Source Map Explorer Audits (0 failures)

## Source Map Explorer Audits

### /home/circleci/repo/examples/angular/dist/example-angular/styles-es2015.js

| Label                                      | Value   | Last Value | Threshold | Success |
| ----                                       |  :---:  |   :---:    |   :---:   |  :---:  |
| src/styles.css                             |  453 B  |            |   500 B   |    ✓    |
| node_modules/style-loader/lib/addStyles.js | 9.78 KB |            |   10 KB   |    ✓    |
| node_modules/style-loader/lib/urls.js      | 2.86 KB |            |   3 KB    |    ✓    |
| src/styles.css?b364                        |  749 B  |            |   800 B   |    ✓    |
| <unmapped>                                 | 1.94 KB |            |   2 KB    |    ✓    |

### /home/circleci/repo/examples/angular/dist/example-angular/styles-es5.js

| Label                                      | Value   | Last Value | Threshold | Success |
| ----                                       |  :---:  |   :---:    |   :---:   |  :---:  |
| src/styles.css                             |  453 B  |            |   500 B   |    ✓    |
| node_modules/style-loader/lib/addStyles.js | 9.78 KB |            |   10 KB   |    ✓    |
| node_modules/style-loader/lib/urls.js      | 2.86 KB |            |   3 KB    |    ✓    |
| src/styles.css?b364                        |  749 B  |            |   800 B   |    ✓    |
| <unmapped>                                 | 1.94 KB |            |   2 KB    |    ✓    |

### /home/circleci/repo/examples/angular/dist/example-angular/main-es2015.js

| Label                                       | Value   | Last Value | Threshold | Success |
| ----                                        |  :---:  |   :---:    |   :---:   |  :---:  |
| $_lazy_route_resource lazy namespace object |  538 B  |            |   600 B   |    ✓    |
| src/app/app.component.html                  | 1.19 KB |            |  1.5 KB   |    ✓    |
| src/app/app-routing.module.ts               |  377 B  |            |   600 B   |    ✓    |
| src/app/app.component.css                   |  402 B  |            |   600 B   |    ✓    |
| src/app/app.component.ts                    |  389 B  |            |   600 B   |    ✓    |
| src/app/app.module.ts                       |  484 B  |            |   600 B   |    ✓    |
| src/environments/environment.ts             |  494 B  |            |   550 B   |    ✓    |
| src/main.ts                                 | 1.1 KB  |            |  1.5 KB   |    ✓    |
| <unmapped>                                  | 5.21 KB |            |  5.5 KB   |    ✓    |

### /home/circleci/repo/examples/angular/dist/example-angular/main-es5.js

| Label                                       | Value   | Last Value | Threshold | Success |
| ----                                        |  :---:  |   :---:    |   :---:   |  :---:  |
| $_lazy_route_resource lazy namespace object |  538 B  |            |   600 B   |    ✓    |
| src/app/app.component.html                  | 1.19 KB |            |  1.5 KB   |    ✓    |
| src/app/app-routing.module.ts               |  436 B  |            |   600 B   |    ✓    |
| src/app/app.component.css                   |  402 B  |            |   600 B   |    ✓    |
| src/app/app.component.ts                    |  430 B  |            |   600 B   |    ✓    |
| src/app/app.module.ts                       |  538 B  |            |   600 B   |    ✓    |
| src/environments/environment.ts             |  492 B  |            |   550 B   |    ✓    |
| src/main.ts                                 | 1.11 KB |            |  1.5 KB   |    ✓    |
| <unmapped>                                  | 5.32 KB |            |  5.5 KB   |    ✓    |

Size Checks (0 failures)

## Size Checks

| Label                                    | Value     | Last Value | Threshold | Success |
| ----                                     |   :---:   |   :---:    |   :---:   |  :---:  |
| dist/example-angular/favicon.ico         |  1.35 KB  |  1.35 KB   |   4 KB    |    ✓    |
| dist/example-angular/index.html          |   304 B   |   304 B    |   3 KB    |    ✓    |
| dist/example-angular                     | 16.86 MB  |  16.86 MB  |   17 MB   |    ✓    |
| dist/example-angular/main-es2015.js      |  2.8 KB   |   2.8 KB   |   3 KB    |    ✓    |
| dist/example-angular/main-es5.js         |  2.82 KB  |  2.82 KB   |   3 KB    |    ✓    |
| dist/example-angular/polyfills-es5.js    | 87.22 KB  |  87.22 KB  |   90 KB   |    ✓    |
| dist/example-angular/polyfills-es2015.js |  44.4 KB  |  44.4 KB   |   45 KB   |    ✓    |
| dist/example-angular/runtime-es2015.js   |  1.65 KB  |  1.65 KB   |  1.75 KB  |    ✓    |
| dist/example-angular/runtime-es5.js      |  1.65 KB  |  1.65 KB   |  1.75 KB  |    ✓    |
| dist/example-angular/styles-es2015.js    |  5.17 KB  |  5.17 KB   |  5.25 KB  |    ✓    |
| dist/example-angular/styles-es5.js       |  5.16 KB  |  5.16 KB   |  5.25 KB  |    ✓    |
| dist/example-angular/vendor-es2015.js    | 672.4 KB  |  672.4 KB  |  700 KB   |    ✓    |
| dist/example-angular/vendor-es5.js       | 686.07 KB | 686.07 KB  |  700 KB   |    ✓    |

Heap Snapshot Checks (0 failures)

## Heap Snapshot Checks

| Label            | Value    | Last Value  | Threshold | Success |
| ----             |  :---:   |    :---:    |   :---:   |  :---:  |
| Documents        |    5     |      5      |     5     |    ✓    |
| Frames           |    2     |      2      |     2     |    ✓    |
| JSHeapTotalSize  | 22183936 |  22446080   |           |    ✓    |
|                  |          |    +256 KB  |           |         |
| JSHeapUsedSize   | 15000160 |  15037968   |           |    ✓    |
|                  |          |   +36.92 KB |           |         |
| LayoutCount      |    2     |      2      |     5     |    ✓    |
| Nodes            |    81    |     81      |    81     |    ✓    |
| RecalcStyleCount |    3     |      3      |     6     |    ✓    |

Axe Audits (0 failures)

## Axe Audits

| Label                             | Value    | Last Value | Threshold | Success |
| ----                              |  :---:   |   :---:    |   :---:   |  :---:  |
| aria-hidden-body                  |          |            |   none    |    ✓    |
| bypass                            |          |            |   none    |    ✓    |
| color-contrast                    |          |            |   none    |    ✓    |
| document-title                    |          |            |   none    |    ✓    |
| empty-heading                     |          |            |   none    |    ✓    |
| heading-order                     |          |            |   none    |    ✓    |
| html-has-lang                     |          |            |   none    |    ✓    |
| html-lang-valid                   |          |            |   none    |    ✓    |
| image-alt                         |          |            |   none    |    ✓    |
| image-redundant-alt               |          |            |   none    |    ✓    |
| landmark-no-duplicate-banner      |          |            |   none    |    ✓    |
| landmark-no-duplicate-contentinfo |          |            |   none    |    ✓    |
| link-name                         |          |            |   none    |    ✓    |
| list                              |          |            |   none    |    ✓    |
| listitem                          |          |            |   none    |    ✓    |
| meta-viewport-large               |          |            |   none    |    ✓    |
| meta-viewport                     |          |            |   none    |    ✓    |
| page-has-heading-one              |          |            |   none    |    ✓    |
| landmark-one-main                 | moderate |  moderate  | moderate  |    ✓    |
| region                            | moderate |  moderate  | moderate  |    ✓    |

Unused Source Checks (0 failures)

## Unused Source Checks

| Label                                                  | Value  | Last Value | Threshold | Success |
| ----                                                   | :---:  |   :---:    |   :---:   |  :---:  |
| http://localhost:3000/                                 | 51.80% |   51.80%   |           |    ✓    |
| http://localhost:3000/runtime-es2015.js                | 13.93% |   13.93%   |    70%    |    ✓    |
| http://localhost:3000/styles-es2015.js                 | 49.85% |   49.85%   |    70%    |    ✓    |
| http://localhost:3000/main-es2015.js                   | 6.64%  |   6.64%    |    70%    |    ✓    |
| http://localhost:3000/polyfills-es2015.js              | 33.16% |   33.16%   |    70%    |    ✓    |
| http://localhost:3000/vendor-es2015.js                 | 53.65% |   53.65%   |    70%    |    ✓    |
| ... ///RouterModule/_EmptyOutletComponent.ngfactory.js | 27.79% |   27.79%   |    70%    |    ✓    |
| ng:///AppModule/AppComponent.ngfactory.js              | 0.02%  |   0.02%    |    70%    |    ✓    |
| ... uterModule/_EmptyOutletComponent_Host.ngfactory.js | 29.16% |   29.16%   |    70%    |    ✓    |
| ng:///AppModule/AppComponent_Host.ngfactory.js         | 0.10%  |   0.10%    |    70%    |    ✓    |
| ng:///AppModule/module.ngfactory.js                    | 0.01%  |   0.01%    |    70%    |    ✓    |

