в самом начале разметки это проговаривалось, вот и оставил, сейчас понимаю, что так не пойдет


![Difference between blocks](https://raw.githubusercontent.com/dylan0000/projectilesincomplete/d0ab17d815dca5ecd906713a64c766ca6d0dbae3/.github/makecode/blocksdiff.png)


![Difference between blocks](https://raw.githubusercontent.com/avedag/shoot/4794e2d29eca5f5e3820329be6f847b88a699f26/.github/makecode/blocksdiff.png)


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/terminus-build-tools-plugin/master/assets/images/visit-site-36.png)](https://pr-64-gregory-industries.pantheonsite.io/)

Created multidev environment [pr-64](https://dashboard.pantheon.io/sites/6a63ef8e-11f2-468f-86b6-5973ebf0ffbd#pr-64) for gregory-industries.


Successfully deployed to following URLs:

* https://mangirishwaglegithubio-pulsa9lun.now.sh
* https://mangirishwagle.now.sh
* https://mangirishwaglegithubio.mangirishwagle.now.sh
* https://mangirishwaglegithubio-git-master.mangirishwagle.now.sh


Deploy preview for _website_ ready!

Built with commit ebb9fdaae62ab626c1dd94fcb2c29770262cf07b

https://atlas-u29hlszet.now.sh


ignore this... mistakes were made.


![](https://github.trello.services/images/mini-trello-icon.png) [Create a proper setup for defining mission on the frontend](https://trello.com/c/0bUkl9CB/15-create-a-proper-setup-for-defining-mission-on-the-frontend)


![](https://github.trello.services/images/mini-trello-icon.png) [Make drag and drop setup for defining missions](https://trello.com/c/5HbRXrzz/47-make-drag-and-drop-setup-for-defining-missions)


Successfully deployed to following URLs:

* https://shaikheena-njbwklook.now.sh
* https://shaikheena.now.sh
* https://heena.me
* https://shaikheena.shaikheena.now.sh
* https://shaikheena-git-master.shaikheena.now.sh


Could you probably suggest this as a pull request against Choco, please?


Hi, I am trying to train two models using the RCF algorithm and deploy them to a multi-model endpoint. However, I get some errors that I don’t know how to troubleshoot, and I was wondering if someone came across this before and could give me a bit of help. I copy pasted some of the logs below. Thank you!

Natalia

[ERROR] 2020-01-08T14:51:07.572Z bf193acb-85b8-46a5-a45d-b7ecb6d68b5b An error occurred (ModelError) when calling the InvokeEndpoint operation: Received server error (500) from model with message:
{
"code": 500,
"type": "InternalServerException",
"message": "Failed to start workers"
}
See https://eu-west-1.console.aws.amazon.com/cloudwatch/home?region=eu-west-1#logEventViewer:group=/aws/sagemaker/Endpoints/[my endpoint] in account [my account no] for more information (copy pasted below)

Warning: Calling MMS with mxnet-model-server. Please move to multi-model-server.
2020-01-08 14:06:06,601 [INFO ] epollEventLoopGroup-3-1 com.amazonaws.ml.mms.wlm.ModelManager - Model 4af28fd3c2e275f27e28fb93ec9b1750 loaded.
2020-01-08 14:06:06,741 [INFO ] W-9000-4af28fd3c2e275f27e28fb93e-stdout com.amazonaws.ml.mms.wlm.WorkerLifeCycle - MXNet worker started.
2020-01-08 14:06:08,000 [INFO ] W-9001-4af28fd3c2e275f27e28fb93e-stdout com.amazonaws.ml.mms.wlm.WorkerLifeCycle - Backend worker process die.
2020-01-08 14:06:08,003 [INFO ] epollEventLoopGroup-4-1 com.amazonaws.ml.mms.wlm.WorkerThread - 9001 Worker disconnected. WORKER_STARTED
2020-01-08 14:06:08,004 [INFO ] W-9000-4af28fd3c2e275f27e28fb93e-stdout com.amazonaws.ml.mms.wlm.WorkerLifeCycle - checkpoint_prefix_filename = glob.glob(checkpoint_prefix_regex)[0] # Ex output: /opt/ml/models/resnet-18/model/resnet18-symbol.json
2020-01-08 14:06:08,004 [INFO ] W-9000-4af28fd3c2e275f27e28fb93e-stdout com.amazonaws.ml.mms.wlm.WorkerLifeCycle - IndexError: list index out of range
2020-01-08 14:06:08,005 [WARN ] W-9001-4af28fd3c2e275f27e28fb93e com.amazonaws.ml.mms.wlm.BatchAggregator - Load model failed: 4af28fd3c2e275f27e28fb93ec9b1750, error: Worker died.
2020-01-08 14:06:08,006 [INFO ] epollEventLoopGroup-4-2 com.amazonaws.ml.mms.wlm.WorkerThread - 9000 Worker disconnected. WORKER_STARTED


This change causes (my particular error message comes from `tsc`) :
```
node_modules/@types/connect/index.d.ts:21:42 - error TS2689: Cannot extend an interface 'http.IncomingMessage'. Did you mean 'implements'?

21     export class IncomingMessage extends http.IncomingMessage {
                                            ~~~~~~~~~~~~~~~~~~~~
```

A workaround may be forcing older version in `package.json` file `"@types/connect": "3.4.32"`  or explicitly installing `npm install @types/connect@3.4.32`.

