleci.com/gh/cypress-io/cypress/238967) the `linux 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/3.8.4/linux-x64/circle-issue-1096-firefox-support-fb400dd163983e8d314c35e8d90e6913c07ddfba-238964/cypress.zip
    npm install https://cdn.cypress.io/beta/npm/3.8.4/circle-issue-1096-firefox-support-fb400dd163983e8d314c35e8d90e6913c07ddfba-238954/cypress.tgz


Please review


Successfully deployed to following URLs:

* https://reacnetgenerator-qlpu0rftt.now.sh
* https://reacnetgenerator.njzjz.now.sh
* https://reacnetgenerator-git-master.njzjz.now.sh


It's better to have your commit messages `concise` and in `present tense`, describing as to what are you particularly doing in that commit. Refer [Git Docs](https://git.kernel.org/pub/scm/git/git.git/tree/Documentation/SubmittingPatches?id=HEAD#n124). It will help you a lot later when you want to `revert` or `Search` for a particular commit 🙂 .


Lol thanks, it’s still WIP

[idimage001.png@01D4B30C.9D4DAD40]

DAVID FELDBAUM  |  Front End Web Developer

w: 312.800.6962 | c: 901.848.6450

david.feldbaum@icfnext.com<mailto:david.feldbaum@icfnext.com>

Chicago, IL

—

LinkedIn<https://www.linkedin.com/company/icf-next/>  |  Twitter<https://twitter.com/ICFNext>  |  ICF Next<https://www.icf.com/next>

From: Brian Shimkus <notifications@github.com>
Reply-To: Dfeldbaum/aem-fed-mixins <reply@reply.github.com>
Date: Thursday, January 30, 2020 at 1:13 PM
To: Dfeldbaum/aem-fed-mixins <aem-fed-mixins@noreply.github.com>
Cc: "Feldbaum, David" <David.Feldbaum@icfnext.com>, Author <author@noreply.github.com>
Subject: Re: [Dfeldbaum/aem-fed-mixins] added general, typography and media query mixins (f56b1af)

Nice work kiddo!

—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<https://github.com/Dfeldbaum/aem-fed-mixins/commit/f56b1af502403520917efabfa04f885436cdf248?email_source=notifications&email_token=AKBTJKJTK3LPU7ZE5Y2U2M3RAMRGNA5CNFSM4KN3MAOKYY3PNVWWK3TUL52HS4DFVVBW63LNNF2EG33NNVSW45FKMNXW23LFNZ2F62LEZYBDKSS2#commitcomment-37046874>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AKBTJKKAW3GYYQSHQWCNJNLRAMRGNANCNFSM4KN3MAOA>.


What happens if Kafka consumer.poll() itself throws an exception e.g a deserialization error
. will  Camel do exchange.setException()? If not will the pipeline stall


Successfully deployed to following URLs:

* https://og-image-builder-50vhnd24m.now.sh
* https://og-image-builder.now.sh
* https://og-image-builder.uninen.now.sh
* https://og-image-builder-git-master.uninen.now.sh


Successfully deployed to following URLs:

* https://chat-app-client-experiment-498rnxkt5.now.sh
* https://chat-app-client-experiment.now.sh
* https://chat-app-client-experiment.paradoxinversion.now.sh
* https://chat-app-client-experiment-git-master.paradoxinversion.now.sh


error_custom_meter (LipingWang) - x86_64-MacOS-10.13-clang: OK (2619 of 2620 tests passed, 6 test warnings)

Messages:\n
 * 6 tests had: RDD diffs.

Failures:\n

PTHPFixture Test Summary
 * Passed: 2
 * Failed: 1

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.96%25-yellow.png)


The code is getting more and more complicated. It could be fatal.


OK, cool.  We accept PRs. :smile:
See the CONTRIBUTING.md guide in the top-level of this repo for more information.


@JuliaRegistrator register()


Registration pull request created: [JuliaRegistries/General/8680](https://github.com/JuliaRegistries/General/pull/8680)

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 v0.0.5 -m "<description of version>" bac88c3c8aa60bd35f774c7ad6e220f1821bef67
git push origin v0.0.5
```


# Specs execution successful
:scroll: [View logs](http://bamboo.comnull)
### Plans updated

Bamboo specs have been successfully imported and the following plans have been updated.

Project | Plan | Build
---|---|---
[Test](http://bamboo.com/browse/TEST) | [Comment test](http://bamboo.com/browse/TEST-CTEST)  | :white_check_mark: [\#1](http://bamboo.com/browse/TEST-CTEST-1)
[New project](http://bamboo.com/browse/NEW) | [Disabled plan](http://bamboo.com/browse/NEW-DISABLED) **disabled** | :white_check_mark: [\#1](http://bamboo.com/browse/NEW-DISABLED-1)

### Deployments updated

Bamboo specs have been successfully imported and the following deployment projects have been updated.

|Deployment project |
----|
[Deployment test](http://bamboo.com/deploy/viewDeploymentProjectVersions.action?id=2162689)|


Successfully deployed to following URLs:

* https://guimini-c5c1zomoz.now.sh
* https://guimini.lacoludo.now.sh
* https://guimini-git-master.lacoludo.now.sh


s


sd


Successfully deployed to following URLs:

* https://now-av73b8qy5.now.sh
* https://now-rho-two.now.sh
* https://api-frameworks.zeit.sh
* https://now.zeit.now.sh
* https://now-git-master.zeit.now.sh


7640-Remove-a-wrong-error-message (lgu1234) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-UnitTestsCoverage-Debug: OK (1272 of 1272 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-43.71%25-green.png)


TeamCity Glyssen / Glyssen pull requests (64-bit) [Build *.*.883.701d75c7dba5c69d5d3adf5e3cda558580ad6e3f](https://build.palaso.org/viewLog.html?buildId=180150&buildTypeId=Glyssen_GlyssenPullRequests64bitWithSilNuGetPackages) outcome was **SUCCESS**
Summary: Tests passed: 2414, ignored: 18 Build time: 00:10:30


Deployment failed with the following error:

~~~
ENOENT: no such file or directory, stat '/tmp/bC3iVuB9MEWtnWxCNc6560ZP/repo/node/bin/create-react-app'
~~~


Successfully deployed to following URLs:

* https://omdb-app-c6ze1k44q.now.sh
* https://omdb-app.now.sh
* https://omdb.willcodefor.beer
* https://omdb-app.believer.now.sh
* https://omdb-app-git-master.believer.now.sh


This fixes a buffer overlow.
renderer_vk uses an array of write descriptor sets, sized as MAX_TEXTURE_SAMPLERS.
It then proceeds to fill up this array.
After which, two more entries are written: uniform bindings for vs and fs, causing it to overrun by 2 elements.


Copy of this build can be found at
https://www.mewbuilds.com/build/931e5c3db04730db5002f051cb3d214f554d3368/index.html
                       https://www.cloudflare-ipfs.com/ipfs/QmamJnPFnZoFxDCVpELjhTCF5nDq55CTfEtY3ZZxpfrpi5
                       Virus Total analysis
                       https://www.virustotal.com/file/22f8f94bb4ae27fe77950d511d8f59d0a9a14db9be5eed7dd4ca559f9377a21f/analysis/1580414791/


Successfully deployed to following URLs:

* https://chat-app-client-experiment-kvb6duu04.now.sh
* https://chat-app-client-experiment.now.sh
* https://chat-app-client-experiment.paradoxinversion.now.sh
* https://chat-app-client-experiment-git-master.paradoxinversion.now.sh


Successfully deployed to following URLs:

* https://me-hidu12uw4.now.sh
* https://cevr.ca
* https://cevr.now.sh
* https://me.cevr.now.sh
* https://me-git-master.cevr.now.sh


Deployment failed with the following error:

~~~
ENOENT: no such file or directory, stat '/tmp/qh9UzWBLbFICXiCmrokqNZes/repo/node/bin/create-react-app'
~~~


Successfully deployed to following URLs:

* https://contract-generator-kzefpllbo.now.sh
* https://contract.vacuumlabs.com
* https://contract-generator.vacuumlabs1.now.sh
* https://contract-generator-git-master.vacuumlabs1.now.sh


numbers < 0*


@JuliaRegistrator register


Registration pull request created: [JuliaRegistries/General/8684](https://github.com/JuliaRegistries/General/pull/8684)

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 v0.1.0 -m "<description of version>" fba649a9c97e252635beffa4f05d51613012b7d3
git push origin v0.1.0
```


Deployment failed with the following error:

~~~
Configuring `regions` is not necessary for Static Files. Deploying Serverless Functions to multiple regions is restricted to paid plans. Upgrade here: https://zeit.co/account/billing.
~~~


test


✅ Device tests passed on TvOS on [Azure DevOps](https://dev.azure.com/devdiv/DevDiv/_build/index?buildId=3426736)(TvOS): [Html Report](http://xamarin-storage/jenkins/xamarin-macios/pull-request/f08c4640e96362d351c39b72921b9e894aa23e38/3426736/device-tests/jenkins-results/tests/index.html) ✅

# :tada: All 142 tests passed :tada:


Cool!