Lighthouse Audits (0 failures)

## Lighthouse Audits

| Label               | Value | Last Value | Threshold | Success |
| ----                | :---: |   :---:    |   :---:   |  :---:  |
| Performance         |   1   |     1      |     1     |    ✓    |
| Accessibility       |  100  |    100     |    100    |    ✓    |
| Best Practices      |  100  |    100     |    100    |    ✓    |
| SEO                 |  91   |     91     |    90     |    ✓    |
| Progressive Web App |  20   |     20     |    20     |    ✓    |


Size Checks (0 failures)

No Failures

Source Map Explorer Audits (0 failures)

No Failures

Heap Snapshot Checks (0 failures)

No Failures

Unused Source Checks (0 failures)

No Failures

Axe Audits (0 failures)

No Failures

Lighthouse Audits (0 failures)

No Failures


Source Map Explorer Audits (0 failures)

## Source Map Explorer Audits

### /home/circleci/repo/examples/angular/dist/example-angular/styles-es2015.js

| Label                                      | Value   | Last Value | Threshold | Success |
| ----                                       |  :---:  |   :---:    |   :---:   |  :---:  |
| src/styles.css                             |  453 B  |            |   500 B   |    ✓    |
| node_modules/style-loader/lib/addStyles.js | 9.78 KB |            |   10 KB   |    ✓    |
| node_modules/style-loader/lib/urls.js      | 2.86 KB |            |   3 KB    |    ✓    |
| src/styles.css?b364                        |  749 B  |            |   800 B   |    ✓    |
| <unmapped>                                 | 1.94 KB |            |   2 KB    |    ✓    |

### /home/circleci/repo/examples/angular/dist/example-angular/styles-es5.js

| Label                                      | Value   | Last Value | Threshold | Success |
| ----                                       |  :---:  |   :---:    |   :---:   |  :---:  |
| src/styles.css                             |  453 B  |            |   500 B   |    ✓    |
| node_modules/style-loader/lib/addStyles.js | 9.78 KB |            |   10 KB   |    ✓    |
| node_modules/style-loader/lib/urls.js      | 2.86 KB |            |   3 KB    |    ✓    |
| src/styles.css?b364                        |  749 B  |            |   800 B   |    ✓    |
| <unmapped>                                 | 1.94 KB |            |   2 KB    |    ✓    |

### /home/circleci/repo/examples/angular/dist/example-angular/main-es2015.js

| Label                                       | Value   | Last Value | Threshold | Success |
| ----                                        |  :---:  |   :---:    |   :---:   |  :---:  |
| $_lazy_route_resource lazy namespace object |  538 B  |            |   600 B   |    ✓    |
| src/app/app.component.html                  | 1.19 KB |            |  1.5 KB   |    ✓    |
| src/app/app-routing.module.ts               |  377 B  |            |   600 B   |    ✓    |
| src/app/app.component.css                   |  402 B  |            |   600 B   |    ✓    |
| src/app/app.component.ts                    |  389 B  |            |   600 B   |    ✓    |
| src/app/app.module.ts                       |  484 B  |            |   600 B   |    ✓    |
| src/environments/environment.ts             |  494 B  |            |   550 B   |    ✓    |
| src/main.ts                                 | 1.1 KB  |            |  1.5 KB   |    ✓    |
| <unmapped>                                  | 5.21 KB |            |  5.5 KB   |    ✓    |

### /home/circleci/repo/examples/angular/dist/example-angular/main-es5.js

| Label                                       | Value   | Last Value | Threshold | Success |
| ----                                        |  :---:  |   :---:    |   :---:   |  :---:  |
| $_lazy_route_resource lazy namespace object |  538 B  |            |   600 B   |    ✓    |
| src/app/app.component.html                  | 1.19 KB |            |  1.5 KB   |    ✓    |
| src/app/app-routing.module.ts               |  436 B  |            |   600 B   |    ✓    |
| src/app/app.component.css                   |  402 B  |            |   600 B   |    ✓    |
| src/app/app.component.ts                    |  430 B  |            |   600 B   |    ✓    |
| src/app/app.module.ts                       |  538 B  |            |   600 B   |    ✓    |
| src/environments/environment.ts             |  492 B  |            |   550 B   |    ✓    |
| src/main.ts                                 | 1.11 KB |            |  1.5 KB   |    ✓    |
| <unmapped>                                  | 5.32 KB |            |  5.5 KB   |    ✓    |

Size Checks (0 failures)

## Size Checks

| Label                                    | Value     | Last Value | Threshold | Success |
| ----                                     |   :---:   |   :---:    |   :---:   |  :---:  |
| dist/example-angular/favicon.ico         |  1.35 KB  |  1.35 KB   |   4 KB    |    ✓    |
| dist/example-angular/index.html          |   304 B   |   304 B    |   3 KB    |    ✓    |
| dist/example-angular                     | 16.86 MB  |  16.86 MB  |   17 MB   |    ✓    |
| dist/example-angular/main-es2015.js      |  2.8 KB   |   2.8 KB   |   3 KB    |    ✓    |
| dist/example-angular/main-es5.js         |  2.82 KB  |  2.82 KB   |   3 KB    |    ✓    |
| dist/example-angular/polyfills-es5.js    | 87.22 KB  |  87.22 KB  |   90 KB   |    ✓    |
| dist/example-angular/polyfills-es2015.js |  44.4 KB  |  44.4 KB   |   45 KB   |    ✓    |
| dist/example-angular/runtime-es2015.js   |  1.65 KB  |  1.65 KB   |  1.75 KB  |    ✓    |
| dist/example-angular/runtime-es5.js      |  1.65 KB  |  1.65 KB   |  1.75 KB  |    ✓    |
| dist/example-angular/styles-es2015.js    |  5.17 KB  |  5.17 KB   |  5.25 KB  |    ✓    |
| dist/example-angular/styles-es5.js       |  5.16 KB  |  5.16 KB   |  5.25 KB  |    ✓    |
| dist/example-angular/vendor-es2015.js    | 672.4 KB  |  672.4 KB  |  700 KB   |    ✓    |
| dist/example-angular/vendor-es5.js       | 686.07 KB | 686.07 KB  |  700 KB   |    ✓    |

Heap Snapshot Checks (0 failures)

## Heap Snapshot Checks

| Label            | Value    | Last Value   | Threshold | Success |
| ----             |  :---:   |    :---:     |   :---:   |  :---:  |
| Documents        |    5     |      5       |     5     |    ✓    |
| Frames           |    2     |      2       |     2     |    ✓    |
| JSHeapTotalSize  | 23756800 |   22183936   |           |    ✓    |
|                  |          |    +1.5 MB   |           |         |
| JSHeapUsedSize   | 14268296 |   15000160   |           |    ✓    |
|                  |          |   +714.71 KB |           |         |
| LayoutCount      |    2     |      2       |     5     |    ✓    |
| Nodes            |    81    |      81      |    81     |    ✓    |
| RecalcStyleCount |    3     |      3       |     6     |    ✓    |

Axe Audits (0 failures)

## Axe Audits

| Label                             | Value    | Last Value | Threshold | Success |
| ----                              |  :---:   |   :---:    |   :---:   |  :---:  |
| aria-hidden-body                  |          |            |   none    |    ✓    |
| bypass                            |          |            |   none    |    ✓    |
| color-contrast                    |          |            |   none    |    ✓    |
| document-title                    |          |            |   none    |    ✓    |
| empty-heading                     |          |            |   none    |    ✓    |
| heading-order                     |          |            |   none    |    ✓    |
| html-has-lang                     |          |            |   none    |    ✓    |
| html-lang-valid                   |          |            |   none    |    ✓    |
| image-alt                         |          |            |   none    |    ✓    |
| image-redundant-alt               |          |            |   none    |    ✓    |
| landmark-no-duplicate-banner      |          |            |   none    |    ✓    |
| landmark-no-duplicate-contentinfo |          |            |   none    |    ✓    |
| link-name                         |          |            |   none    |    ✓    |
| list                              |          |            |   none    |    ✓    |
| listitem                          |          |            |   none    |    ✓    |
| meta-viewport-large               |          |            |   none    |    ✓    |
| meta-viewport                     |          |            |   none    |    ✓    |
| page-has-heading-one              |          |            |   none    |    ✓    |
| landmark-one-main                 | moderate |  moderate  | moderate  |    ✓    |
| region                            | moderate |  moderate  | moderate  |    ✓    |