...I am adding this comment to be indexed by search engines and maybe helps other :)


Instead of map all the badges, we could do this?

```ruby
return true if user.badges
  .where(allow_title: true)
  .pluck(:name)
  .any? { |name| Badge.display_name(name) == title }
```


blah blah


desuperheater_remain_issues (yzhou601) - x86_64-Linux-Ubuntu-18.04-gcc-7.4-UnitTestsCoverage-Debug: OK (1255 of 1255 tests passed, 0 test warnings)

![Build Badge](http://img.shields.io/badge/build%20status-passing-green.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-100.0%25-green.png) ![Coverage Badge](http://img.shields.io/badge/coverage%20status-43.51%25-green.png)


Successfully deployed to following URLs:

* https://github-e2e-tests-dev-alias-v2-without-alias-jxgq5khst.now.sh
* https://github-e2e-tests-dev-alias-v2-without-alias.zeit-github-test-dev1.now.sh
* https://github-e2e-tests-dev-alias-v2-without-alias-git-master.zeit-github-test-dev1.now.sh


Successfully deployed to following URLs:

* https://github-e2e-tests-dev-alias-v1-with-alias-suvwdhzglk.now.sh
* https://z-github-e2e-tests-dev-only.now.sh


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

~~~
The domain peebnkw43o.com is not verfied and cannot be used as an alias.
~~~

([Learn more](http://localhost:3000/zeit-github-test-dev/github-e2e-test-dev-domain-issues/n73oc4yf2) or [visit](https://github-e2e-test-dev-domain-issues-n73oc4yf2.now.sh) the non-aliased deployment)


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

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

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

### Deployments updated

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

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


Successfully deployed to following URLs:

* https://carga-logistica-4pz84ehya.now.sh
* https://carga-logistica.now.sh
* https://carga-logistica.andresmontoyain.now.sh
* https://carga-logistica-git-master.andresmontoyain.now.sh


- Add dynamo DB support using boto3
- Change the "on or off" logic from new_state's value of "true/false" (string) to True/False (Boolean)
- Split up environment variable validation
- For creating file: Change new_state to state so it uses the value "on/off" instead of "True/False"


only thing I found was https://stackoverflow.com/questions/28222533/polymorphism-for-foreign-key-constraints
+ the link in the comments


Successfully deployed to following URLs:

* https://bsd-weekly-eyrl2lw21.now.sh
* https://bsd-weekly.now.sh
* https://bsdweekly.com
* https://www.bsdweekly.com
* https://bsd-weekly.hovancik.now.sh
* https://bsd-weekly-git-master.hovancik.now.sh


Names copied directly from IDA DB, since it's safer to use distinct enum names in 3.8 codebase.


hello


cntrl  .
0001?


Successfully deployed to following URLs:

* https://docs-5pithlk6o.now.sh
* https://docs.zeit.sh
* https://docs.zeit.now.sh
* https://docs-git-master.zeit.now.sh


Why would anyone want this?
It opens the system, from the start, to a backdoored/compromised setup of jeedom.


Successfully deployed to following URLs:

* https://zenunu-7bhn1noz1.now.sh
* https://zenunu.now.sh
* https://zenunu.dtox-consulting.now.sh
* https://zenunu-git-master.dtox-consulting.now.sh


Interesting, thanks!


prefix shouldn't be "clamped", there is no reason to do this.


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/terminus-build-tools-plugin/master/assets/images/visit-site-36.png)](https://pr-6-dasjo-be.pantheonsite.io/)

Created multidev environment [pr-6](https://dashboard.pantheon.io/sites/c63ab8da-cec4-4d01-b9c0-198938b4328c#pr-6) for dasjo-be.


This is a simple reply!


You can use `null_resource` with count for expanding: https://github.com/flexkube/libflexkube/blob/master/e2e/main.tf#L51-L59


Newline missing.


первый кормит


This contains some code for sorting and stuff.


They may be succeeding when running them in the TestRunner on your machine, but they seem to be failing on our CI (see for example https://travis-ci.org/hpi-swa/graalsqueak/jobs/632322106#L4014). Yes, this is an obscure bug.


### TinyCI build failure:
[make -j 3] returned [2]:
```[  0%] Built target json11
[  6%] Built target lua
[  7%] Built target miniz
[ 16%] Built target box2d
[ 42%] Built target sp2freetype
[ 71%] Built target bullet
Scanning dependencies of target Pokemon
[ 71%] Building CXX object CMakeFiles/Pokemon.dir/home/tinyci/builds/daid/SeriousProton2/src/timer.cpp.o
CMakeFiles/Pokemon.dir/build.make:3566: recipe for target 'CMakeFiles/Pokemon.dir/home/tinyci/builds/daid/SeriousProton2/src/timer.cpp.o' failed
CMakeFiles/Makefile2:220: recipe for target 'CMakeFiles/Pokemon.dir/all' failed
Makefile:105: recipe for target 'all' failed

/home/tinyci/builds/daid/SeriousProton2/src/timer.cpp: In static member function 'static sp::EngineTime::time_point sp::EngineTime::now()':
/home/tinyci/builds/daid/SeriousProton2/src/timer.cpp:8:62: error: 'class sp::Engine' has no member named 'getElapsedGameTime'
     return EngineTime::time_point(sp::Engine::getInstance()->getElapsedGameTime());
                                                              ^~~~~~~~~~~~~~~~~~
make[2]: *** [CMakeFiles/Pokemon.dir/home/tinyci/builds/daid/SeriousProton2/src/timer.cpp.o] Error 1
make[1]: *** [CMakeFiles/Pokemon.dir/all] Error 2
make: *** [all] Error 2
```


Successfully deployed to following URLs:

* https://chronarium-2ct5rfqy6.now.sh
* https://chronarium.now.sh
* https://chronarium.danilex.now.sh
* https://chronarium-git-master.danilex.now.sh


Finally, here is 1.0.0, Great job @ged-odoo and Team :clap::heart:


### TinyCI build failure:
[make -j 3] returned [2]:
```[  1%] Built target json11
[  7%] Built target lua
[  7%] Built target miniz
[ 16%] Built target box2d
[ 43%] Built target sp2freetype
[ 73%] Built target bullet
Scanning dependencies of target ZeroRho
[ 73%] Building CXX object CMakeFiles/ZeroRho.dir/home/tinyci/builds/daid/SeriousProton2/src/timer.cpp.o
CMakeFiles/ZeroRho.dir/build.make:3278: recipe for target 'CMakeFiles/ZeroRho.dir/home/tinyci/builds/daid/SeriousProton2/src/timer.cpp.o' failed
CMakeFiles/Makefile2:294: recipe for target 'CMakeFiles/ZeroRho.dir/all' failed
Makefile:105: recipe for target 'all' failed

/home/tinyci/builds/daid/SeriousProton2/src/timer.cpp: In static member function 'static sp::EngineTime::time_point sp::EngineTime::now()':
/home/tinyci/builds/daid/SeriousProton2/src/timer.cpp:8:62: error: 'class sp::Engine' has no member named 'getElapsedGameTime'
     return EngineTime::time_point(sp::Engine::getInstance()->getElapsedGameTime());
                                                              ^~~~~~~~~~~~~~~~~~
make[2]: *** [CMakeFiles/ZeroRho.dir/home/tinyci/builds/daid/SeriousProton2/src/timer.cpp.o] Error 1
make[1]: *** [CMakeFiles/ZeroRho.dir/all] Error 2
make: *** [all] Error 2
```