Public score -13.46, Private score -23.02


Successfully deployed to following URLs:

* https://surreal-jfc4vb9ek.now.sh
* https://surreal.now.sh
* https://surreal.af
* https://surreal.benjamintanghz.now.sh
* https://surreal-git-master.benjamintanghz.now.sh


Successfully deployed to following URLs:

* https://blocks-93a6qvtn5.now.sh
* https://blocks-ui.com
* https://blocks.blocks-ui.now.sh
* https://blocks-git-master.blocks-ui.now.sh


If it is already NULL, it is a redundant NULL set, but this is not a bug.


Successfully deployed to following URLs:

* https://ssrtodo-11genlm3v.now.sh
* https://ssrtodo.now.sh
* https://ssrtodo.jnovaxer.now.sh
* https://ssrtodo-git-master.jnovaxer.now.sh


![](https://github.trello.services/images/mini-trello-icon.png) [google analytics setup](https://trello.com/c/eOwLdWKq/12-google-analytics-setup)


Gotta celebrate even the little victories at this point, after all.


docs excluded from *app* folder


Niño un respeto con el trabajo de los demás y su persona! ,yo no se a que entro el compañero a su discord ni me interesa, seria para preguntar algo xq se compro un tv box!, pero bueno a mi lo que me importa es que este hablando de mi y de mi otro compañero que somos los 2 que programamos y hacemos lo que podemos ya que tampoco somos expertos y otro compi haciendo imágenes pre-configuradas,los otros dos por desgracia no pueden hacer nada ya sea xq no tienen tiempo o no saben mucho. Por ejemplo que usted solo tenga forks en sus repos de github y tenga poca cosa creada por usted desde cero por no decir nada... no quiere decir que emuelec sea coreELEC con la imagen de intro cambiada ,el emulationstation de batocera y blablabla.... Yo no lo e probado xq no tengo tv box pero por lo que dice la gente esta de lujo ,bien por ti! Pero eso antes de volver a criticar dale un ojo a mi github pera que sepas de lo que hablas. Un saludo y espero no tener mas malos royos de estos ,no tengo tiempo ;-) prefiero perder lo haciendo algo que me guste!


Successfully deployed to following URLs:

* https://blocks-2phnzxp7p.now.sh
* https://blocks-ui.com
* https://blocks.blocks-ui.now.sh
* https://blocks-git-master.blocks-ui.now.sh


Related to this issue: https://github.com/Xruptor/BagSync/issues/97


170926542_Issue7681 (Unknown) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-IntegrationCoverage-Debug: OK (677 of 678 tests passed, 0 test warnings)

Failures:\n

integration Test Summary
 * Passed: 677
 * Timeout: 1

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.85%25-yellow.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-68.33%25-green.png)


# Specs execution successful
:scroll: [View logs](http://bamboo.comnull)
### Plans updated

Bamboo specs have been successfully imported and the following plans have been updated.

Project | Plan | Build
---|---|---
[Test](http://bamboo.com/browse/TEST) | [Comment test](http://bamboo.com/browse/TEST-CTEST)  | :white_check_mark: [\#1](http://bamboo.com/browse/TEST-CTEST-1)
[New project](http://bamboo.com/browse/NEW) | [Disabled plan](http://bamboo.com/browse/NEW-DISABLED) **disabled** | :white_check_mark: [\#1](http://bamboo.com/browse/NEW-DISABLED-1)

### Deployments updated

Bamboo specs have been successfully imported and the following deployment projects have been updated.

|Deployment project |
----|
[Deployment test](http://bamboo.com/deploy/viewDeploymentProjectVersions.action?id=2162689)|


Successfully deployed to following URLs:

* https://github-e2e-tests-dev-alias-v2-with-alias-3ilr4e6ga.now.sh
* https://z-github-e2e-tests-dev-alias-v2-with-alias.now.sh
* https://github-e2e-tests-dev-alias-v2-with-alias.zeit-github-test-dev1.now.sh
* https://github-e2e-tests-dev-alias-v2-with-alias-git-master.zeit-github-test-dev1.now.sh


Successfully deployed to following URLs:

* https://github-e2e-tests-dev-alias-v2-without-alias-1z4xjvi2l.now.sh
* https://github-e2e-tests-dev-alias-v2-without-alias.zeit-github-test-dev1.now.sh
* https://github-e2e-tests-dev-alias-v2-without-alias-git-master.zeit-github-test-dev1.now.sh


Successfully deployed to following URLs:

* https://ccc-dht0n86y8.now.sh
* https://ccc.zeit-github-test-dev1.now.sh
* https://ccc-git-master.zeit-github-test-dev1.now.sh


Sube el código hola mundo


Deployment failed with the following error:

~~~
You defined 1 build that did not match any source files (please ensure they are NOT defined in .nowignore):
~~~


Successfully deployed to following URLs:

* https://github-e2e-tests-dev-alias-v1-with-alias-gqt7a4sp6.now.sh
* https://z-github-e2e-tests-dev-only.now.sh
* https://github-e2e-tests-dev-alias-v1-with-alias-git-master.zeit-github-test-dev1.now.sh


Failed to assign a domain to your deployment due to the following error:

~~~
The domain zm1icsjocn.com is not verfied and cannot be used as an alias.
~~~

([Learn more](http://localhost:3000/zeit-github-test-dev/github-e2e-test-dev-domain-issues/ld4lwplu5) or [visit](https://github-e2e-test-dev-domain-issues-ld4lwplu5.now.sh) the non-aliased deployment)


ok, I understood differently from the paper. Still, its impressive speed. Do you guys use some custom architecture for this? Can you share any details ?


"process_hcoh" is not extra. Please bring it back. Thanks


```if (N > 1 ) for (auto i = N - 2; i--; ) if (fullpath[i] == '/' || fullpath[i] == '\\') return &fullpath[i+1];```


Successfully deployed to following URLs:

* https://beam-invoice-kanalmiks.now.sh
* https://beam-invoice.now.sh
* https://beam-invoice.clementdlc.now.sh
* https://beam-invoice-git-master.clementdlc.now.sh


Successfully deployed to following URLs:

* https://weather-app-2-0-q1vi8m4ck.now.sh
* https://weather-app-2-0.aleksassincreed.now.sh
* https://weather-app-2-0-git-master.aleksassincreed.now.sh


> 忘记上来说下了，仔细看了编译信息，发现编译V2RAY时一个链接失败（GO），编译不成功是墙加高造成的，全局翻就编译成功了。

你可以试试这个 [dev](https://github.com/Mattraks/lede/tree/dev)
coolsnowwolf/lede#2855


Deployment failed with the following error:

~~~
Configuring `regions` is not necessary for Static Files. Deploying Serverless Functions to multiple regions is restricted to paid plans. Upgrade here: https://zeit.co/account/billing.
~~~


Can we just create one file? What I did in the past in Rattlesnake is to let all processors hold a xml doc and they can append node and attributes separately. When outputting, all non-masters will send the date to master under their own node and then empty their docs, then master proceed to write the file. In this way, most operations are in memory and only master does the file writing and only one single file is created. If we have hundreds of processors or more, this can make the output much cleaner. The output object in Rattlesnake is called XMLOut.


wen


*unlock


*goto out


> Hi, how would I change direction / language after editor is ready? say by clicking a button (switching between laguages)

There's no way to do that at this moment. Destroy the editor and re-create it with a different language configuration.

FYI: Both the BiDi support and the ["text part language"](https://ckeditor.com/docs/ckeditor4/latest/examples/language.html) (like in v4) are on our roadmap but without strong ETAs.


Successfully deployed to following URLs:

* https://leeyawnz-4y03opruf.now.sh
* https://leeyawnz.now.sh
* https://leeyawnz.leeyawnz.now.sh
* https://leeyawnz-git-master.leeyawnz.now.sh


This is the from the December 8th service change.


🔥 Device tests completed (Failed) on TvOS on [Azure DevOps](https://dev.azure.com/devdiv/DevDiv/_build/index?buildId=3429140)(TvOS): [Html Report](http://xamarin-storage/jenkins/xamarin-macios/mono-2019-12/b660546b2f601af89769b29bac28598009dbbc56/3429140/device-tests/jenkins-results/tests/index.html) 🔥

# Test results

<details>
<summary>72 tests failed, 70 tests passed.</summary>

## Failed tests

 * [NUnit] Mono BCL tests group 1/tvOS - device/Debug: Failed
 * [NUnit] Mono BCL tests group 2/tvOS - device/Debug: Failed
 * [xUnit] Mono BCL tests group 3/tvOS - device/Debug: Failed
 * [xUnit] Mono BCL tests group 4/tvOS - device/Debug: Failed
 * [xUnit] Mono BCL tests group 5/tvOS - device/Debug: Failed
 * mscorlib Part 1/tvOS - device/Debug: Failed
 * mscorlib Part 2/tvOS - device/Debug: Failed
 * [xUnit] Mono SystemCoreXunit Part 1/tvOS - device/Debug: Failed
 * [xUnit] Mono SystemCoreXunit Part 2/tvOS - device/Debug: Failed
 * [xUnit] Mono SystemXunit/tvOS - device/Debug: Failed
 * [NUnit] Mono BCL tests group 1/tvOS - device/AssemblyBuildTarget: dylib (debug): Failed
 * [NUnit] Mono BCL tests group 1/tvOS - device/AssemblyBuildTarget: SDK framework (debug): Failed
 * [NUnit] Mono BCL tests group 1/tvOS - device/AssemblyBuildTarget: dylib (debug, profiling): Failed
 * [NUnit] Mono BCL tests group 1/tvOS - device/AssemblyBuildTarget: SDK framework (debug, profiling): Failed
 * [NUnit] Mono BCL tests group 1/tvOS - device/Release: Failed (MT1032: This application executable might be too large (921 MB) to execute on device. If bitcode was enabled you might want to disable it for development, it is only required to submit applications to Apple.)
 * [NUnit] Mono BCL tests group 1/tvOS - device/AssemblyBuildTarget: SDK framework (release): Failed
 * [NUnit] Mono BCL tests group 2/tvOS - device/AssemblyBuildTarget: dylib (debug): Failed
 * [NUnit] Mono BCL tests group 2/tvOS - device/AssemblyBuildTarget: SDK framework (debug): Failed
 * [NUnit] Mono BCL tests group 2/tvOS - device/AssemblyBuildTarget: dylib (debug, profiling): Failed
 * [NUnit] Mono BCL tests group 2/tvOS - device/AssemblyBuildTarget: SDK framework (debug, profiling): Failed
 * [NUnit] Mono BCL tests group 2/tvOS - device/Release: Failed (MT1032: This application executable might be too large (1098 MB) to execute on device. If bitcode was enabled you might want to disable it for development, it is only required to submit applications to Apple.)
 * [NUnit] Mono BCL tests group 2/tvOS - device/AssemblyBuildTarget: SDK framework (release): Failed
 * [xUnit] Mono BCL tests group 3/tvOS - device/AssemblyBuildTarget: dylib (debug): Failed
 * [xUnit] Mono BCL tests group 3/tvOS - device/AssemblyBuildTarget: SDK framework (debug): Failed
 * [xUnit] Mono BCL tests group 3/tvOS - device/AssemblyBuildTarget: dylib (debug, profiling): Failed
 * [xUnit] Mono BCL tests group 3/tvOS - device/AssemblyBuildTarget: SDK framework (debug, profiling): Failed
 * [xUnit] Mono BCL tests group 3/tvOS - device/Release: Failed (MT1032: This application executable might be too large (762 MB) to execute on device. If bitcode was enabled you might want to disable it for development, it is only required to submit applications to Apple.)
 * [xUnit] Mono BCL tests group 3/tvOS - device/AssemblyBuildTarget: SDK framework (release): Failed
 * [xUnit] Mono BCL tests group 4/tvOS - device/AssemblyBuildTarget: dylib (debug): Failed
 * [xUnit] Mono BCL tests group 4/tvOS - device/AssemblyBuildTarget: SDK framework (debug): Failed
 * [xUnit] Mono BCL tests group 4/tvOS - device/AssemblyBuildTarget: dylib (debug, profiling): Failed
 * [xUnit] Mono BCL tests group 4/tvOS - device/AssemblyBuildTarget: SDK framework (debug, profiling): Failed
 * [xUnit] Mono BCL tests group 4/tvOS - device/Release: Failed (MT1032: This application executable might be too large (638 MB) to execute on device. If bitcode was enabled you might want to disable it for development, it is only required to submit applications to Apple.)
 * [xUnit] Mono BCL tests group 4/tvOS - device/AssemblyBuildTarget: SDK framework (release): Failed
 * [xUnit] Mono BCL tests group 5/tvOS - device/AssemblyBuildTarget: dylib (debug): Failed
 * [xUnit] Mono BCL tests group 5/tvOS - device/AssemblyBuildTarget: SDK framework (debug): Failed
 * [xUnit] Mono BCL tests group 5/tvOS - device/AssemblyBuildTarget: dylib (debug, profiling): Failed
 * [xUnit] Mono BCL tests group 5/tvOS - device/AssemblyBuildTarget: SDK framework (debug, profiling): Failed
 * [xUnit] Mono BCL tests group 5/tvOS - device/Release: Failed
 * [xUnit] Mono BCL tests group 5/tvOS - device/AssemblyBuildTarget: SDK framework (release): Failed
 * mscorlib Part 1/tvOS - device/AssemblyBuildTarget: dylib (debug): Failed
 * mscorlib Part 1/tvOS - device/AssemblyBuildTarget: SDK framework (debug): Failed
 * mscorlib Part 1/tvOS - device/AssemblyBuildTarget: dylib (debug, profiling): Failed
 * mscorlib Part 1/tvOS - device/AssemblyBuildTarget: SDK framework (debug, profiling): Failed
 * mscorlib Part 1/tvOS - device/Release: Failed (MT1032: This application executable might be too large (728 MB) to execute on device. If bitcode was enabled you might want to disable it for development, it is only required to submit applications to Apple.)
 * mscorlib Part 1/tvOS - device/AssemblyBuildTarget: SDK framework (release): Failed
 * mscorlib Part 1/tvOS - device/Debug: SGenConc: Failed
 * mscorlib Part 2/tvOS - device/AssemblyBuildTarget: dylib (debug): Failed
 * mscorlib Part 2/tvOS - device/AssemblyBuildTarget: SDK framework (debug): Failed
 * mscorlib Part 2/tvOS - device/AssemblyBuildTarget: dylib (debug, profiling): Failed
 * mscorlib Part 2/tvOS - device/AssemblyBuildTarget: SDK framework (debug, profiling): Failed
 * mscorlib Part 2/tvOS - device/Release: Failed (MT1032: This application executable might be too large (798 MB) to execute on device. If bitcode was enabled you might want to disable it for development, it is only required to submit applications to Apple.)
 * mscorlib Part 2/tvOS - device/AssemblyBuildTarget: SDK framework (release): Failed
 * mscorlib Part 2/tvOS - device/Debug: SGenConc: Failed
 * [xUnit] Mono SystemCoreXunit Part 1/tvOS - device/AssemblyBuildTarget: dylib (debug): Failed
 * [xUnit] Mono SystemCoreXunit Part 1/tvOS - device/AssemblyBuildTarget: SDK framework (debug): Failed
 * [xUnit] Mono SystemCoreXunit Part 1/tvOS - device/AssemblyBuildTarget: dylib (debug, profiling): Failed
 * [xUnit] Mono SystemCoreXunit Part 1/tvOS - device/AssemblyBuildTarget: SDK framework (debug, profiling): Failed
 * [xUnit] Mono SystemCoreXunit Part 1/tvOS - device/Release: Failed (MT1032: This application executable might be too large (720 MB) to execute on device. If bitcode was enabled you might want to disable it for development, it is only required to submit applications to Apple.)
 * [xUnit] Mono SystemCoreXunit Part 1/tvOS - device/AssemblyBuildTarget: SDK framework (release): Failed
 * [xUnit] Mono SystemCoreXunit Part 2/tvOS - device/AssemblyBuildTarget: dylib (debug): Failed
 * [xUnit] Mono SystemCoreXunit Part 2/tvOS - device/AssemblyBuildTarget: SDK framework (debug): Failed
 * [xUnit] Mono SystemCoreXunit Part 2/tvOS - device/AssemblyBuildTarget: dylib (debug, profiling): Failed
 * [xUnit] Mono SystemCoreXunit Part 2/tvOS - device/AssemblyBuildTarget: SDK framework (debug, profiling): Failed
 * [xUnit] Mono SystemCoreXunit Part 2/tvOS - device/Release: Failed (MT1032: This application executable might be too large (792 MB) to execute on device. If bitcode was enabled you might want to disable it for development, it is only required to submit applications to Apple.)
 * [xUnit] Mono SystemCoreXunit Part 2/tvOS - device/AssemblyBuildTarget: SDK framework (release): Failed
 * [xUnit] Mono SystemXunit/tvOS - device/AssemblyBuildTarget: dylib (debug): Failed
 * [xUnit] Mono SystemXunit/tvOS - device/AssemblyBuildTarget: SDK framework (debug): Failed
 * [xUnit] Mono SystemXunit/tvOS - device/AssemblyBuildTarget: dylib (debug, profiling): Failed
 * [xUnit] Mono SystemXunit/tvOS - device/AssemblyBuildTarget: SDK framework (debug, profiling): Failed
 * [xUnit] Mono SystemXunit/tvOS - device/Release: Failed (MT1032: This application executable might be too large (533 MB) to execute on device. If bitcode was enabled you might want to disable it for development, it is only required to submit applications to Apple.)
 * [xUnit] Mono SystemXunit/tvOS - device/AssemblyBuildTarget: SDK framework (release): Failed
</details>


@cyberorg This implementation only brings the keyboard on the screen. What is being typed using the tablet does not fill the field? Assuming you have tested this at your end, what needs to be done differently by me.


TeamCity MAS / MAS [Build 1.1.0.801-MAS-150-WeeklyEmailN](https://teamcity.nice.org.uk/viewLog.html?buildId=65279&buildTypeId=Mas_Mas) outcome was **SUCCESS**
Summary: Tests passed: 43 Build time: 00:01:28


Fixed at https://github.com/openmrs/openmrs-module-appui/commit/3c5a6a0203e48431ac2f016748248006a29b33dc


Successfully deployed to following URLs:

* https://relational-playground-k0ps5ts83.now.sh
* https://relationalplayground.com
* https://relational-playground.michaelmior.now.sh
* https://relational-playground-git-master.michaelmior.now.sh


Failed to assign a domain to your deployment due to the following error:

~~~
We could not create a certificate for hackinthenorth.com because HTTP pretest failed. Please ensure the CNAME for hackinthenorth.com points to "alias.zeit.co". You can find more information at https://err.sh/now-cli/cant-solve-challenge.
~~~

([Learn more](https://zeit.co/hackinthenorth/hackinthenorthgithubio/l6s1ls2r7) or [visit](https://hackinthenorthgithubio-l6s1ls2r7.now.sh) the non-aliased deployment)


That's because I was testing those methods in the console. So, I put that.


Ah, ok. Thank you for the explanation!


[R/calc_K.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calc_K.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the average number of junctions after an infinite number of generations, provided information on the initial heterozygosity, population size and the number of generations.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_K.R:6:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calc_K.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_K.R:11:20:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calc_K.R#L11) *style:* **Variable and function name style should be snake_case.**
```r
calc_k <- function(N = Inf,
                   ^
```
[R/calc_K.R:12:20:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calc_K.R#L12) *style:* **Variable and function name style should be snake_case.**
```r
                   R = Inf,
                   ^
```
[R/calc_K.R:13:20:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calc_K.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
                   H_0 = 0.5,
                   ^~~
```
[R/calc_K.R:14:20:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calc_K.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                   C = 1) {
                   ^
```
[R/calc_K.R:16:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calc_K.R#L16) *style:* **Variable and function name style should be snake_case.**
```r
  K <- H_0 * C * 2 * N * R / (2 * N * C + R)
  ^
```
[R/calc_K.R:19:5:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calc_K.R#L19) *style:* **Variable and function name style should be snake_case.**
```r
    K <- H_0 * R
    ^
```
[R/calc_K.R:23:5:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calc_K.R#L23) *style:* **Variable and function name style should be snake_case.**
```r
    K <- H_0 * C * 2 * N
    ^
```
[R/calc_K.R:27:5:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calc_K.R#L27) *style:* **Variable and function name style should be snake_case.**
```r
    K <- Inf
    ^
```
[R/calculate_error.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_error.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the error in the estimate of the onset of hybridisation, following Equations 3 & 4 in the Supplementary information of Janzen et al. 2018.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_error.R:7:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_error.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_error.R:9:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_error.R#L9) *style:* **Lines should not be more than 80 characters.**
```r
#' @param relative Boolean flag, if TRUE: return the relative error, if FALSE: return error in generations
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_error.R:15:24:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_error.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
time_error <- function(J = NA,
                       ^
```
[R/calculate_error.R:16:24:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_error.R#L16) *style:* **Variable and function name style should be snake_case.**
```r
                       N = Inf,
                       ^
```
[R/calculate_error.R:17:24:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_error.R#L17) *style:* **Variable and function name style should be snake_case.**
```r
                       R = Inf,
                       ^
```
[R/calculate_error.R:18:24:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_error.R#L18) *style:* **Variable and function name style should be snake_case.**
```r
                       H_0 = 0.5,
                       ^~~
```
[R/calculate_error.R:19:24:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_error.R#L19) *style:* **Variable and function name style should be snake_case.**
```r
                       C = 1,
                       ^
```
[R/calculate_error.R:24:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_error.R#L24) *style:* **Variable and function name style should be snake_case.**
```r
  K <- junctions::calc_k(N, R, H_0, C)
  ^
```
[R/calculate_error.R:30:7:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_error.R#L30) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( relative) return(  error)
      ^
```
[R/calculate_error.R:30:25:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_error.R#L30) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if ( relative) return(  error)
                        ^
```
[R/calculate_MAT.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_MAT.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Function that calculates the maximum time after hybridization after which the number of junctions can still be reliably used to estimate the onset of hybridization. This is following equation 15 in Janzen et al. 2018.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_MAT.R:6:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_MAT.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_MAT.R:12:27:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_MAT.R#L12) *style:* **Variable and function name style should be snake_case.**
```r
calculate_mat <- function(N = Inf,
                          ^
```
[R/calculate_MAT.R:13:27:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_MAT.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
                          R = Inf,
                          ^
```
[R/calculate_MAT.R:14:27:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_MAT.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                          H_0 = 0.5,
                          ^~~
```
[R/calculate_MAT.R:15:27:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_MAT.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                          C = 1) {
                          ^
```
[R/calculate_MAT.R:20:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_MAT.R#L20) *style:* **Variable and function name style should be snake_case.**
```r
  K <- junctions::calc_k(N, R, H_0, C)
  ^
```
[R/calculate_time.R:1:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_time.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' Estimate the time since the onset of hybridization, using the number of junctions
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_time.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_time.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Estimate the time since the onset of hybridization, following equation 14 in Janzen et al. 2018
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_time.R:7:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_time.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_time.R:11:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_time.R#L11) *style:* **Lines should not be more than 80 characters.**
```r
#' estimate_time(J = J, N = 100, R = 1000, H_0 = 0.5, C = 1)  # should be 200 again
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calculate_time.R:13:27:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_time.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
estimate_time <- function(J = NA,
                          ^
```
[R/calculate_time.R:14:27:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_time.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                          N = Inf,
                          ^
```
[R/calculate_time.R:15:27:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_time.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                          R = Inf,
                          ^
```
[R/calculate_time.R:16:27:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_time.R#L16) *style:* **Variable and function name style should be snake_case.**
```r
                          H_0 = 0.5,
                          ^~~
```
[R/calculate_time.R:17:27:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_time.R#L17) *style:* **Variable and function name style should be snake_case.**
```r
                          C = 1) {
                          ^
```
[R/calculate_time.R:28:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/calculate_time.R#L28) *style:* **Variable and function name style should be snake_case.**
```r
  K <- junctions::calc_k(N, R, H_0, C)
  ^
```
[R/estimate_time_markers.R:1:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_markers.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' Estimate the time since the onset of hybridization, using the observed number of junctions, taking into account the distribution of markers
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_markers.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Estimate the time since the onset of hybridization, following equation 1 in Janzen et al. unpublished
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:6:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_markers.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param marker_distribution A vector containing the position of all markers in Morgan.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:7:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_markers.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param lower_lim lower limit of the optimization algorithm. Increase if the expected admixture time is relatively ancient
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:8:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_markers.R#L8) *style:* **Lines should not be more than 80 characters.**
```r
#' @param upper_lim upper limit of hte optimization algorithm. If set too large, recent admixture events can be overlooked - best to set as low as possible.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:12:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_markers.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
#' J <- number_of_junctions_markers(N = 100, H_0 = 0.5, t = 200, marker_distribution = markers)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_markers.R:18:35:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_markers.R#L18) *style:* **Variable and function name style should be snake_case.**
```r
estimate_time_markers <- function(J = NA,
                                  ^
```
[R/estimate_time_markers.R:19:35:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_markers.R#L19) *style:* **Variable and function name style should be snake_case.**
```r
                                  N = Inf,
                                  ^
```
[R/estimate_time_markers.R:20:35:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_markers.R#L20) *style:* **Variable and function name style should be snake_case.**
```r
                                  H_0 = 0.5,
                                  ^~~
```
[R/estimate_time_markers.R:34:71:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_markers.R#L34) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  fitted <- stats::optimize(to_fit, interval = c(lower_lim, upper_lim) )
                                                                      ^
```
[R/estimate_time_phased.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L2) *style:* **functions should have cyclomatic complexity of less than 15, this has 49.**
```r
get_prob_from_matrix_phased <- function(left, right, p, P) {
^
```
[R/estimate_time_phased.R:2:57:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L2) *style:* **Variable and function name style should be snake_case.**
```r
get_prob_from_matrix_phased <- function(left, right, p, P) {
                                                        ^
```
[R/estimate_time_phased.R:108:19:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L108) *warning:* **no visible global function definition for ‘single_state’**
```r
  seven_states <- single_state(local_time, N = pop_size, d = di)
                  ^~~~~~~~~~~~
```
[R/estimate_time_phased.R:122:23:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L122) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                      ^
```
[R/estimate_time_phased.R:122:32:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L122) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                               ^
```
[R/estimate_time_phased.R:125:10:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L125) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  return( log(focal_prob))
         ^
```
[R/estimate_time_phased.R:129:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L129) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_cond_prob_vector_phased_inf <- function(info_vector,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:137:19:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L137) *warning:* **no visible global function definition for ‘single_state_inf’**
```r
  seven_states <- single_state_inf(local_time, d = di)
                  ^~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:151:23:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L151) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                      ^
```
[R/estimate_time_phased.R:151:32:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L151) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                               ^
```
[R/estimate_time_phased.R:154:10:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L154) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  return( log(focal_prob))
         ^
```