Unused Source Checks (0 failures)

## Unused Source Checks

| Label                                                  | Value  | Last Value | Threshold | Success |
| ----                                                   | :---:  |   :---:    |   :---:   |  :---:  |
| http://localhost:3000/                                 | 51.80% |   51.80%   |           |    ✓    |
| http://localhost:3000/runtime-es2015.js                | 13.93% |   13.93%   |    70%    |    ✓    |
| http://localhost:3000/styles-es2015.js                 | 49.85% |   49.85%   |    70%    |    ✓    |
| http://localhost:3000/main-es2015.js                   | 6.64%  |   6.64%    |    70%    |    ✓    |
| http://localhost:3000/polyfills-es2015.js              | 33.16% |   33.16%   |    70%    |    ✓    |
| http://localhost:3000/vendor-es2015.js                 | 53.65% |   53.65%   |    70%    |    ✓    |
| ... ///RouterModule/_EmptyOutletComponent.ngfactory.js | 27.79% |   27.79%   |    70%    |    ✓    |
| ng:///AppModule/AppComponent.ngfactory.js              | 0.02%  |   0.02%    |    70%    |    ✓    |
| ... uterModule/_EmptyOutletComponent_Host.ngfactory.js | 29.16% |   29.16%   |    70%    |    ✓    |
| ng:///AppModule/AppComponent_Host.ngfactory.js         | 0.10%  |   0.10%    |    70%    |    ✓    |
| ng:///AppModule/module.ngfactory.js                    | 0.01%  |   0.01%    |    70%    |    ✓    |

Lighthouse Audits (0 failures)

## Lighthouse Audits

| Label               | Value | Last Value | Threshold | Success |
| ----                | :---: |   :---:    |   :---:   |  :---:  |
| Performance         |   1   |     1      |     1     |    ✓    |
| Accessibility       |  100  |    100     |    100    |    ✓    |
| Best Practices      |  100  |    100     |    100    |    ✓    |
| SEO                 |  91   |     91     |    90     |    ✓    |
| Progressive Web App |  20   |     20     |    20     |    ✓    |


Поступил иначе: по сути на странице нет ничего кроме перфораторов, значит максимально подходящий h1 для неё - "перфораторы", который я уже написал.
 чтобы не плодить лишние сущности, я просто перенёс заголовок h1 внутрь section


Successfully aliased the URL <https://iandaley-dot-ninja-d5lthk1wb.now.sh> to the following aliases:

* https://iandaley-dot-ninja.iandaley23.now.sh
* https://iandaley-dot-ninja-git-master.iandaley23.now.sh


Закоментил пока


Successfully aliased the URL <https://ishakuni-frontend-l7r3trr93.now.sh> to the following aliases:

* https://ishakuni.com
* https://www.ishakuni.com
* https://ishakuni-frontend.caulagi.now.sh
* https://ishakuni-frontend-git-master.caulagi.now.sh


Successfully aliased the URL <https://ui-8wwlcusjv.now.sh> to the following aliases:

* https://ui.manifold.now.sh
* https://ui-git-master.manifold.now.sh


<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

end of the stream or a document separator is expected at line 4, column 1:
    version
    ^

</details>


[vg CI tests](https://ucsc-ci.com/vgteam/vg/pipelines/1592) complete for branch protobuf-backport.  View the [full report here](http://vg-data.s3.amazonaws.com/vg_ci/vgci_reports/commit/e939e2ee4d9fa34e4173fa0a3f1afba4e9125d4a/index.html).

19 tests passed, 0 tests failed and 0 tests skipped in 13397 seconds

Tests produced 382 warnings. 382 were for lower-than-expected alignment scores


This commit has been mentioned on **Discourse Meta**. There might be relevant details there:

https://meta.discourse.org/t/google-not-working-as-a-login-for-some-devices-on-meta/127576/13


Successfully aliased the URL <https://danestves-sjg5oonyp.now.sh> to the following aliases:

* https://dev.danestves.com
* https://danestves.danestves.now.sh
* https://danestves-git-master.danestves.now.sh


The <li> have been removed, but not the closing tag here.


Successfully aliased the URL <https://my-choreo-d1bu15z1h.now.sh> to the following aliases:

* https://choreo.now.sh
* https://my-choreo.danielschmidt.now.sh
* https://my-choreo-git-master.danielschmidt.now.sh


I believe we might be missing some configuration for asyncio / domain context here. Right now I'm not seeing any of the child spans show up, which I assume means they're being associated with other contexts (or, unlikely, they just haven't existed in the samples ive reviewed).


Successfully aliased the URL <https://studentexternalprofile-7xzogoxa9.now.sh> to the following aliases:

* https://sep.4geeksacademy.co
* https://student-external-profile.geeksacademy.now.sh
* https://student-external-profile-git-master.geeksacademy.now.sh


Yeah and the xml version might not even be available at the time it crashes. I'm going to add a /Dmacro to override the value for the releases so it is available at all times.


last fixes


А там же есть состояние наведения на превьюхе. И там изображение товара перекрывается кнопками "купить" и "в закладки", действия по нажатию этих кнопок прописаны, ни одна из них не ведёт на страницу товара, а что-то же должно вести. Выходит что изображение не может вести - оно закрыто кнопками, кнопки тоже не ведут, выходит, что самое логичное - повесить ссылку на название товара.


I just bought you a couple of coffees, as I very much appreciate you maintaining this!

I'm seeing a bug in FF69 when dragging a tab from one FF window to another.  In the destination, the tab shows up as kind of "fused" to the adjacent tab, which leaves it in a state where one of the two tabs is inaccessible.


It worked as I tested it, yes. On my X10 and on the X9D+ I think. Don't remember exactly.


But yes, it is possibly a problem since some things went south with the serial driver since then. I remember some options crashing the radio (like serial trainer).


Should be python instead of pyton - make install err's on this


Successfully aliased the URL <https://react-boilerplate-js-hn1hqh69q.now.sh> to the following aliases:

* https://react-boilerplate-js.arpanlaha.now.sh
* https://react-boilerplate-js-git-master.arpanlaha.now.sh


т.к. у вас тут срабатывает понятие `forward declaration`


cache-glyc (energy-plus) - Win64-Windows-10-VisualStudio-16: OK (2535 of 2553 tests passed, 365 test warnings)

Messages:\n
 * 283 tests had: EIO diffs.
 * 354 tests had: ESO small diffs.
 * 210 tests had: Table small diffs.
 * 320 tests had: MTR small diffs.
 * 14 tests had: ESO big diffs.
 * 10 tests had: MTR big diffs.
 * 15 tests had: Table big diffs.
 * 13 tests had: ERR diffs.
 * 1 test had: JSON big diffs.
 * 2 tests had: AUD diffs.
 * 1 test had: EDD diffs.

Failures:\n

regression Test Summary
 * Passed: 650
 * Failed: 18

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-99.29%25-yellow.png)


Successfully aliased the URL <https://matchbox-okr-agz093pwu.now.sh> to the following aliases:

* https://matchbox-okr.jambas.now.sh
* https://matchbox-okr-git-master.jambas.now.sh