:trollface:


### TinyCI build failure:
[make -j 3] returned [2]:
```[  1%] Built target json11
[  7%] Built target lua
[  7%] Built target miniz
[ 16%] Built target box2d
[ 42%] Built target sp2freetype
[ 70%] Built target bullet
Scanning dependencies of target Fuseblaze
[ 70%] Building CXX object CMakeFiles/Fuseblaze.dir/home/tinyci/builds/daid/SeriousProton2/src/timer.cpp.o
CMakeFiles/Fuseblaze.dir/build.make:3758: recipe for target 'CMakeFiles/Fuseblaze.dir/home/tinyci/builds/daid/SeriousProton2/src/timer.cpp.o' failed
CMakeFiles/Makefile2:146: recipe for target 'CMakeFiles/Fuseblaze.dir/all' failed
Makefile:105: recipe for target 'all' failed

/home/tinyci/builds/daid/SeriousProton2/src/timer.cpp: In static member function 'static sp::EngineTime::time_point sp::EngineTime::now()':
/home/tinyci/builds/daid/SeriousProton2/src/timer.cpp:8:62: error: 'class sp::Engine' has no member named 'getElapsedGameTime'
     return EngineTime::time_point(sp::Engine::getInstance()->getElapsedGameTime());
                                                              ^~~~~~~~~~~~~~~~~~
make[2]: *** [CMakeFiles/Fuseblaze.dir/home/tinyci/builds/daid/SeriousProton2/src/timer.cpp.o] Error 1
make[1]: *** [CMakeFiles/Fuseblaze.dir/all] Error 2
make: *** [all] Error 2
```


### TinyCI build failure:
[make -j 3] returned [2]:
```[  0%] Built target json11
[  6%] Built target lua
[  6%] Built target miniz
[ 15%] Built target box2d
[ 42%] Built target sp2freetype
[ 72%] Built target bullet
Scanning dependencies of target Geroniwar
[ 72%] Building CXX object CMakeFiles/Geroniwar.dir/data/tinyci_build/daid/SeriousProton2/src/timer.cpp.o
CMakeFiles/Geroniwar.dir/build.make:3446: recipe for target 'CMakeFiles/Geroniwar.dir/data/tinyci_build/daid/SeriousProton2/src/timer.cpp.o' failed
CMakeFiles/Makefile2:220: recipe for target 'CMakeFiles/Geroniwar.dir/all' failed
Makefile:105: recipe for target 'all' failed

/data/tinyci_build/daid/SeriousProton2/src/timer.cpp: In static member function 'static sp::EngineTime::time_point sp::EngineTime::now()':
/data/tinyci_build/daid/SeriousProton2/src/timer.cpp:8:62: error: 'class sp::Engine' has no member named 'getElapsedGameTime'
     return EngineTime::time_point(sp::Engine::getInstance()->getElapsedGameTime());
                                                              ^~~~~~~~~~~~~~~~~~
make[2]: *** [CMakeFiles/Geroniwar.dir/data/tinyci_build/daid/SeriousProton2/src/timer.cpp.o] Error 1
make[1]: *** [CMakeFiles/Geroniwar.dir/all] Error 2
make: *** [all] Error 2
```


### TinyCI build failure:
[make -j 3] returned [2]:
```[  1%] Built target json11
[  7%] Built target lua
[  7%] Built target miniz
[ 16%] Built target box2d
[ 43%] Built target sp2freetype
[ 72%] Built target bullet
Scanning dependencies of target ZeroRho
[ 73%] Building CXX object CMakeFiles/ZeroRho.dir/home/tinyci/builds/daid/SeriousProton2/src/timer.cpp.o
CMakeFiles/ZeroRho.dir/build.make:3374: recipe for target 'CMakeFiles/ZeroRho.dir/home/tinyci/builds/daid/SeriousProton2/src/timer.cpp.o' failed
CMakeFiles/Makefile2:294: recipe for target 'CMakeFiles/ZeroRho.dir/all' failed
Makefile:105: recipe for target 'all' failed

/home/tinyci/builds/daid/SeriousProton2/src/timer.cpp: In static member function 'static sp::EngineTime::time_point sp::EngineTime::now()':
/home/tinyci/builds/daid/SeriousProton2/src/timer.cpp:8:62: error: 'class sp::Engine' has no member named 'getElapsedGameTime'
     return EngineTime::time_point(sp::Engine::getInstance()->getElapsedGameTime());
                                                              ^~~~~~~~~~~~~~~~~~
make[2]: *** [CMakeFiles/ZeroRho.dir/home/tinyci/builds/daid/SeriousProton2/src/timer.cpp.o] Error 1
make[1]: *** [CMakeFiles/ZeroRho.dir/all] Error 2
make: *** [all] Error 2
```


So when EnableBuckets was set to false, the text variable wasn't set.