[R/estimate_time_phased.R:158:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L158) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculates the time since admixture, given unphased ancestry data.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:159:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L159) *style:* **Lines should not be more than 80 characters.**
```r
#' @param local_anc_matrix Local_anc can be provided as either matrix with two columns, where the first column represents ancestry on chromosome 1, and the second column represents ancestry on chromosome 2. Ancestry labels used should be [0, 1], where 0 indicates the first ancestor, and 1 indicates the second ancestor. Alternatively, the user can provide a vector using labels indicating whether at the specific marker, the focal individual is homozygous for the first ancestor (label = 1), homozygous for the second ancestor (label = 2), heterozygous [0,1] (label = 3) or heterozygous [1, 0] (label = 4).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:163:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L163) *style:* **Lines should not be more than 80 characters.**
```r
#' @param lower_lim lower limit of the optimization algorithm. Increase if the expected admixture time is relatively ancient
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:164:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L164) *style:* **Lines should not be more than 80 characters.**
```r
#' @param upper_lim upper limit of hte optimization algorithm. If set too large, recent admixture events can be overlooked - best to set as low as possible.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:165:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L165) *style:* **Lines should not be more than 80 characters.**
```r
#' @param optim_pop_size If TRUE, population size is also optimized. Starting point of the optimizaton will then be on the given population size, and half the maximum time.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:200:11:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L200) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (sum( labels %in% 1:4) != length(labels)) {
          ^
```
[R/estimate_time_phased.R:207:58:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L207) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[R/estimate_time_phased.R:257:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L257) *style:* **Lines should not be more than 80 characters.**
```r
#' estimates the time since admixture, given unphased ancestry data and assuming infinite population size.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:258:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L258) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculates the time since admixture, given unphased ancestry data.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:259:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L259) *style:* **Lines should not be more than 80 characters.**
```r
#' @param local_anc_matrix Local_anc can be provided as either matrix with two columns, where the first column represents ancestry on chromosome 1, and the second column represents ancestry on chromosome 2. Ancestry labels used should be [0, 1], where 0 indicates the first ancestor, and 1 indicates the second ancestor. Alternatively, the user can provide a vector using labels indicating whether at the specific marker, the focal individual is homozygous for the first ancestor (label = 1), homozygous for the second ancestor (label = 2), heterozygous [0,1] (label = 3) or heterozygous [1, 0] (label = 4).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:262:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L262) *style:* **Lines should not be more than 80 characters.**
```r
#' @param lower_lim lower limit of the optimization algorithm. Increase if the expected admixture time is relatively ancient
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:263:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L263) *style:* **Lines should not be more than 80 characters.**
```r
#' @param upper_lim upper limit of hte optimization algorithm. If set too large, recent admixture events can be overlooked - best to set as low as possible.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/estimate_time_phased.R:296:11:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L296) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (sum( labels %in% 1:4) != length(labels)) {
          ^
```
[R/estimate_time_phased.R:303:58:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_phased.R#L303) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[R/estimate_time_unphased.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_unphased.R#L2) *style:* **functions should have cyclomatic complexity of less than 15, this has 28.**
```r
get_prob_from_matrix <- function(left, right, p, P) {
^
```
[R/estimate_time_unphased.R:2:50:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_unphased.R#L2) *style:* **Variable and function name style should be snake_case.**
```r
get_prob_from_matrix <- function(left, right, p, P) {
                                                 ^
```
[R/estimate_time_unphased.R:12:24:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_unphased.R#L12) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    prob <- (p ^ 2) * ( P[1] + P[4] + P[7] ) +
                       ^
```
[R/estimate_time_unphased.R:12:43:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_unphased.R#L12) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    prob <- (p ^ 2) * ( P[1] + P[4] + P[7] ) +
                                          ^
```
[R/estimate_time_unphased.R:18:22:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_unphased.R#L18) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    prob <- p * q * ( p * q * P[3] +
                     ^
```
[R/estimate_time_unphased.R:35:24:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_unphased.R#L35) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    prob <- (q ^ 2) * ( P[1] + P[4] + P[7]) +
                       ^
```
[R/estimate_time_unphased.R:88:19:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_unphased.R#L88) *warning:* **no visible global function definition for ‘single_state’**
```r
  seven_states <- single_state(local_time, N = pop_size, d = di)
                  ^~~~~~~~~~~~
```
[R/estimate_time_unphased.R:102:23:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_unphased.R#L102) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                      ^
```
[R/estimate_time_unphased.R:102:32:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_unphased.R#L102) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    final_prob <- log( rel_prob )
                               ^
```
[R/estimate_time_unphased.R:105:12:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_unphased.R#L105) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    return( log(focal_prob))
           ^
```
[R/estimate_time_unphased.R:160:11:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_unphased.R#L160) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (sum( labels %in% 1:3) != length(labels)) {
          ^
```
[R/estimate_time_unphased.R:167:58:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/estimate_time_unphased.R#L167) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[R/number_of_junctions_backcross.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions_backcross.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the expected number of junctions after t generations, in a backcrossing mating scheme.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_backcross.R:4:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions_backcross.R#L4) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_backcross.R:10:43:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions_backcross.R#L10) *style:* **Variable and function name style should be snake_case.**
```r
number_of_junctions_backcross <- function(H_0 = 0.5,
                                          ^~~
```
[R/number_of_junctions_backcross.R:11:43:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions_backcross.R#L11) *style:* **Variable and function name style should be snake_case.**
```r
                                          C = 1,
                                          ^
```
[R/number_of_junctions_di.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions_di.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' Calculate the expected number of junctions between two markers separated by a given amount of recombination
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_di.R:3:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions_di.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the expected number of junctions after t generations, provided information on the initial heterozygosity, population size, the number of generations since the onset of admixture and the distance between two markers.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_di.R:12:36:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions_di.R#L12) *style:* **Variable and function name style should be snake_case.**
```r
number_of_junctions_di <- function(N = Inf,
                                   ^
```
[R/number_of_junctions_di.R:13:36:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions_di.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
                                   H_0 = 0.5,
                                   ^~~
```
[R/number_of_junctions_markers.R:1:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions_markers.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' Calculate the expected total number of junctions in a chromosome, given the distribution of markers
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_markers.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions_markers.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the expected number of junctions after t generations, provided information on the initial heterozygosity, population size, the number of generations since the onset of admixture and the distribution of markers.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_markers.R:6:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions_markers.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param marker_distribution A vector containing the position of all markers in Morgan.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions_markers.R:20:41:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions_markers.R#L20) *style:* **Variable and function name style should be snake_case.**
```r
number_of_junctions_markers <- function(N = Inf,
                                        ^
```
[R/number_of_junctions_markers.R:21:41:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions_markers.R#L21) *style:* **Variable and function name style should be snake_case.**
```r
                                        H_0 = 0.5,
                                        ^~~
```
[R/number_of_junctions_markers.R:32:27:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions_markers.R#L32) *warning:* **no visible global function definition for ‘number_of_junctions_di’**
```r
    expected_junctions <- number_of_junctions_di(N, H_0, t, di)
                          ^~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculate the average number of junctions after t generations, provided information on the initial heterozygosity, population size and the number of generations.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions.R:6:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param C Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/number_of_junctions.R:13:33:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
number_of_junctions <- function(N = Inf,
                                ^
```
[R/number_of_junctions.R:14:33:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                                R = Inf,
                                ^
```
[R/number_of_junctions.R:15:33:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                                H_0 = 0.5,
                                ^~~
```
[R/number_of_junctions.R:16:33:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions.R#L16) *style:* **Variable and function name style should be snake_case.**
```r
                                C = 1,
                                ^
```
[R/number_of_junctions.R:28:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/number_of_junctions.R#L28) *style:* **Variable and function name style should be snake_case.**
```r
  K <- junctions::calc_k(N, R, H_0, C)
  ^
```
[R/optim_limits.R:5:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/optim_limits.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
#' @param calc_func function to calculate the time, should accept two arguments: upper, lower and should return a stats::optimize object with two properties: $minimum and $objective
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/optim_limits.R:6:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/optim_limits.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param iterations number of times the boundaries should be adjusted to obtain an estimate that is not close to the boundaries. After this number of iterations is exceeded, NA is returned
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/phased_log_likelihood.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/phased_log_likelihood.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculates the log likelihood of observing the phased data, given the population size, initial heterozygosity and time since admixture