[R/cla_secsse_loglik.R:1:37:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L1) *style:* **Commas should always have a space after.**
```r
cla_secsse_loglik_rhs <- function(t,y,parameter){
                                    ^
```
[R/cla_secsse_loglik.R:1:39:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L1) *style:* **Commas should always have a space after.**
```r
cla_secsse_loglik_rhs <- function(t,y,parameter){
                                      ^
```
[R/cla_secsse_loglik.R:3:10:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L3) *style:* **Put spaces around all infix operators.**
```r
  d <- ly/2
        ~^~
```
[R/cla_secsse_loglik.R:4:3:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L4) *style:* **Variable and function name style should be snake_case.**
```r
  Es <- y[1:d]
  ^~
```
[R/cla_secsse_loglik.R:5:3:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L5) *style:* **Variable and function name style should be snake_case.**
```r
  Ds <- y[(d+1):ly]
  ^~
```
[R/cla_secsse_loglik.R:5:13:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L5) *style:* **Put spaces around all infix operators.**
```r
  Ds <- y[(d+1):ly]
           ~^~
```
[R/cla_secsse_loglik.R:8:3:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L8) *style:* **Variable and function name style should be snake_case.**
```r
  Q <- parameter[[3]]
  ^
```
[R/cla_secsse_loglik.R:10:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L10) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:11:26:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L11) *style:* **Commas should always have a space after.**
```r
  all_states <- cbind(Ds,Es)
                         ^
```
[R/cla_secsse_loglik.R:12:26:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L12) *style:* **Commas should always have a space after.**
```r
  a <- cbind(all_states[,2],all_states[,1])
                         ^
```
[R/cla_secsse_loglik.R:12:29:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L12) *style:* **Commas should always have a space after.**
```r
  a <- cbind(all_states[,2],all_states[,1])
                            ^
```
[R/cla_secsse_loglik.R:12:41:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L12) *style:* **Commas should always have a space after.**
```r
  a <- cbind(all_states[,2],all_states[,1])
                                        ^
```
[R/cla_secsse_loglik.R:14:3:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
  cross_D_E <- a%*%b
  ^~~~~~~~~
```
[R/cla_secsse_loglik.R:14:17:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L14) *style:* **Put spaces around all infix operators.**
```r
  cross_D_E <- a%*%b
               ~^~~~
```
[R/cla_secsse_loglik.R:16:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L16) *style:* **Lines should not be more than 80 characters.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:16:3:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L16) *style:* **Variable and function name style should be snake_case.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
  ^~
```
[R/cla_secsse_loglik.R:16:10:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L16) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
         ^
```
[R/cla_secsse_loglik.R:16:34:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L16) *style:* **Commas should always have a space after.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
                                 ^
```
[R/cla_secsse_loglik.R:16:62:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L16) *style:* **Commas should always have a space after.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
                                                             ^
```
[R/cla_secsse_loglik.R:16:73:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L16) *style:* **Put spaces around all infix operators.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
                                                                        ^~
```
[R/cla_secsse_loglik.R:16:74:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L16) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
                                                                         ^
```
[R/cla_secsse_loglik.R:16:75:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L16) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
                                                                          ^
```
[R/cla_secsse_loglik.R:16:84:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L16) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
                                                                                ^
```
[R/cla_secsse_loglik.R:16:118:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L16) *style:* **Commas should always have a space after.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
                                                                                ^
```
[R/cla_secsse_loglik.R:16:122:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L16) *style:* **Commas should always have a space after.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
                                                                                ^
```
[R/cla_secsse_loglik.R:16:133:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L16) *style:* **Commas should always have a space after.**
```r
  dD <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Ds +( Q %*% Ds ) + unlist(lapply(lapply(lambdas,"*",cross_D_E),sum))
                                                                                ^
```
[R/cla_secsse_loglik.R:17:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L17) *style:* **Lines should not be more than 80 characters.**
```r
  dE <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Es + ( Q %*% Es ) + mus + unlist(lapply(lapply(lambdas,"*",Es%*%t(Es)),sum))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:17:3:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L17) *style:* **Variable and function name style should be snake_case.**
```r
  dE <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Es + ( Q %*% Es ) + mus + unlist(lapply(lapply(lambdas,"*",Es%*%t(Es)),sum))
  ^~
```
[R/cla_secsse_loglik.R:17:10:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L17) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  dE <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Es + ( Q %*% Es ) + mus + unlist(lapply(lapply(lambdas,"*",Es%*%t(Es)),sum))
         ^
```
[R/cla_secsse_loglik.R:17:34:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L17) *style:* **Commas should always have a space after.**
```r
  dE <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Es + ( Q %*% Es ) + mus + unlist(lapply(lapply(lambdas,"*",Es%*%t(Es)),sum))
                                 ^
```
[R/cla_secsse_loglik.R:17:62:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L17) *style:* **Commas should always have a space after.**
```r
  dE <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Es + ( Q %*% Es ) + mus + unlist(lapply(lapply(lambdas,"*",Es%*%t(Es)),sum))
                                                             ^
```
[R/cla_secsse_loglik.R:17:76:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L17) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  dE <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Es + ( Q %*% Es ) + mus + unlist(lapply(lapply(lambdas,"*",Es%*%t(Es)),sum))
                                                                           ^
```
[R/cla_secsse_loglik.R:17:85:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L17) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  dE <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Es + ( Q %*% Es ) + mus + unlist(lapply(lapply(lambdas,"*",Es%*%t(Es)),sum))
                                                                                ^
```
[R/cla_secsse_loglik.R:17:125:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L17) *style:* **Commas should always have a space after.**
```r
  dE <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Es + ( Q %*% Es ) + mus + unlist(lapply(lapply(lambdas,"*",Es%*%t(Es)),sum))
                                                                                ^
```
[R/cla_secsse_loglik.R:17:129:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L17) *style:* **Commas should always have a space after.**
```r
  dE <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Es + ( Q %*% Es ) + mus + unlist(lapply(lapply(lambdas,"*",Es%*%t(Es)),sum))
                                                                                ^
```
[R/cla_secsse_loglik.R:17:131:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L17) *style:* **Put spaces around all infix operators.**
```r
  dE <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Es + ( Q %*% Es ) + mus + unlist(lapply(lapply(lambdas,"*",Es%*%t(Es)),sum))
                                                                                ~^~~~
```
[R/cla_secsse_loglik.R:17:141:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L17) *style:* **Commas should always have a space after.**
```r
  dE <- -((unlist(lapply(lambdas,sum))) + mus + Q %*% (rep(1,d)))  * Es + ( Q %*% Es ) + mus + unlist(lapply(lapply(lambdas,"*",Es%*%t(Es)),sum))
                                                                                ^
```
[R/cla_secsse_loglik.R:18:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L18) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:19:20:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L19) *style:* **Commas should always have a space after.**
```r
  return(list(c(dE,dD)))
                   ^
```
[R/cla_secsse_loglik.R:23:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L23) *style:* **Variable and function name style should be snake_case.**
```r
cla_calThruNodes <- function(
^~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:27:3:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L27) *style:* **Variable and function name style should be snake_case.**
```r
  forTime,
  ^~~~~~~
```
[R/cla_secsse_loglik.R:34:3:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L34) *warning:* **local variable ‘mus’ assigned but may not be used**
```r
  mus <- parameter[[2]]
  ^~~
```
[R/cla_secsse_loglik.R:36:3:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L36) *warning:* **local variable ‘Q’ assigned but may not be used**
```r
  Q <- parameter[[3]]
  ^
```
[R/cla_secsse_loglik.R:36:3:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L36) *style:* **Variable and function name style should be snake_case.**
```r
  Q <- parameter[[3]]
  ^
```
[R/cla_secsse_loglik.R:37:3:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L37) *warning:* **local variable ‘nb_node’ assigned but may not be used**
```r
  nb_node <- phy$Nnode
  ^~~~~~~
```
[R/cla_secsse_loglik.R:40:3:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L40) *warning:* **local variable ‘hmax’ assigned but may not be used**
```r
  hmax <- NULL
  ^~~~
```
[R/cla_secsse_loglik.R:41:3:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L41) *warning:* **local variable ‘ly’ assigned but may not be used**
```r
  ly <- ncol(states)
  ^~
```
[R/cla_secsse_loglik.R:42:20:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L42) *style:* **Put spaces around all infix operators.**
```r
  d <- ncol(states)/2
                  ~^~
```
[R/cla_secsse_loglik.R:43:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L43) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:44:4:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L44) *style:* **Commented code should be removed.**
```r
  #ances <- ances[1] #########################  REMOVE!!!!!!!!!!!!
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:45:4:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L45) *style:* **Commented code should be removed.**
```r
  #desIndex <- 1
   ^~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:46:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L46) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:48:3:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L48) *style:* **Variable and function name style should be snake_case.**
```r
  desRows <- which(phy$edge[, 1] == focal)
  ^~~~~~~
```
[R/cla_secsse_loglik.R:49:3:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L49) *style:* **Variable and function name style should be snake_case.**
```r
  desNodes <- phy$edge[desRows, 2]
  ^~~~~~~~
```
[R/cla_secsse_loglik.R:50:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L50) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:51:3:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L51) *style:* **Variable and function name style should be snake_case.**
```r
  nodeM <- numeric()
  ^~~~~
```
[R/cla_secsse_loglik.R:52:3:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L52) *style:* **Variable and function name style should be snake_case.**
```r
  nodeN <- numeric()
  ^~~~~
```
[R/cla_secsse_loglik.R:54:6:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L54) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(desIndex in 1:2){
     ^
```
[R/cla_secsse_loglik.R:55:36:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L55) *style:* **Commas should always have a space after.**
```r
    y <- states[desNodes[desIndex],]
                                   ^
```
[R/cla_secsse_loglik.R:56:5:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L56) *style:* **Variable and function name style should be snake_case.**
```r
    timeInte <- forTime[which(forTime[,2] == desNodes[desIndex]),3]
    ^~~~~~~~
```
[R/cla_secsse_loglik.R:56:40:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L56) *style:* **Commas should always have a space after.**
```r
    timeInte <- forTime[which(forTime[,2] == desNodes[desIndex]),3]
                                       ^
```
[R/cla_secsse_loglik.R:56:66:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L56) *style:* **Commas should always have a space after.**
```r
    timeInte <- forTime[which(forTime[,2] == desNodes[desIndex]),3]
                                                                 ^
```
[R/cla_secsse_loglik.R:58:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L58) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/cla_secsse_loglik.R:59:7:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L59) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(use_fortran == FALSE){
      ^
```
[R/cla_secsse_loglik.R:60:8:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L60) *style:* **Variable and function name style should be snake_case.**
```r
       nodeMN <- deSolve::ode(y = y, func = cla_secsse_loglik_rhs,
       ^~~~~~
```
[R/cla_secsse_loglik.R:61:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L61) *style:* **Lines should not be more than 80 characters.**
```r
                           times = c(0,timeInte), parms = parameter,rtol = reltol, atol = abstol,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:61:40:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L61) *style:* **Commas should always have a space after.**
```r
                           times = c(0,timeInte), parms = parameter,rtol = reltol, atol = abstol,