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

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

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

### Deployments updated

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

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


Successfully deployed to following URLs:

* https://graphql-ide-a9gp74rr2.now.sh
* https://graphql-ide.now.sh
* https://graphql-ide.yooo.now.sh
* https://graphql-ide-git-master.yooo.now.sh


運営がんば


Successfully deployed to following URLs:

* https://tsps-69u90ezvo.now.sh
* https://tsps.now.sh
* https://tsps.wangchenxu.now.sh
* https://tsps-git-master.wangchenxu.now.sh


thats why it is in experimental branch and for sh4 only. feel free to revert it anytime.


a


The following change fixes the build by adding a stub getcallerpc:

https://github.com/9fans/plan9port/pull/326


Successfully deployed to following URLs:

* https://domus-61fww8bri.now.sh
* https://domus.now.sh
* https://cogito.study
* https://www.cogito.study
* https://domus.cogito-study.now.sh
* https://domus-git-master.cogito-study.now.sh


Successfully deployed to following URLs:

* https://cinemaddict-react-app-9ya92cs93.now.sh
* https://cinemaddict-react-app.now.sh
* https://cinemaddict-react-app.zhukovaxenia.now.sh
* https://cinemaddict-react-app-git-master.zhukovaxenia.now.sh


O verdinho foi a nova implementação necessária


*This is a story of someone trying to learn:*

*HTML
*Css
*Javascript
*Php <br>
 with <h1> Becode </h1>
![Image of Yaktocat](https://octodex.github.com/images/yaktocat.png)


Successfully deployed to following URLs:

* https://sui-components-dikw9sqq2.now.sh
* https://sui-components.now.sh
* https://suicomponents.now.sh
* https://sui-components.schibstedspain.now.sh
* https://sui-components-git-master.schibstedspain.now.sh


with jitter right??


hello, how can i build the database?


Successfully deployed to following URLs:

* https://angularspa-rk798k3tz.now.sh
* https://angularspa.now.sh
* https://angularspa.asadsahi.now.sh
* https://angularspa-git-master.asadsahi.now.sh


@kocsismate thanks for your support

https://github.com/chubbyphp/chubbyphp-container/commit/df51e8998d8b661a267a95c69686c5e4dbce8a5d


Successfully deployed to following URLs:

* https://immobilienconsultingaktuell-keyb16rvz.now.sh
* https://immobilienconsultingaktuell.barbar.now.sh
* https://immobilienconsultingaktuell-git-master.barbar.now.sh


remove_objexx_gio (lefticus) - x86_64-MacOS-10.13-clang: OK (2596 of 2596 tests passed, 670 test warnings)

Messages:\n
 * 670 tests had: EIO diffs.
 * 1 test had: Table small diffs.

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


Successfully deployed to following URLs:

* https://sample-esribpipi.now.sh
* https://sample-alpha-nine.now.sh
* https://sample.masanari.now.sh
* https://sample-git-master.masanari.now.sh