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/phased_log_likelihood.R:3:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/phased_log_likelihood.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @param local_anc_matrix Local_anc can be provided as either matrix with two columns, where the first column represents ancestry on chromosome 1, and the second column represents ancestry on chromosome 2. Ancestry labels used should be [0, 1], where 0 indicates the first ancestor, and 1 indicates the second ancestor. Alternatively, the user can provide a vector indicating whether at the specific marker, the focal individual is homozygous for the first ancestor (0), homozygous for the second ancestor (1) or heterozygous (2).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/phased_log_likelihood.R:38:11:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/phased_log_likelihood.R#L38) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (sum( labels %in% 1:4) != length(labels)) {
          ^
```
[R/phased_log_likelihood.R:45:58:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/phased_log_likelihood.R#L45) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[R/sim_backcrossing.R:7:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_backcrossing.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param size_in_morgan Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_backcrossing.R:11:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_backcrossing.R#L11) *style:* **Lines should not be more than 80 characters.**
```r
#' recorded to be returned at the end of the simulation. If left at -1, ancestry is recorded at every generation (computationally heavy).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_backcrossing.R:12:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_backcrossing.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
#' @return List with five entries: average_junctions: average number of junctions over time, detected_junctions: average number of detected junctions, given the markers. markers: vector with the locations of the molecular markers, junction_distribution: distribution of junctions per time step average_heterozygosity: average heterozygosity.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_fin_chrom.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_fin_chrom.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Individual based simulation of the accumulation of junctions for a chromosome with regularly distributed markers.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_fin_chrom.R:5:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_fin_chrom.R#L5) *style:* **Lines should not be more than 80 characters.**
```r
#' @param morgan Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_fin_chrom.R:9:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_fin_chrom.R#L9) *style:* **Lines should not be more than 80 characters.**
```r
#' @return \item{avgJunctions}{vector of the average number of junctions at time = [0, total_runtime]}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_fin_chrom.R:17:27:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_fin_chrom.R#L17) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
sim_fin_chrom <- function (pop_size = 100,
                          ^
```
[R/sim_fin_chrom.R:22:28:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_fin_chrom.R#L22) *style:* **Variable and function name style should be snake_case.**
```r
                           R = 100) {
                           ^
```
[R/sim_inf_chrom.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_inf_chrom.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Individual based simulation of the accumulation of junctions for a chromosome with an infinite number of recombination sites.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_inf_chrom.R:6:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_inf_chrom.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param morgan Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_inf_chrom.R:7:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_inf_chrom.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param markers The number of genetic markers superimposed on the chromosome. If markers is set to -1, no markers are superimposed (faster simulation)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_inf_chrom.R:9:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_inf_chrom.R#L9) *style:* **Lines should not be more than 80 characters.**
```r
#' @return \item{avgJunctions}{vector of the average number of junctions at time = [0, total_runtime]}
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_unphased.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_phased_unphased.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Individual based simulation of the accumulation of junctions, returning phased and unphased data. Ancestry on both chromosomes of 10 randomly sampled individuals per generations is returned.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_unphased.R:6:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_phased_unphased.R#L6) *style:* **Lines should not be more than 80 characters.**
```r
#' @param size_in_morgan Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_unphased.R:7:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_phased_unphased.R#L7) *style:* **Lines should not be more than 80 characters.**
```r
#' @param number_of_markers The number of genetic markers superimposed on the chromosome.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_unphased.R:8:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_phased_unphased.R#L8) *style:* **Lines should not be more than 80 characters.**
```r
#' @param time_points vector with time points at which local ancestry has to be recorded to be returned at the end of the simulation. If left at -1, ancestry is recorded at every generation (computationally heavy).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_unphased.R:12:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_phased_unphased.R#L12) *style:* **Lines should not be more than 80 characters.**
```r
#' @return a tibble with five columns: [time, individual, marker location, ancestry chromosome 1, ancestry chromosome 2]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_with_error.R:1:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_phased_with_error.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' Individual Based Simulation of the accumulation of junctions, given phasing error
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_with_error.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_phased_with_error.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Individual based simulation of the accumulation of junctions, returning phased and unphased data. Phased data is
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_with_error.R:3:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_phased_with_error.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' generated using a user-provided error rate. Ancestry on both chromosomes of 10 randomly sampled individuals per generations is
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_with_error.R:8:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_phased_with_error.R#L8) *style:* **Lines should not be more than 80 characters.**
```r
#' @param size_in_morgan Mean number of crossovers per meiosis (e.g. size in Morgan of the chromosome)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_with_error.R:9:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_phased_with_error.R#L9) *style:* **Lines should not be more than 80 characters.**
```r
#' @param number_of_markers The number of genetic markers superimposed on the chromosome.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_with_error.R:10:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_phased_with_error.R#L10) *style:* **Lines should not be more than 80 characters.**
```r
#' @param time_points vector with time points at which local ancestry has to be recorded to be returned at the end of the simulation. If left at -1, ancestry is recorded at every generation (computationally heavy).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_with_error.R:15:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_phased_with_error.R#L15) *style:* **Lines should not be more than 80 characters.**
```r
#' @param error_rate fraction of markers that are erroneously phased (e.g. swapped)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_phased_with_error.R:16:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/sim_phased_with_error.R#L16) *style:* **Lines should not be more than 80 characters.**
```r
#' @return a tibble with five columns: [time, individual, marker location, ancestry chromosome 1, ancestry chromosome 2]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/unphased_log_likelihood.R:2:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/unphased_log_likelihood.R#L2) *style:* **Lines should not be more than 80 characters.**
```r
#' @description Calculates the log likelihood of observing the unphased data, given the population size, initial heterozygosity and time since admixture
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/unphased_log_likelihood.R:3:1:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/unphased_log_likelihood.R#L3) *style:* **Lines should not be more than 80 characters.**
```r
#' @param local_anc_matrix Local_anc can be provided as either matrix with two columns, where the first column represents ancestry on chromosome 1, and the second column represents ancestry on chromosome 2. Ancestry labels used should be [0, 1], where 0 indicates the first ancestor, and 1 indicates the second ancestor. Alternatively, the user can provide a vector indicating whether at the specific marker, the focal individual is homozygous for the first ancestor (0), homozygous for the second ancestor (1) or heterozygous (2).
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/unphased_log_likelihood.R:34:11:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/unphased_log_likelihood.R#L34) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  if (sum( labels %in% 1:3) != length(labels)) {
          ^
```
[R/unphased_log_likelihood.R:41:58:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/R/unphased_log_likelihood.R#L41) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                      local_anc[2:length(local_anc)]      )
                                                         ^
```
[tests/testthat/test-equations.R:11:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/tests/testthat/test-equations.R#L11) *style:* **Variable and function name style should be snake_case.**
```r
  A <- is.infinite(v3)
  ^
```
[tests/testthat/test-equations.R:18:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/tests/testthat/test-equations.R#L18) *style:* **Variable and function name style should be snake_case.**
```r
  J <- junctions::number_of_junctions(N = 100, R = 1000,
  ^
```
[tests/testthat/test-marker_dist.R:4:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/tests/testthat/test-marker_dist.R#L4) *style:* **Variable and function name style should be snake_case.**
```r
  R <- 1000
  ^
```
[tests/testthat/test-marker_dist.R:16:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/tests/testthat/test-marker_dist.R#L16) *style:* **Variable and function name style should be snake_case.**
```r
  N <- 1e3
  ^
```
[tests/testthat/test-marker_dist.R:17:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/tests/testthat/test-marker_dist.R#L17) *style:* **Variable and function name style should be snake_case.**
```r
  R <- 1000
  ^
```
[tests/testthat/test-marker_dist.R:60:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/tests/testthat/test-marker_dist.R#L60) *style:* **Variable and function name style should be snake_case.**
```r
  N <- 1e3
  ^
```
[tests/testthat/test-marker_dist.R:61:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/tests/testthat/test-marker_dist.R#L61) *style:* **Variable and function name style should be snake_case.**
```r
  R <- 1000
  ^
```
[tests/testthat/test-phased-error.R:53:64:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/tests/testthat/test-phased-error.R#L53) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  expected_heterozygosity <- 2 * 0.5 * 0.5 * (1 - 1 / (2 * 100) ) ^ 200
                                                               ^
```
[tests/testthat/test-sims.R:4:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/tests/testthat/test-sims.R#L4) *style:* **Variable and function name style should be snake_case.**
```r
  R <- 100 #chromosome size
  ^
```
[tests/testthat/test-sims.R:5:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/tests/testthat/test-sims.R#L5) *style:* **Variable and function name style should be snake_case.**
```r
  N <- 100 #population size
  ^
```
[tests/testthat/test-sims.R:6:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/tests/testthat/test-sims.R#L6) *style:* **Variable and function name style should be snake_case.**
```r
  H_0 <- 0.5 #initial heterozygosity
  ^~~
```
[tests/testthat/test-sims.R:7:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/tests/testthat/test-sims.R#L7) *style:* **Variable and function name style should be snake_case.**
```r
  C <- 1 #number of recombinations per meiosis
  ^
```
[tests/testthat/test-sims.R:29:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/tests/testthat/test-sims.R#L29) *style:* **Variable and function name style should be snake_case.**
```r
  N <- 50 #population size
  ^
```
[tests/testthat/test-sims.R:30:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/tests/testthat/test-sims.R#L30) *style:* **Variable and function name style should be snake_case.**
```r
  H_0 <- 0.5 #initial heterozygosity
  ^~~
```
[tests/testthat/test-sims.R:31:3:](https://github.com/thijsjanzen/junctions/blob/d0bc6e6def93cb06defe3e797ab0b223b99072d7/tests/testthat/test-sims.R#L31) *style:* **Variable and function name style should be snake_case.**
```r
  C <- 1 #number of recombinations per meiosis
  ^
```