                                       ^
```
[R/cla_secsse_loglik.R:61:69:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L61) *style:* **Commas should always have a space after.**
```r
                           times = c(0,timeInte), parms = parameter,rtol = reltol, atol = abstol,
                                                                    ^
```
[R/cla_secsse_loglik.R:62:40:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L62) *style:* **Commas should always have a space after.**
```r
                           hmax = NULL,method = methode)
                                       ^
```
[R/cla_secsse_loglik.R:64:8:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L64) *style:* **Variable and function name style should be snake_case.**
```r
       nodeMN <- ode_FORTRAN(y = y, func = "cla_secsse_runmod",
       ^~~~~~
```
[R/cla_secsse_loglik.R:65:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L65) *style:* **Lines should not be more than 80 characters.**
```r
                              times = c(0,timeInte), parms = parameter, rtol = reltol, atol = abstol,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:65:43:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L65) *style:* **Commas should always have a space after.**
```r
                              times = c(0,timeInte), parms = parameter, rtol = reltol, atol = abstol,
                                          ^
```
[R/cla_secsse_loglik.R:68:7:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L68) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(desIndex == 1){
      ^
```
[R/cla_secsse_loglik.R:69:7:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L69) *style:* **Variable and function name style should be snake_case.**
```r
      nodeN <- nodeMN
      ^~~~~
```
[R/cla_secsse_loglik.R:71:7:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L71) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(desIndex == 2){
      ^
```
[R/cla_secsse_loglik.R:72:7:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L72) *style:* **Variable and function name style should be snake_case.**
```r
      nodeM <- nodeMN
      ^~~~~
```
[R/cla_secsse_loglik.R:72:22:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L72) *style:* **Trailing whitespace is superfluous.**
```r
      nodeM <- nodeMN
                     ^
```
[R/cla_secsse_loglik.R:74:6:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L74) *style:* **Commented code should be removed.**
```r
   # print(nodeMN)
     ^~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:77:3:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L77) *style:* **Variable and function name style should be snake_case.**
```r
  nodeM <- as.numeric(nodeM[2,-1])
  ^~~~~
```
[R/cla_secsse_loglik.R:77:31:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L77) *style:* **Commas should always have a space after.**
```r
  nodeM <- as.numeric(nodeM[2,-1])
                              ^
```
[R/cla_secsse_loglik.R:78:3:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L78) *style:* **Variable and function name style should be snake_case.**
```r
  nodeN <- as.numeric(nodeN[2,-1])
  ^~~~~
```
[R/cla_secsse_loglik.R:78:31:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L78) *style:* **Commas should always have a space after.**
```r
  nodeN <- as.numeric(nodeN[2,-1])
                              ^
```
[R/cla_secsse_loglik.R:79:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L79) *style:* **Lines should not be more than 80 characters.**
```r
  ff <- normalize_loglik(nodeM[(1:d) + d],loglik); nodeM[(1:d) + d] <- ff$probs; loglik <- ff$loglik
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:79:9:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L79) *warning:* **no visible global function definition for ‘normalize_loglik’**
```r
  ff <- normalize_loglik(nodeM[(1:d) + d],loglik); nodeM[(1:d) + d] <- ff$probs; loglik <- ff$loglik
        ^~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:79:43:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L79) *style:* **Commas should always have a space after.**
```r
  ff <- normalize_loglik(nodeM[(1:d) + d],loglik); nodeM[(1:d) + d] <- ff$probs; loglik <- ff$loglik
                                          ^
```
[R/cla_secsse_loglik.R:80:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L80) *style:* **Lines should not be more than 80 characters.**
```r
  ff <- normalize_loglik(nodeN[(1:d) + d],loglik); nodeN[(1:d) + d] <- ff$probs; loglik <- ff$loglik
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:80:9:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L80) *warning:* **no visible global function definition for ‘normalize_loglik’**
```r
  ff <- normalize_loglik(nodeN[(1:d) + d],loglik); nodeN[(1:d) + d] <- ff$probs; loglik <- ff$loglik
        ^~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:80:43:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L80) *style:* **Commas should always have a space after.**
```r
  ff <- normalize_loglik(nodeN[(1:d) + d],loglik); nodeN[(1:d) + d] <- ff$probs; loglik <- ff$loglik
                                          ^
```
[R/cla_secsse_loglik.R:81:5:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L81) *style:* **Commented code should be removed.**
```r
  # cat(rbind(nodeM[(d+1):length(nodeM)],nodeN[(d+1):length(nodeN)]),"\n")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:82:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L82) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:83:52:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L83) *style:* **Commas should always have a space after.**
```r
  all_states <- cbind(nodeM[(d + 1):length(nodeM)],nodeN[(d + 1):length(nodeN)])
                                                   ^
```
[R/cla_secsse_loglik.R:84:26:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L84) *style:* **Commas should always have a space after.**
```r
  a <- cbind(all_states[,2],all_states[,1])
                         ^
```
[R/cla_secsse_loglik.R:84:29:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L84) *style:* **Commas should always have a space after.**
```r
  a <- cbind(all_states[,2],all_states[,1])
                            ^
```
[R/cla_secsse_loglik.R:84:41:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L84) *style:* **Commas should always have a space after.**
```r
  a <- cbind(all_states[,2],all_states[,1])
                                        ^
```
[R/cla_secsse_loglik.R:86:3:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L86) *style:* **Variable and function name style should be snake_case.**
```r
  cross_M_N <- a%*%b
  ^~~~~~~~~
```
[R/cla_secsse_loglik.R:86:17:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L86) *style:* **Put spaces around all infix operators.**
```r
  cross_M_N <- a%*%b
               ~^~~~
```
[R/cla_secsse_loglik.R:87:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L87) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:88:5:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L88) *style:* **Commented code should be removed.**
```r
  # mergeBranch <- NULL
    ^~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:90:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L90) *style:* **Lines should not be more than 80 characters.**
```r
  #combProb <- 0.5*sum(lapply(lambdas,"*",cross_M_N)[[1]]) ## multiplication of probabilities of both branches
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:90:4:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L90) *style:* **Commented code should be removed.**
```r
  #combProb <- 0.5*sum(lapply(lambdas,"*",cross_M_N)[[1]]) ## multiplication of probabilities of both branches
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:91:4:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L91) *style:* **Commented code should be removed.**
```r
  #mergeBranch <- c(mergeBranch,combProb)
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:92:3:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L92) *style:* **Variable and function name style should be snake_case.**
```r
  mergeBranch <- 0.5 * (unlist(lapply(lapply(lambdas,"*",cross_M_N),sum)))
  ^~~~~~~~~~~
```
[R/cla_secsse_loglik.R:92:54:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L92) *style:* **Commas should always have a space after.**
```r
  mergeBranch <- 0.5 * (unlist(lapply(lapply(lambdas,"*",cross_M_N),sum)))
                                                     ^
```
[R/cla_secsse_loglik.R:92:58:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L92) *style:* **Commas should always have a space after.**
```r
  mergeBranch <- 0.5 * (unlist(lapply(lapply(lambdas,"*",cross_M_N),sum)))
                                                         ^
```
[R/cla_secsse_loglik.R:92:69:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L92) *style:* **Commas should always have a space after.**
```r
  mergeBranch <- 0.5 * (unlist(lapply(lapply(lambdas,"*",cross_M_N),sum)))
                                                                    ^
```
[R/cla_secsse_loglik.R:94:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L94) *style:* **Lines should not be more than 80 characters.**
```r
  ff <- normalize_loglik(mergeBranch,loglik); mergeBranch <- ff$probs; loglik <- ff$loglik
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:94:9:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L94) *warning:* **no visible global function definition for ‘normalize_loglik’**
```r
  ff <- normalize_loglik(mergeBranch,loglik); mergeBranch <- ff$probs; loglik <- ff$loglik
        ^~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:94:38:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L94) *style:* **Commas should always have a space after.**
```r
  ff <- normalize_loglik(mergeBranch,loglik); mergeBranch <- ff$probs; loglik <- ff$loglik
                                     ^
```
[R/cla_secsse_loglik.R:94:47:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L94) *style:* **Variable and function name style should be snake_case.**
```r
  ff <- normalize_loglik(mergeBranch,loglik); mergeBranch <- ff$probs; loglik <- ff$loglik
                                              ^~~~~~~~~~~
```
[R/cla_secsse_loglik.R:95:4:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L95) *style:* **Commented code should be removed.**
```r
  #sumD <- sum(mergeBranch)
   ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:96:4:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L96) *style:* **Commented code should be removed.**
```r
  #mergeBranch <- mergeBranch/sumD
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:97:4:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L97) *style:* **Commented code should be removed.**
```r
  #loglik <- loglik + log(sumD)
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:98:4:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L98) *style:* **Commented code should be removed.**
```r
  #cat(mergeBranch,"\n")
   ^~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:100:26:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L100) *style:* **Commas should always have a space after.**
```r
  newstate <- c(newstate,mergeBranch)
                         ^
```
[R/cla_secsse_loglik.R:101:16:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L101) *style:* **Commas should always have a space after.**
```r
  states[focal,] <- newstate
               ^
```
[R/cla_secsse_loglik.R:102:4:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L102) *style:* **Commented code should be removed.**
```r
  #print(parameter); print(loglik)
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:103:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L103) *style:* **Lines should not be more than 80 characters.**
```r
  return(list(states = states,loglik = loglik,mergeBranch = mergeBranch,nodeM = nodeM))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:103:31:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L103) *style:* **Commas should always have a space after.**
```r
  return(list(states = states,loglik = loglik,mergeBranch = mergeBranch,nodeM = nodeM))
                              ^
```
[R/cla_secsse_loglik.R:103:47:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L103) *style:* **Commas should always have a space after.**
```r
  return(list(states = states,loglik = loglik,mergeBranch = mergeBranch,nodeM = nodeM))
                                              ^
```
[R/cla_secsse_loglik.R:103:73:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L103) *style:* **Commas should always have a space after.**
```r
  return(list(states = states,loglik = loglik,mergeBranch = mergeBranch,nodeM = nodeM))
                                                                        ^
```
[R/cla_secsse_loglik.R:110:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L110) *style:* **Variable and function name style should be snake_case.**
```r
cla_doParalThing <- function(take_ancesSub,
^~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:110:30:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L110) *style:* **Variable and function name style should be snake_case.**
```r
cla_doParalThing <- function(take_ancesSub,
                             ^~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:113:26:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L113) *style:* **Variable and function name style should be snake_case.**
```r
                         forTime,
                         ^~~~~~~
```
[R/cla_secsse_loglik.R:118:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L118) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:120:4:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L120) *style:* **Commented code should be removed.**
```r
  #cl <- makeCluster(2)
   ^~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:121:4:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L121) *style:* **Commented code should be removed.**
```r
  #registerDoParallel(cl)
   ^~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:122:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L122) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:123:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L123) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:124:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L124) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:128:3:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L128) *style:* **Variable and function name style should be snake_case.**
```r
  statesNEW <- foreach::foreach (ii = 1:2,
  ^~~~~~~~~
```
[R/cla_secsse_loglik.R:128:33:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L128) *style:* **Remove spaces before the left parenthesis in a function call.**
```r
  statesNEW <- foreach::foreach (ii = 1:2,
                                ^
```
[R/cla_secsse_loglik.R:145:47:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L145) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
                                   )) %dopar% {
                                              ^
```