[R/calc_rel_contr_node_time.R:61:1:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/calc_rel_contr_node_time.R#L61) *style:* **Lines should not be more than 80 characters.**
```r
                                   ((1 - s) * (    num_nodes + num_hidden_nodes))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_rel_contr_node_time.R:61:48:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/calc_rel_contr_node_time.R#L61) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                                   ((1 - s) * (    num_nodes + num_hidden_nodes))
                                               ^
```
[R/calc_rel_contr_node_time.R:63:1:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/calc_rel_contr_node_time.R#L63) *style:* **Lines should not be more than 80 characters.**
```r
                                   ((1 - s) * (2 * num_nodes + num_hidden_nodes))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_rel_contr_node_time.R:75:1:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/calc_rel_contr_node_time.R#L75) *style:* **Variable and function names should not be longer than 30 characters.**
```r
calc_expected_hidden_nodes_per_branch <- function(bl, lambda, mu) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_rel_contr_node_time.R:125:3:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/calc_rel_contr_node_time.R#L125) *style:* **Variable and function names should not be longer than 30 characters.**
```r
  calc_expected_hidden_nodes_per_dt <- function(t, lambda, mu) {
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_summary_statistics.R:64:1:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/calc_summary_statistics.R#L64) *style:* **Lines should not be more than 80 characters.**
```r
    # this is rather inefficient off course, RPANDA can do all pairwise comparisons?
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_summary_statistics.R:65:1:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/calc_summary_statistics.R#L65) *style:* **Lines should not be more than 80 characters.**
```r
    local_jsd <- tryCatch(RPANDA::JSDtree(list(true_tree, trees[[i]]), meth = "standard")[1,2],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/calc_summary_statistics.R:65:93:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/calc_summary_statistics.R#L65) *style:* **Commas should always have a space after.**
```r
    local_jsd <- tryCatch(RPANDA::JSDtree(list(true_tree, trees[[i]]), meth = "standard")[1,2],
                                                                                ^
```
[R/calc_summary_statistics.R:79:1:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/calc_summary_statistics.R#L79) *style:* **Lines should not be more than 80 characters.**
```r
                                 "mean_branch_length", "nLTT", "jsd", "topo_dist")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/count_hidden.R:7:1:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/count_hidden.R#L7) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
reduce_tree <- function(tree) {
^
```
[R/create_equal_alignment.R:4:1:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/create_equal_alignment.R#L4) *style:* **Lines should not be more than 80 characters.**
```r
#' @param node_model model used to generate substitutions on the nodes (linked or unlinked)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_equal_alignment.R:10:23:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/create_equal_alignment.R#L10) *warning:* **no visible global function definition for ‘calc_dist’**
```r
  num_emp_subs <- sum(calc_dist(focal_alignment, root_sequence))
                      ^~~~~~~~~
```
[R/create_equal_alignment.R:14:23:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/create_equal_alignment.R#L14) *warning:* **no visible global function definition for ‘count_hidden’**
```r
  num_hidden_nodes <- count_hidden(input_tree)
                      ^~~~~~~~~~~~
```
[R/create_equal_alignment.R:28:24:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/create_equal_alignment.R#L28) *warning:* **no visible global function definition for ‘calc_dist’**
```r
  proposed_subs <- sum(calc_dist(proposed_alignment, root_sequence))
                       ^~~~~~~~~
```
[R/create_equal_alignment.R:39:9:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/create_equal_alignment.R#L39) *warning:* **no visible global function definition for ‘calc_dist’**
```r
    sum(calc_dist(local_alignment, root_sequence))
        ^~~~~~~~~
```
[R/infer_phylogeny.R:8:1:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/infer_phylogeny.R#L8) *style:* **Lines should not be more than 80 characters.**
```r
#' @param sub_rate substitution rate used to generate the original alignment (if available), default is 1
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/infer_phylogeny.R:32:1:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/infer_phylogeny.R#L32) *style:* **Lines should not be more than 80 characters.**
```r
          clock_rate_param = beautier::create_clock_rate_param(value = sub_rate),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_independent.R:1:1:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_independent.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' simulate a sequence assuming node substitutions are shared among the offspring
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_independent.R:13:1:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_independent.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
sim_dual_independent <- function(phy,
^
```
[R/sim_dual_independent.R:14:34:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_independent.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                                 Q1 = NULL,
                                 ^~
```
[R/sim_dual_independent.R:15:34:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_independent.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                                 Q2 = NULL,
                                 ^~
```
[R/sim_dual_independent.R:37:20:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_independent.R#L37) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q1)) Q1 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_independent.R:38:20:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_independent.R#L38) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q2)) Q2 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_independent.R:41:22:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_independent.R#L41) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q1)) Q1 <- Q1[lower.tri(Q1)]
                     ^~
```
[R/sim_dual_independent.R:42:22:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_independent.R#L42) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q2)) Q2 <- Q2[lower.tri(Q2)]
                     ^~
```
[R/sim_dual_independent.R:67:10:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_independent.R#L67) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)
         ^~~~~~~~~~~~
```
[R/sim_dual_independent.R:69:7:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_independent.R#L69) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(number > length(phy$tip.label)) return(TRUE)
      ^
```
[R/sim_dual_independent.R:70:7:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_independent.R#L70) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(number <= length(phy_no_extinct$tip.label)) return(TRUE)
      ^
```
[R/sim_dual_independent.R:79:5:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_independent.R#L79) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)
    ^
```
[R/sim_dual_independent.R:80:6:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_independent.R#L80) *style:* **Commented code should be removed.**
```r
   # P <- nodeSub::slow_matrix(eig_q2, node_time, rate2)
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_independent.R:80:10:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_independent.R#L80) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
    P <- get_p_matrix(tl[i], eig_q1, rate1)
         ^~~~~~~~~~~~
```
[R/sim_dual_independent.R:92:5:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_independent.R#L92) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(tl[i], eig_q1, rate1)
    ^
```
[R/sim_dual_independent.R:93:6:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_independent.R#L93) *style:* **Commented code should be removed.**
```r
    #P <- nodeSub::slow_matrix(eig_q1, tl[i], rate1)
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_independent.R:105:7:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_independent.R#L105) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(check_to_extinct_tip(to)) {
      ^
```
[R/sim_dual_independent.R:105:23:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_independent.R#L105) *warning:* **no visible global function definition for ‘phyDat.DNA’**
```r
  alignment_phydat <- phyDat.DNA( as.data.frame(res, stringsAsFactors = FALSE))
                      ^~~~~~~~~~
```
[R/sim_dual_independent.R:114:42:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_independent.R#L114) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_dual_independent.R:117:34:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_independent.R#L117) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  alignment_phydat <- phyDat.DNA( as.data.frame(res, stringsAsFactors = FALSE))
                                 ^
```
[R/sim_dual_linked.R:35:1:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_linked.R#L35) *style:* **functions should have cyclomatic complexity of less than 15, this has 17.**