Successfully deployed to following URLs:

* https://bsd-weekly-b8x303db8.now.sh
* https://bsd-weekly.now.sh
* https://bsdweekly.com
* https://www.bsdweekly.com
* https://bsd-weekly.hovancik.now.sh
* https://bsd-weekly-git-master.hovancik.now.sh


Successfully deployed to following URLs:

* https://hello-week-1zv16bdj0.now.sh
* https://hello-week.now.sh
* https://hello-week.mauroreisvieira.now.sh
* https://hello-week-git-master.mauroreisvieira.now.sh


Successfully deployed to following URLs:

* https://beam-invoice-b6nihi79i.now.sh
* https://beam-invoice.now.sh
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* https://beam-invoice-git-master.clementdlc.now.sh


Successfully deployed to following URLs:

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* https://personal-website.bjarkt.now.sh
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Successfully deployed to following URLs:

* https://jwt-celupn871.now.sh
* https://jwt-wheat.now.sh
* https://jwt.webapisgithub.now.sh
* https://jwt-git-master.webapisgithub.now.sh


remove_objexx_gio__5 (lefticus) - Win64-Windows-10-VisualStudio-16: OK (2617 of 2618 tests passed, 23 test warnings)

Messages:\n
 * 23 tests had: EIO diffs.
 * 5 tests had: Table small diffs.

Failures:\n

EnergyPlusFixture Test Summary
 * Passed: 771
 * Failed: 1

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.96%25-yellow.png)


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* https://test-task-table-9r0f3h56t.now.sh
* https://test-task-table.now.sh
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* https://test-task-table-git-master.kochewww.now.sh


Successfully deployed to following URLs:

* https://ui-420nnitip.now.sh
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* https://ui.roleypoly.now.sh
* https://ui-git-master.roleypoly.now.sh


Successfully deployed to following URLs:

* https://getbaan-alpmbiucr.now.sh
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* https://getbaan-git-master.niawjunior.now.sh


Successfully deployed to following URLs:

* https://jwt-55t0zuv4f.now.sh
* https://jwt-wheat.now.sh
* https://jwt.webapisgithub.now.sh
* https://jwt-git-master.webapisgithub.now.sh


# Specs execution successful
:scroll: [View logs](http://bamboo.comnull)
### Plans updated

Bamboo specs have been successfully imported and the following plans have been updated.

Project | Plan | Build
---|---|---
[Test](http://bamboo.com/browse/TEST) | [Comment test](http://bamboo.com/browse/TEST-CTEST)  | :white_check_mark: [\#1](http://bamboo.com/browse/TEST-CTEST-1)
[New project](http://bamboo.com/browse/NEW) | [Disabled plan](http://bamboo.com/browse/NEW-DISABLED) **disabled** | :white_check_mark: [\#1](http://bamboo.com/browse/NEW-DISABLED-1)

### Deployments updated

Bamboo specs have been successfully imported and the following deployment projects have been updated.

|Deployment project |
----|
[Deployment test](http://bamboo.com/deploy/viewDeploymentProjectVersions.action?id=2162689)|


TeamCity Bvcms / Build [Build 3486](https://builds.tpsdb.com/viewLog.html?buildId=11747&buildTypeId=Bvcms_Build) outcome was **SUCCESS**
Summary: Tests passed: 229 Build time: 00:26:30


TeamCity Bvcms / Build [Build 3487](https://builds.tpsdb.com/viewLog.html?buildId=11748&buildTypeId=Bvcms_Build) is now running


Emissivity-in-WindowMaterial-ComplexShade (LipingWang) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-IntegrationCoverage-Debug: OK (677 of 678 tests passed, 0 test warnings)

Failures:\n

integration Test Summary
 * Passed: 677
 * Timeout: 1

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.85%25-yellow.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-68.33%25-green.png)


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* https://website-esb7by21n.now.sh
* https://keplersj.com
* https://website.keplersj.now.sh
* https://website-git-master.keplersj.now.sh


Note that all of the `/pathfinding` files will be integrated into the `/robot` folder once completed. There's just a lot so it's separate for now.