[R/cla_secsse_loglik.R:145:48:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L145) *style:* **Trailing whitespace is superfluous.**
```r
                                   )) %dopar% {
                                               ^
```
[R/cla_secsse_loglik.R:146:38:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L146) *style:* **Variable and function name style should be snake_case.**
```r
                                     ancesSub <- take_ancesSub[[ii]]
                                     ^~~~~~~~
```
[R/cla_secsse_loglik.R:147:41:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L147) *style:* **Place a space before left parenthesis, except in a function call.**
```r
                                     for(i in 1:length(ancesSub)){
                                        ^
```
[R/cla_secsse_loglik.R:148:49:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L148) *style:* **Trailing whitespace is superfluous.**
```r
                                       calcul <-
                                                ^
```
[R/cla_secsse_loglik.R:154:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L154) *style:* **Lines should not be more than 80 characters.**
```r
                                                          use_fortran = use_fortran,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:165:28:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L165) *style:* **Trailing whitespace is superfluous.**
```r
#' Logikelihood calculation
                           ^
```
[R/cla_secsse_loglik.R:168:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L168) *style:* **Lines should not be more than 80 characters.**
```r
#' @param parameter list where the first is a table where lambdas across different modes of speciation are shown, the second mus and the third transition rates.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:169:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L169) *style:* **Lines should not be more than 80 characters.**
```r
#' @param phy phylogenetic tree of class phylo, ultrametric, fully-resolved, rooted and with branch lengths.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:170:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L170) *style:* **Lines should not be more than 80 characters.**
```r
#' @param traits vector with trait states, order of states must be the same as tree tips, for help, see vignette.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:171:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L171) *style:* **Lines should not be more than 80 characters.**
```r
#' @param num_concealed_states number of concealed states, generally equivalent to number of examined states.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:172:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L172) *style:* **Lines should not be more than 80 characters.**
```r
#' @param use_fortran Should the Fortran code for numerical integration be called? Default is TRUE.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:174:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L174) *style:* **Lines should not be more than 80 characters.**
```r
#' @param cond condition on the existence of a node root: "maddison_cond","proper_cond"(default). For details, see vignette.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:175:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L175) *style:* **Lines should not be more than 80 characters.**
```r
#' @param root_state_weight the method to weigh the states:"maddison_weights","proper_weights"(default) or "equal_weights". It can also be specified the root state:the vector c(1,0,0) indicates state 1 was the root state.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:176:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L176) *style:* **Lines should not be more than 80 characters.**
```r
#' @param sampling_fraction vector that states the sampling proportion per trait state. It must have as many elements as trait states.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:178:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L178) *style:* **Lines should not be more than 80 characters.**
```r
#' @param setting_calculation argument used internally to speed up calculation. It should be leave blank (default : setting_calculation = NULL)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:179:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L179) *style:* **Lines should not be more than 80 characters.**
```r
#' @param setting_parallel argument used internally to set a parallel calculation. It should be left blank (default : setting_parallel = NULL)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:180:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L180) *style:* **Lines should not be more than 80 characters.**
```r
#' @param see_ancestral_states should the ancestral states be shown? Deafault FALSE
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:181:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L181) *style:* **Lines should not be more than 80 characters.**
```r
#' @param loglik_penalty the size of the penalty for all parameters; default is 0 (no penalty)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:182:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L182) *style:* **Lines should not be more than 80 characters.**
```r
#' @note To run in parallel it is needed to load the following libraries when windows: apTreeshape, doparallel and foreach. When unix, it requires: apTreeshape, doparallel, foreach and doMC
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:207:52:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L207) *style:* **Trailing whitespace is superfluous.**
```r
#'masterBlock <- matrix(4,ncol=3,nrow=3,byrow=TRUE)
                                                   ^
```
[R/cla_secsse_loglik.R:211:67:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L211) *style:* **Trailing whitespace is superfluous.**
```r
#'prepare_full_lambdas(traits,num_concealed_states,idparlist[[1]])
                                                                  ^
```
[R/cla_secsse_loglik.R:212:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L212) *style:* **Lines should not be more than 80 characters.**
```r
#'# which is a list with 9 matrices, corresponding to the 9 states (0A,1A,2A,0B,etc)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:217:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L217) *style:* **Lines should not be more than 80 characters.**
```r
#'parameter[[1]] <- prepare_full_lambdas(traits,num_concealed_states,lambd_and_modeSpe)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:217:88:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L217) *style:* **Trailing whitespace is superfluous.**
```r
#'parameter[[1]] <- prepare_full_lambdas(traits,num_concealed_states,lambd_and_modeSpe)
                                                                                ^
```
[R/cla_secsse_loglik.R:219:55:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L219) *style:* **Trailing whitespace is superfluous.**
```r
#'masterBlock <- matrix(0.07,ncol=3,nrow=3,byrow=TRUE)
                                                      ^
```
[R/cla_secsse_loglik.R:223:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L223) *style:* **Lines should not be more than 80 characters.**
```r
#'                  use_fortran = FALSE, methode = "ode45", cond = "maddison_cond",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:230:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L230) *style:* **functions should have cyclomatic complexity of less than 15, this has 26.**
```r
cla_secsse_loglik <- function(parameter,
^
```
[R/cla_secsse_loglik.R:245:3:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L245) *warning:* **local variable ‘mus’ assigned but may not be used**
```r
  mus <- parameter[[2]]
  ^~~
```
[R/cla_secsse_loglik.R:247:3:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L247) *warning:* **local variable ‘Q’ assigned but may not be used**
```r
  Q <- parameter[[3]]
  ^
```
[R/cla_secsse_loglik.R:247:3:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L247) *style:* **Variable and function name style should be snake_case.**
```r
  Q <- parameter[[3]]
  ^
```
[R/cla_secsse_loglik.R:248:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L248) *style:* **Trailing whitespace is superfluous.**
```r

^~
```
[R/cla_secsse_loglik.R:249:5:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L249) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(run_parallel == TRUE){
    ^
```
[R/cla_secsse_loglik.R:249:27:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L249) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
  if(run_parallel == TRUE){
                          ^
```
[R/cla_secsse_loglik.R:249:28:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L249) *style:* **Trailing whitespace is superfluous.**
```r
  if(run_parallel == TRUE){
                           ^
```
[R/cla_secsse_loglik.R:250:7:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L250) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(is.null(setting_calculation)){
      ^
```
[R/cla_secsse_loglik.R:251:7:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L251) *warning:* **no visible global function definition for ‘check_input’**
```r
      check_input(traits,phy,sampling_fraction,root_state_weight)
      ^~~~~~~~~~~
```
[R/cla_secsse_loglik.R:251:26:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L251) *style:* **Commas should always have a space after.**
```r
      check_input(traits,phy,sampling_fraction,root_state_weight)
                         ^
```
[R/cla_secsse_loglik.R:251:30:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L251) *style:* **Commas should always have a space after.**
```r
      check_input(traits,phy,sampling_fraction,root_state_weight)
                             ^
```
[R/cla_secsse_loglik.R:251:48:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L251) *style:* **Commas should always have a space after.**
```r
      check_input(traits,phy,sampling_fraction,root_state_weight)
                                               ^
```
[R/cla_secsse_loglik.R:252:29:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L252) *style:* **Trailing whitespace is superfluous.**
```r
      setting_calculation <-
                            ^
```
[R/cla_secsse_loglik.R:253:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L253) *style:* **Lines should not be more than 80 characters.**
```r
        build_initStates_time_bigtree(phy, traits, num_concealed_states, sampling_fraction)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:255:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L255) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/cla_secsse_loglik.R:257:5:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L257) *style:* **Variable and function name style should be snake_case.**
```r
    forTime <- setting_calculation$forTime
    ^~~~~~~
```
[R/cla_secsse_loglik.R:258:5:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L258) *style:* **Variable and function name style should be snake_case.**
```r
    ancesSub1 <- setting_calculation$ancesSub1
    ^~~~~~~~~
```
[R/cla_secsse_loglik.R:259:5:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L259) *style:* **Variable and function name style should be snake_case.**
```r
    ancesSub2 <- setting_calculation$ancesSub2
    ^~~~~~~~~
```
[R/cla_secsse_loglik.R:260:5:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L260) *style:* **Variable and function name style should be snake_case.**
```r
    ancesRest <- setting_calculation$ancesRest
    ^~~~~~~~~
```
[R/cla_secsse_loglik.R:261:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L261) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/cla_secsse_loglik.R:262:7:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L262) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(num_concealed_states != round(num_concealed_states)){ # for testing
      ^
```
[R/cla_secsse_loglik.R:262:60:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L262) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
    if(num_concealed_states != round(num_concealed_states)){ # for testing
                                                           ^
```
[R/cla_secsse_loglik.R:262:75:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L262) *style:* **Trailing whitespace is superfluous.**
```r
    if(num_concealed_states != round(num_concealed_states)){ # for testing
                                                                          ^
```
[R/cla_secsse_loglik.R:263:28:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L263) *style:* **Trailing whitespace is superfluous.**
```r
      d <- ncol(states) / 2
                           ^
```
[R/cla_secsse_loglik.R:264:29:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L264) *style:* **Commas should always have a space after.**
```r
      new_states <- states[,c(1:sqrt(d),(d + 1):((d + 1) + sqrt(d) - 1))]
                            ^
```
[R/cla_secsse_loglik.R:264:41:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L264) *style:* **Commas should always have a space after.**
```r
      new_states <- states[,c(1:sqrt(d),(d + 1):((d + 1) + sqrt(d) - 1))]
                                        ^
```
[R/cla_secsse_loglik.R:264:41:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L264) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      new_states <- states[,c(1:sqrt(d),(d + 1):((d + 1) + sqrt(d) - 1))]
                                        ^
```
[R/cla_secsse_loglik.R:265:29:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L265) *style:* **Commas should always have a space after.**
```r
      new_states <- states[,c(1,2,3,10,11,12)]
                            ^
```
[R/cla_secsse_loglik.R:265:33:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L265) *style:* **Commas should always have a space after.**
```r
      new_states <- states[,c(1,2,3,10,11,12)]
                                ^
```
[R/cla_secsse_loglik.R:265:35:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L265) *style:* **Commas should always have a space after.**
```r
      new_states <- states[,c(1,2,3,10,11,12)]
                                  ^
```
[R/cla_secsse_loglik.R:265:37:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L265) *style:* **Commas should always have a space after.**
```r
      new_states <- states[,c(1,2,3,10,11,12)]
                                    ^
```
[R/cla_secsse_loglik.R:265:40:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L265) *style:* **Commas should always have a space after.**
```r
      new_states <- states[,c(1,2,3,10,11,12)]
                                       ^
```
[R/cla_secsse_loglik.R:265:43:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L265) *style:* **Commas should always have a space after.**
```r
      new_states <- states[,c(1,2,3,10,11,12)]
                                          ^
```
[R/cla_secsse_loglik.R:268:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L268) *style:* **Trailing whitespace is superfluous.**
```r