```r
make_transition_matrix <- function(mut_double) {
^
```
[R/sim_dual_linked.R:86:12:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_linked.R#L86) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
      P <- get_p_matrix(branch_length, eig_q, rate)
           ^~~~~~~~~~~~
```
[R/sim_dual_linked.R:111:1:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_linked.R#L111) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
sim_dual_linked <- function(phy,
^
```
[R/sim_dual_linked.R:112:29:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_linked.R#L112) *style:* **Variable and function name style should be snake_case.**
```r
                            Q = NULL,
                            ^
```
[R/sim_dual_linked.R:113:23:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_linked.R#L113) *warning:* **no visible global function definition for ‘phyDat.DNA’**
```r
  alignment_phydat <- phyDat.DNA(as.data.frame(res, stringsAsFactors = FALSE))
                      ^~~~~~~~~~
```
[R/sim_dual_linked.R:132:19:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_linked.R#L132) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q)) Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                  ^
```
[R/sim_dual_linked.R:135:21:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_linked.R#L135) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[R/sim_dual_linked.R:171:7:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_linked.R#L171) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(number > length(phy$tip.label)) return(TRUE)
      ^
```
[R/sim_dual_linked.R:172:7:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_linked.R#L172) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(number <= length(phy_no_extinct$tip.label)) return(TRUE)
      ^
```
[R/sim_dual_linked.R:191:6:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_linked.R#L191) *style:* **Commented code should be removed.**
```r
   # total_node_subs <- total_node_subs + node_subs_1 + node_subs_2
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_linked.R:196:7:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_linked.R#L196) *style:* **Variable and function name style should be snake_case.**
```r
      P <- get_p_matrix(branch_length, eig_q, rate)
      ^
```
[R/sim_dual_linked.R:210:9:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_linked.R#L210) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      if(check_to_extinct_tip(offspring[i])) {
        ^
```
[R/sim_dual_linked.R:220:42:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_linked.R#L220) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_dual_parent.R:1:1:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_parent.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' simulate a sequence assuming node substitutions are shared among the offspring
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_dual_parent.R:13:1:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_parent.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 18.**
```r
sim_dual_parent <- function(phy,
^
```
[R/sim_dual_parent.R:14:27:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_parent.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                          Q1 = NULL,
                          ^~
```
[R/sim_dual_parent.R:15:27:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_parent.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                          Q2 = NULL,
                          ^~
```
[R/sim_dual_parent.R:29:20:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_parent.R#L29) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q1)) Q1 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_parent.R:30:20:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_parent.R#L30) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q2)) Q2 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_dual_parent.R:33:22:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_parent.R#L33) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q1)) Q1 <- Q1[lower.tri(Q1)]
                     ^~
```
[R/sim_dual_parent.R:34:22:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_parent.R#L34) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q2)) Q2 <- Q2[lower.tri(Q2)]
                     ^~
```
[R/sim_dual_parent.R:52:10:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_parent.R#L52) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)
         ^~~~~~~~~~~~
```
[R/sim_dual_parent.R:64:5:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_parent.R#L64) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)
    ^
```
[R/sim_dual_parent.R:71:22:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_parent.R#L71) *warning:* **no visible global function definition for ‘get_index’**
```r
      local_index <- get_index(edge, parent, offspring)
                     ^~~~~~~~~
```
[R/sim_dual_parent.R:74:12:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_parent.R#L74) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
      P <- get_p_matrix(branch_length, eig_q1, rate1)
           ^~~~~~~~~~~~
```
[R/sim_dual_parent.R:86:7:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_parent.R#L86) *style:* **Variable and function name style should be snake_case.**
```r
      P <- get_p_matrix(branch_length, eig_q1, rate1)
      ^
```
[R/sim_dual_parent.R:96:23:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_parent.R#L96) *warning:* **no visible global function definition for ‘phyDat.DNA’**
```r
  alignment_phydat <- phyDat.DNA(as.data.frame(res, stringsAsFactors = FALSE))
                      ^~~~~~~~~~
```
[R/sim_dual_parent.R:105:42:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_dual_parent.R#L105) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_linked.R:12:1:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_linked.R#L12) *style:* **functions should have cyclomatic complexity of less than 15, this has 16.**
```r
sim_linked <- function(phy,
^
```
[R/sim_linked.R:13:24:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_linked.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
                       Q = NULL,
                       ^
```
[R/sim_linked.R:33:19:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_linked.R#L33) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q)) Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                  ^
```
[R/sim_linked.R:36:21:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_linked.R#L36) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[R/sim_linked.R:51:29:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_linked.R#L51) *warning:* **no visible global function definition for ‘make_transition_matrix’**
```r
  node_transition_matrix <- make_transition_matrix(node_mut_rate_double)
                            ^~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_linked.R:77:12:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_linked.R#L77) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
      P <- get_p_matrix(branch_length, eig_q, rate)
           ^~~~~~~~~~~~
```
[R/sim_linked.R:88:7:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_linked.R#L88) *style:* **Variable and function name style should be snake_case.**
```r
      P <- get_p_matrix(branch_length, eig_q, rate)
      ^
```
[R/sim_linked.R:100:23:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_linked.R#L100) *warning:* **no visible global function definition for ‘phyDat.DNA’**
```r
  alignment_phydat <- phyDat.DNA(as.data.frame(res, stringsAsFactors = FALSE))
                      ^~~~~~~~~~
```
[R/sim_linked.R:108:42:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_linked.R#L108) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_normal.R:31:24:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_normal.R#L31) *style:* **Variable and function name style should be snake_case.**
```r
                       Q = NULL,
                       ^
```
[R/sim_normal.R:39:10:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_normal.R#L39) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
    P <- get_p_matrix(tl[i], eig, rate)
         ^~~~~~~~~~~~
```
[R/sim_normal.R:43:5:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_normal.R#L43) *style:* **Variable and function name style should be snake_case.**
```r
    Q <- rep(1, lbf * (lbf - 1) / 2)
    ^
```
[R/sim_normal.R:45:21:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_normal.R#L45) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[R/sim_normal.R:56:23:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_normal.R#L56) *warning:* **no visible global function definition for ‘phyDat.DNA’**
```r
  alignment_phydat <- phyDat.DNA(as.data.frame(res, stringsAsFactors = FALSE))
                      ^~~~~~~~~~
```
[R/sim_normal.R:67:5:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_normal.R#L67) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(tl[i], eig, rate)
    ^
```
[R/sim_normal.R:81:40:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_normal.R#L81) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(x$tip.label, as.character( (k + 1):num_nodes))
                                       ^
```
[R/sim_unlinked_tree.R:10:5:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L10) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(class(phy) != "phylo") {
    ^
```
[R/sim_unlinked_tree.R:29:23:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L29) *warning:* **no visible global function definition for ‘calc_dist’**
```r
  num_emp_subs <- sum(calc_dist(focal_alignment, rootseq))
                      ^~~~~~~~~
```