Successfully deployed to following URLs:

* https://aremycolorsaccessible-cqnygac5a.now.sh
* https://aremycoloursaccessible.com
* https://aremycolorsaccessible.com
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* https://www.aremycoloursaccessible.com
* https://aremycolorsaccessible.sitaggart.now.sh
* https://aremycolorsaccessible-git-master.sitaggart.now.sh


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* https://contenteditable.now.sh
* https://writingtoolkit.online
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* https://contenteditable-git-master.thaddeusmccleary.now.sh


"There is NO ..."


Successfully deployed to following URLs:

* https://firebase-handson-mov9tzptr.now.sh
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自动构建 [auto-dragalia-bd7a2e70.zip](https://circleci.com/gh/NateScarlet/auto-dragalia/951/artifacts/0/home/circleci/project/artifacts/auto-dragalia-bd7a2e70.zip)


The following doc(s) have been deployed to the [popcards](https:///popcards-static-docs.pantheonsite.io/docs) Multidev environment:
- [gatsby/src/layout/popCards/index.js](https://github.com/pantheon-systems/documentation/commit/a12d4122f4ae9119bc53fa8e676850a7b1b6ea2f/gatsby/src/layout/popCards/index.js)
- [gatsby/src/layout/popCards/style.css](https://github.com/pantheon-systems/documentation/commit/a12d4122f4ae9119bc53fa8e676850a7b1b6ea2f/gatsby/src/layout/popCards/style.css)
- [gatsby/src/pages/index.js](https://github.com/pantheon-systems/documentation/commit/a12d4122f4ae9119bc53fa8e676850a7b1b6ea2f/gatsby/src/pages/index.js)
- [source/data/home.yaml](https://github.com/pantheon-systems/documentation/commit/a12d4122f4ae9119bc53fa8e676850a7b1b6ea2f/source/data/home.yaml)


Successfully deployed to following URLs:

* https://personal-website-project-2zb8v2jx5.now.sh
* https://davidegiovanni.com
* https://www.davidegiovanni.com
* https://personal-website-project.davidegiovanni.now.sh
* https://personal-website-project-git-master.davidegiovanni.now.sh


Typo that we fixed later.


Successfully deployed to following URLs:

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* https://pluto-beta.now.sh
* https://pluto.dimitrimichel.now.sh
* https://pluto-git-master.dimitrimichel.now.sh


The file should be saved in the offline data folder next to the cache.


Minor: fetch?


Successfully deployed to following URLs:

* https://personal-website-3cfcpeo8l.now.sh
* https://personal-website-six.now.sh
* https://personal-website.mathieutheriault89.now.sh
* https://personal-website-git-master.mathieutheriault89.now.sh


@pullmoll any reason this has been dropped on 32-bit?


Very Nice Punjabi


Hum, that already went in https://github.com/jitsi/jitsi-meet/commit/5cfae2c419624892aea9f8b030aa7328a1fc546c


All Rules (3 / 3) Passed

      :crown: Good job! this pull request is aligned with your organization's best practices!

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:point_right: click here to view a full list of the events :point_left:


Also the assumption that musl "defines PAGE_SIZE" is entirely wrong, it only defines it on platforms where it's a constant, and this breaks everywhere else. I have a correct fix available.


Apple notarization warns "The binary uses an SDK older than the 10.9 SDK" for Contents/Java/arduino-builder.

Ok for now, but will need to be updated for future releases, after Apple starts requiring >= 10.9 SDK for notarization.


Successfully deployed to following URLs:

* https://revoltuigithubio-2kd867h8r.now.sh
* https://revoltui.now.sh
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* https://revoltuigithubio-git-master.pedroladeira.now.sh


Change step name to: "I have the following user with expiration date in the "future"" so it can be reused.


Successfully deployed to following URLs:

* https://final-floorbazaarcom-1buq4jp25.now.sh
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* https://final-floorbazaarcom-git-master.saurabharyan30.now.sh


Successfully deployed to following URLs:

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* https://gata-calendar-demo.now.sh
* https://gata-calendar-demo.cschweda.now.sh
* https://gata-calendar-demo-git-master.cschweda.now.sh


TeamCity MAS / MAS [Build 1.1.0.758](https://teamcity.nice.org.uk/viewLog.html?buildId=65142&buildTypeId=Mas_Mas) outcome was **FAILURE**
Summary: Artifacts size 0 B is 100% different from 3.7 MB in build #1.1.0.719-MAS-150-WeeklyEmailN; exit code 1 (Step: Set build number (Command Line)) (new) Build time: 00:00:12


Change method so it accepts date parameter as string (future, today, past).


$ devtools::install_github("ACEMS/r2vr", force = T, build_vignettes = T)

$ vignette("interactions", package = "r2vr")

- install/update packages
- install rmarkdown and pandoc

https://github.com/rstudio/rstudio/issues/3661#issuecomment-475705806


TeamCity MAS / MAS [Build 1.1.0.759-MAS-150-WeeklyEmailN](https://teamcity.nice.org.uk/viewLog.html?buildId=65143&buildTypeId=Mas_Mas) outcome was **FAILURE**
Summary: Tests failed: 2, passed: 41 Build time: 00:01:27
### Failed tests
```
Test collection for MAS.Tests.IntegrationTests.WeeklyEmailTests (1): MAS.Tests.IntegrationTests.WeeklyEmailTests.EmailBodyHtmlMatchesApprovedWithMEC: <no details avaliable>

Test collection for MAS.Tests.IntegrationTests.WeeklyEmailTests (1): MAS.Tests.IntegrationTests.WeeklyEmailTests.EmailBodyHtmlMatchesApprovedWithoutMEC: <no details avaliable>

```


@JuliaRegistrator register


I want ask you a question, i dont know why "imx-drm" is need? what the etnaviv not enough?


@xoto10
NO, i have only replaced PvNode by ttPv


The original line here explains why this plug-in can't be disabled: If you disable the Toolbox, you've disabled the interface to disable/enable plug-ins, so you couldn't change it back. To prevent this we've made the Toolbox a required plug-in.


Successfully deployed to following URLs:

* https://temp-841wrggnp.now.sh
* https://temp-nine.now.sh
* https://temp.efcjunior.now.sh
* https://temp-git-master.efcjunior.now.sh


This is a singleton, so don't cache it.


Should be a RuntimeError.


7507-Load-introduced-by-ZoneHVACEnergyRecoveryVentilator-not-always-met-by-AirLoop-systems (lgu1234) - Win64-Windows-10-VisualStudio-16: OK (2619 of 2619 tests passed, 1 test warnings)

Messages:\n
 * 1 test had: EIO diffs.
 * 1 test had: ESO small diffs.
 * 1 test had: MTR small diffs.
 * 1 test had: Table small diffs.

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png)


Failed to assign a domain to your deployment due to the following error:

~~~
The domain kinthedev.ga is not verfied and cannot be used as an alias.
~~~

([Learn more](https://zeit.co/senpaikin/kinssite/n6bprd783) or [visit](https://kinssite-n6bprd783.now.sh) the non-aliased deployment)


So instead of reordering the migrations to happen in the correct order, you'd rather remove the foreign keys all together? Specially in a "security related" package like passport, it sounds dangerous to do so for any new install. I strongly suggest to reconsider this


Successfully deployed to following URLs:

* https://next-with-moxy-2v7sh7hyg.now.sh
* https://next-with-moxy.now.sh
* https://next-with-moxy.moxystudio.now.sh
* https://next-with-moxy-git-master.moxystudio.now.sh