^~~~~~~~
```
[R/cla_secsse_loglik.R:270:5:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L270) *warning:* **local variable ‘ly’ assigned but may not be used**
```r
    ly <- ncol(states)
    ^~
```
[R/cla_secsse_loglik.R:272:5:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L272) *style:* **Variable and function name style should be snake_case.**
```r
    take_ancesSub <- list(ancesSub1, ancesSub2)
    ^~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:273:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L273) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/cla_secsse_loglik.R:274:7:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L274) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(is.null(setting_parallel)){
      ^
```
[R/cla_secsse_loglik.R:278:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L278) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/cla_secsse_loglik.R:279:5:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L279) *style:* **Variable and function name style should be snake_case.**
```r
    statesNEW <- cla_doParalThing(take_ancesSub,
    ^~~~~~~~~
```
[R/cla_secsse_loglik.R:288:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L288) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/cla_secsse_loglik.R:289:5:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L289) *style:* **Variable and function name style should be snake_case.**
```r
    comingfromSub1 <- statesNEW[[1]][[1]]
    ^~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:290:5:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L290) *style:* **Variable and function name style should be snake_case.**
```r
    comingfromSub2 <- statesNEW[[2]][[1]]
    ^~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:292:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L292) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/cla_secsse_loglik.R:293:5:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L293) *style:* **Variable and function name style should be snake_case.**
```r
    thoseCalculated <-
    ^~~~~~~~~~~~~~~
```
[R/cla_secsse_loglik.R:293:23:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L293) *style:* **Trailing whitespace is superfluous.**
```r
    thoseCalculated <-
                      ^
```
[R/cla_secsse_loglik.R:297:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L297) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/cla_secsse_loglik.R:300:1:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L300) *style:* **Trailing whitespace is superfluous.**
```r