[R/sim_unlinked_tree.R:34:51:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L34) *style:* **Put spaces around all infix operators.**
```r
      to_add <- c(start_node, end_node, t0, t1, t0-t1)
                                                 ~^~
```
[R/sim_unlinked_tree.R:40:3:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L40) *style:* **Variable and function names should not be longer than 30 characters.**
```r
  calc_expected_hidden_nodes_per_dt <- function(t, lambda, mu) {
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:45:9:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L45) *warning:* **no visible global function definition for ‘calc_dist’**
```r
    sum(calc_dist(local_alignment, rootseq))
        ^~~~~~~~~
```
[R/sim_unlinked_tree.R:50:35:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L50) *style:* **Commas should always have a space after.**
```r
                  apply(branches[,c(3,4)], 1,
                                  ^
```
[R/sim_unlinked_tree.R:50:39:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L50) *style:* **Commas should always have a space after.**
```r
                  apply(branches[,c(3,4)], 1,
                                      ^
```
[R/sim_unlinked_tree.R:52:36:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L52) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
                        lambda, mu) )
                                   ^
```
[R/sim_unlinked_tree.R:63:1:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L63) *style:* **Lines should not be more than 80 characters.**
```r
#' simulate a sequence assuming node substitutions are shared among the offspring
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:77:1:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L77) *style:* **functions should have cyclomatic complexity of less than 15, this has 43.**
```r
sim_unlinked_tree <- function(phy,
^
```
[R/sim_unlinked_tree.R:78:31:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L78) *style:* **Variable and function name style should be snake_case.**
```r
                              Q1 = NULL,
                              ^~
```
[R/sim_unlinked_tree.R:79:31:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L79) *style:* **Variable and function name style should be snake_case.**
```r
                              Q2 = NULL,
                              ^~
```
[R/sim_unlinked_tree.R:104:10:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L104) *style:* **Only use double-quotes.**
```r
    stop('lambda and mu have to be provided')
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:113:20:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L113) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q1)) Q1 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_unlinked_tree.R:114:20:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L114) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q2)) Q2 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_unlinked_tree.R:117:22:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L117) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q1)) Q1 <- Q1[lower.tri(Q1)]
                     ^~
```
[R/sim_unlinked_tree.R:118:22:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L118) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q2)) Q2 <- Q2[lower.tri(Q2)]
                     ^~
```
[R/sim_unlinked_tree.R:131:51:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L131) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  hidden_nodes <- add_hidden_nodes(phy, lambda, mu )
                                                  ^
```
[R/sim_unlinked_tree.R:146:1:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L146) *style:* **Lines should not be more than 80 characters.**
```r
  P_n <- nodeSub::slow_matrix(eig_q2, node_time, rate2)    #get_p_matrix(node_time, eig_q2, rate2)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:146:3:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L146) *style:* **Variable and function name style should be snake_case.**
```r
  P_n <- nodeSub::slow_matrix(eig_q2, node_time, rate2)    #get_p_matrix(node_time, eig_q2, rate2)
  ^~~
```
[R/sim_unlinked_tree.R:146:61:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L146) *style:* **Commented code should be removed.**
```r
  P_n <- nodeSub::slow_matrix(eig_q2, node_time, rate2)    #get_p_matrix(node_time, eig_q2, rate2)
                                                            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:151:7:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L151) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(number > length(phy$tip.label)) return(TRUE)
      ^
```
[R/sim_unlinked_tree.R:152:7:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L152) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(number <= length(phy_no_extinct$tip.label)) return(TRUE)
      ^
```
[R/sim_unlinked_tree.R:181:9:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L181) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
    if ( obs_hidden_nodes[i] > 0) {
        ^
```
[R/sim_unlinked_tree.R:186:10:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L186) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      for(j in 1:obs_hidden_nodes[i]) {
         ^
```
[R/sim_unlinked_tree.R:188:14:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L188) *style:* **Place a space before left parenthesis, except in a function call.**
```r
        while(focal_t + dt >= total_bl) {
             ^
```
[R/sim_unlinked_tree.R:197:23:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L197) *warning:* **no visible global function definition for ‘phyDat.DNA’**
```r
  alignment_phydat <- phyDat.DNA( as.data.frame(res, stringsAsFactors = FALSE))
                      ^~~~~~~~~~
```
[R/sim_unlinked_tree.R:198:8:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L198) *style:* **Commented code should be removed.**
```r
      #P_b <- get_p_matrix(bl[1], eig_q1, rate1)
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:199:7:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L199) *style:* **Variable and function name style should be snake_case.**
```r
      P_b <-  nodeSub::slow_matrix(eig_q1, bl[1], rate1)
      ^~~
```
[R/sim_unlinked_tree.R:214:10:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L214) *style:* **Place a space before left parenthesis, except in a function call.**
```r
      for(h in 1:obs_hidden_nodes[i]) {
         ^
```
[R/sim_unlinked_tree.R:227:10:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L227) *style:* **Commented code should be removed.**
```r
        #P_b <- get_p_matrix(bl[1], eig_q1, rate1)
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:228:9:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L228) *style:* **Variable and function name style should be snake_case.**
```r
        P_b <-  nodeSub::slow_matrix(eig_q1, bl[1], rate1)
        ^~~
```
[R/sim_unlinked_tree.R:247:8:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L247) *style:* **Commented code should be removed.**
```r
      #P <- get_p_matrix(tl[i], eig_q1, rate1)
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:248:7:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L248) *style:* **Variable and function name style should be snake_case.**
```r
      P <-  nodeSub::slow_matrix(eig_q1, tl[i], rate1)
      ^
```
[R/sim_unlinked_tree.R:263:7:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L263) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(check_to_extinct_tip(to)) {
      ^
```
[R/sim_unlinked_tree.R:270:42:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L270) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_unlinked_tree.R:273:34:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L273) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  alignment_phydat <- phyDat.DNA( as.data.frame(res, stringsAsFactors = FALSE))
                                 ^
```
[R/sim_unlinked_tree.R:282:1:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L282) *style:* **Lines should not be more than 80 characters.**
```r
#' simulate a sequence assuming node substitutions are shared among the offspring
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:301:40:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L301) *style:* **Variable and function name style should be snake_case.**
```r
                                       Q1 = NULL,
                                       ^~
```
[R/sim_unlinked_tree.R:302:40:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L302) *style:* **Variable and function name style should be snake_case.**
```r
                                       Q2 = NULL,
                                       ^~
```
[R/sim_unlinked_tree.R:313:5:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L313) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(length(geiger::is.extinct(input_tree)) > 0) {
    ^
```
[R/sim_unlinked_tree.R:320:5:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L320) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(is.null(focal_alignment)) {
    ^
```
[R/sim_unlinked_tree.R:322:1:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L322) *style:* **Lines should not be more than 80 characters.**
```r
    focal_alignment <- nodeSub::sim_normal(input_tree, l = l, Q = Q1, bf = bf, rootseq = rootseq, rate = rate1)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:336:1:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L336) *style:* **Lines should not be more than 80 characters.**
```r
    proposed_alignment <- nodeSub::sim_unlinked_tree(input_tree, Q1 = Q1, Q2 = Q2,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:337:1:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L337) *style:* **Lines should not be more than 80 characters.**