^~~~
```
[R/cla_secsse_loglik.R:301:8:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L301) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    for(i in 1:length(ancesRest)){
       ^
```
[R/cla_secsse_loglik.R:302:16:](https://github.com/rsetienne/secsse/blob/e22fa181a4ff83be6c194c831400b5c23c395256/R/cla_secsse_loglik.R#L302) *style:* **Trailing whitespace is superfluous.**
```r
      calcul <-
               ^
```


<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

Schema Validation Failed!
Rejecting Schema: https://schemas.taskcluster.net/github/v1/taskcluster-github-config.json#
Errors:
  * data should NOT have additional properties: "scopes"
  * data.metadata.source should be string

</details>


ну по тз они никуда не ведут, они попап только открывают
![2019-09-06_23-33-32](https://user-images.githubusercontent.com/42157058/64458762-db3d2980-d0fe-11e9-91dc-d7bd1b492a50.png)


<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

end of the stream or a document separator is expected at line 4, column 1:
    version
    ^

</details>


I did a text search and found only one instance of ```[`compute_Mlincomb!`](@ref)```, which probably can be changed for the other one. What do you think of including the docs only for `compute_Mlincomb`? (Possibly with a rewrite of the doc-string if needed)


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-128-aledade.pantheonsite.io/)

Created multidev environment [pr-128](https://dashboard.pantheon.io/sites/533c69ec-70af-4cb2-af59-49d50e7d05f7#pr-128) for aledade.


does this close #26?


FYI I have just flashed a Sonoff POWR2 with the flash.sh and it works fine.


That's probably older code


CoolingTowerPlantComponent (Myoldmopar) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-IntegrationCoverage-Debug: OK (673 of 673 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-68.43%25-green.png)


![Turtle Art Gallery](https://user-images.githubusercontent.com/54724853/64458968-5df0c500-d0bc-11e9-9492-e9e72cc2ba0c.PNG)


The `snr` parameter is used to track the referrer


немного неправильное возращемое значение
смотрите вот например вы инстанцируете класс `stack` с таким типом
```
struct Test {
  int a;
};

....
stack<Test> st;
```
как вы думаете будет в таком случае ваш код будет компилироваться???
нет. Т.к. нет способа преобразования структуры `Test` в `int`
Поэтому возращаемое значение должно быть
```
return Type{};
```


Hi - yeah, I didn't think it was just this commit - but the commit and my particular configuration of Emacs.  As usual. :)

I did some debugging, and saw the cache file was fresh - so it's not the URL directly.  It was able to get that and pull the data from openweathermap just fine.

Some more debugging and I see the wrong type argument is coming from a round() call passed a nil value -
in the line:
   (cons 'min (format "%s %s" (round (cdr (assoc 'min (cdr (assoc 'temp day))))) temp-symbol))

I was suspecting perhaps the version cl (or cl-lib) I have wasn't right.  I'm running Emacs 27.0.50 from the latest pretest build on savannah (x64 on windows [sigh]) and it says cl-lib 1.0 is built-in.  So that's probably not it.

I'll contact you via email to continue this and not clutter this commit - I wanted to state for others though that I didn't think it was just this commit but running it in my Emacs with my configuration. :)

Rob


TeamCity Bvcms / Build [Build 1973](https://builds.tpsdb.com/viewLog.html?buildId=8271&buildTypeId=Bvcms_Build) outcome was **SUCCESS**
Summary: Tests passed: 91 Build time: 00:20:40


TeamCity Bvcms / Build [Build 1974](https://builds.tpsdb.com/viewLog.html?buildId=8272&buildTypeId=Bvcms_Build) is now running


🔥 Device tests completed (Failed) on iOS-Beta on [Azure DevOps](https://dev.azure.com/devdiv/DevDiv/_build/index?buildId=3026056)(iOS-Beta): [Html Report](http://xamarin-storage/jenkins/xamarin-macios/xcode11/a9abc07cb357f9f012e3da66c70fa09d96bf02f7/3026056/device-tests/jenkins-results/tests/index.html) 🔥

# Test results

<details>
<summary>66 tests failed, 11 tests passed.</summary>

## Failed tests

 * monotouch-test/iOS Unified 64-bits - device/Debug: Crashed
 * framework-test/iOS Unified 64-bits - device/Debug: Crashed
 * interdependent-binding-projects/iOS Unified 64-bits - device/Debug: Crashed
 * fsharp/iOS Unified 64-bits - device/Debug: Crashed
 * dont link/iOS Unified 64-bits - device/Debug: Crashed
 * link all/iOS Unified 64-bits - device/Debug: Crashed
 * link sdk/iOS Unified 64-bits - device/Debug: Crashed
 * mono-native-compat/iOS Unified 64-bits - device/Debug: Crashed
 * mono-native-unified/iOS Unified 64-bits - device/Debug: Crashed
 * monotouch-test/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug): Crashed
 * monotouch-test/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug): Crashed
 * monotouch-test/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug, profiling): Crashed
 * monotouch-test/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug, profiling): Crashed
 * monotouch-test/iOS Unified 64-bits - device/Release: Crashed
 * monotouch-test/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (release): Crashed
 * monotouch-test/iOS Unified 64-bits - device/Release (all optimizations): Crashed
 * monotouch-test/iOS Unified 64-bits - device/Debug (all optimizations): Crashed
 * monotouch-test/iOS Unified 64-bits - device/Debug: SGenConc: Crashed
 * framework-test/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug): Crashed
 * framework-test/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug): Crashed
 * framework-test/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug, profiling): Crashed
 * framework-test/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug, profiling): Crashed
 * framework-test/iOS Unified 64-bits - device/Release: Crashed
 * framework-test/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (release): Crashed
 * interdependent-binding-projects/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug): Crashed
 * interdependent-binding-projects/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug): Crashed
 * interdependent-binding-projects/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug, profiling): Crashed
 * interdependent-binding-projects/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug, profiling): Crashed
 * interdependent-binding-projects/iOS Unified 64-bits - device/Release: Crashed
 * interdependent-binding-projects/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (release): Crashed
 * fsharp/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug): Crashed
 * fsharp/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug): Crashed
 * fsharp/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug, profiling): Crashed
 * fsharp/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug, profiling): Crashed
 * fsharp/iOS Unified 64-bits - device/Release: Crashed
 * fsharp/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (release): Crashed
 * dont link/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug): Crashed
 * dont link/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug): Crashed
 * dont link/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug, profiling): Crashed
 * dont link/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug, profiling): Crashed
 * dont link/iOS Unified 64-bits - device/Release: Crashed
 * dont link/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (release): Crashed
 * link all/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug): Crashed
 * link all/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug): Crashed
 * link all/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug, profiling): Crashed
 * link all/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug, profiling): Crashed
 * link all/iOS Unified 64-bits - device/Release: Crashed
 * link all/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (release): Crashed
 * link sdk/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug): Crashed
 * link sdk/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug): Crashed
 * link sdk/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug, profiling): Crashed
 * link sdk/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug, profiling): Crashed
 * link sdk/iOS Unified 64-bits - device/Release: Crashed
 * link sdk/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (release): Crashed
 * mono-native-compat/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug): Crashed
 * mono-native-compat/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug): Crashed
 * mono-native-compat/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug, profiling): Crashed
 * mono-native-compat/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug, profiling): Crashed
 * mono-native-compat/iOS Unified 64-bits - device/Release: Crashed
 * mono-native-compat/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (release): Crashed
 * mono-native-unified/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug): Crashed
 * mono-native-unified/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug): Crashed
 * mono-native-unified/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug, profiling): Crashed
 * mono-native-unified/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug, profiling): Crashed
 * mono-native-unified/iOS Unified 64-bits - device/Release: Crashed
 * mono-native-unified/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (release): Crashed
</details>


используйте  вместо такого способа, более привычный способ для работы с указателями для структуры или класса


Commit


ну наверное лучше будет использовать `new`


@KPrasch I thought I already left a comment here but I no longer see it. This added `if` check was causing Ursula status page to not load since the nickname attribute was not set for Ursula. Try running an Ursula status page.


возращаемое значение не верно, т.к. не будет работать для всех типов