```r
                                                     rate1 = focal_rate, rate2 = focal_rate, l = l, bf = bf, rootseq = rootseq,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:338:1:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L338) *style:* **Lines should not be more than 80 characters.**
```r
                                                     node_time = node_time, lambda = lambda, mu = mu)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked_tree.R:347:1:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked_tree.R#L347) *style:* **Lines should not be more than 80 characters.**
```r
  proposed_alignment <- propose_alignments(buffer = c(), focal_rate = adjusted_rate)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked.R:1:1:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked.R#L1) *style:* **Lines should not be more than 80 characters.**
```r
#' simulate a sequence assuming node substitutions are shared among the offspring
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_unlinked.R:13:1:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 18.**
```r
sim_unlinked <- function(phy,
^
```
[R/sim_unlinked.R:14:26:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked.R#L14) *style:* **Variable and function name style should be snake_case.**
```r
                         Q1 = NULL,
                         ^~
```
[R/sim_unlinked.R:15:26:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked.R#L15) *style:* **Variable and function name style should be snake_case.**
```r
                         Q2 = NULL,
                         ^~
```
[R/sim_unlinked.R:37:20:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked.R#L37) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q1)) Q1 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_unlinked.R:38:20:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked.R#L38) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.null(Q2)) Q2 <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
                   ^~
```
[R/sim_unlinked.R:41:22:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked.R#L41) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q1)) Q1 <- Q1[lower.tri(Q1)]
                     ^~
```
[R/sim_unlinked.R:42:22:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked.R#L42) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q2)) Q2 <- Q2[lower.tri(Q2)]
                     ^~
```
[R/sim_unlinked.R:59:10:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked.R#L59) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)
         ^~~~~~~~~~~~
```
[R/sim_unlinked.R:71:5:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked.R#L71) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(node_time, eig_q2, rate2)
    ^
```
[R/sim_unlinked.R:72:10:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked.R#L72) *warning:* **no visible global function definition for ‘get_p_matrix’**
```r
    P <- get_p_matrix(tl[i], eig_q1, rate1)
         ^~~~~~~~~~~~
```
[R/sim_unlinked.R:84:5:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked.R#L84) *style:* **Variable and function name style should be snake_case.**
```r
    P <- get_p_matrix(tl[i], eig_q1, rate1)
    ^
```
[R/sim_unlinked.R:95:23:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked.R#L95) *warning:* **no visible global function definition for ‘phyDat.DNA’**
```r
  alignment_phydat <- phyDat.DNA( as.data.frame(res, stringsAsFactors = FALSE))
                      ^~~~~~~~~~
```
[R/sim_unlinked.R:104:42:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked.R#L104) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  label <- c(phy$tip.label, as.character( (k + 1):num_nodes))
                                         ^
```
[R/sim_unlinked.R:107:34:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/sim_unlinked.R#L107) *style:* **Do not place spaces around code in parentheses or square brackets.**
```r
  alignment_phydat <- phyDat.DNA( as.data.frame(res, stringsAsFactors = FALSE))
                                 ^
```
[R/util.R:2:1:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/util.R#L2) *style:* **Variable and function name style should be snake_case.**
```r
fast.table <- function(data) {
^~~~~~~~~~
```
[R/util.R:2:10:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/util.R#L2) *warning:* **no visible global function definition for ‘get_p_m_rcpp’**
```r
  res <- get_p_m_rcpp(eig, branch_length, rate)
         ^~~~~~~~~~~~
```
[R/util.R:20:1:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/util.R#L20) *style:* **Variable and function name style should be snake_case.**
```r
phyDat.DNA <- function(data) {
^~~~~~~~~~
```
[R/util.R:35:3:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/util.R#L35) *style:* **Variable and function name style should be snake_case.**
```r
  AC <- matrix(c(c(1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 1, 1, 1),
  ^~
```
[R/util.R:108:1:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/util.R#L108) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
slow_matrix <- function(eig, branch_length, rate) {
^
```
[R/util.R:116:3:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/R/util.R#L116) *style:* **Variable and function name style should be snake_case.**
```r
  P <- matrix(NA, nrow = dim_size, ncol = dim_size)
  ^
```
[tests/testthat/test-dual_independent.R:10:3:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/tests/testthat/test-dual_independent.R#L10) *style:* **Variable and function name style should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-dual_parent.R:9:3:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/tests/testthat/test-dual_parent.R#L9) *style:* **Variable and function name style should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-dual-linked.R:9:3:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/tests/testthat/test-dual-linked.R#L9) *style:* **Variable and function name style should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-relative_node_time.R:22:1:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/tests/testthat/test-relative_node_time.R#L22) *style:* **Lines should not be more than 80 characters.**
```r
  obs_fraction <- ali$total_node_substitutions / (ali$total_node_substitutions + ali$total_branch_substitutions)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-sim_normal.R:20:3:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/tests/testthat/test-sim_normal.R#L20) *style:* **Variable and function name style should be snake_case.**
```r
  Q_JC <- matrix(1, nrow = 4, ncol = 4)
  ^~~~
```
[tests/testthat/test-substitution.R:10:3:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/tests/testthat/test-substitution.R#L10) *style:* **Variable and function name style should be snake_case.**
```r
  Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
  ^
```
[tests/testthat/test-substitution.R:13:21:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/tests/testthat/test-substitution.R#L13) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[tests/testthat/test-substitution.R:29:5:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/tests/testthat/test-substitution.R#L29) *style:* **Variable and function name style should be snake_case.**
```r
    P <- nodeSub::slow_matrix(eig = eig_q,
    ^
```
[tests/testthat/test-substitution.R:84:3:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/tests/testthat/test-substitution.R#L84) *style:* **Variable and function name style should be snake_case.**
```r
  Q <- rep(1, lbf * (lbf - 1) / 2) # default is JC69
  ^
```
[tests/testthat/test-substitution.R:87:21:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/tests/testthat/test-substitution.R#L87) *style:* **Variable and function name style should be snake_case.**
```r
  if (is.matrix(Q)) Q <- Q[lower.tri(Q)]
                    ^
```
[tests/testthat/test-substitution.R:94:3:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/tests/testthat/test-substitution.R#L94) *style:* **Variable and function name style should be snake_case.**
```r
  P1 <- nodeSub::slow_matrix(eig = eig_q,
  ^~
```
[tests/testthat/test-substitution.R:98:3:](https://github.com/thijsjanzen/nodeSub/blob/b2a68f0440ebd8fc6bd2693f215a97dbb010bfab/tests/testthat/test-substitution.R#L98) *style:* **Variable and function name style should be snake_case.**
```r
  P2 <- get_p_matrix(branch_length, eig_q, rate)
  ^~
```


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


Personal preference and size of the project. If this was a fully developed app it would probably be better to just create a set of buttons using BEM for clarity and reusability.


[R/drake_config.R:478:1:](https://github.com/ropensci/drake/blob/df5577ebeb4aee9d6e8ab8d2da9c09011c39a9d6/R/drake_config.R#L478) *style:* **Lines should not be more than 80 characters.**
```r
#'   then the cache will stay locked, and you will need to manually unlock it with
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


I should have, but I needed the data to be inside the project while working on the plane. I forgot to delete it once landed.


Deployment failed with the following error:

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


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Oh interesting.


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Message:
 ```7aa6cd97afc2e0bf02f7f67cc525c3c7502bf7596a9a797425f59ae06971b1c4```
 Genesis Address:
 ```19Wt6q5eK3scFcvVTUMkG3gwaCaDughBig```
 Signature:
 ```Hx699Q34yci0PUAITbCHBFY1bwnhabGCOID53ebxWrTyfmsx9His66qiNlqETXJjLM5czUPOV/rF9tTbTqQXrdM=```


Copy of this build can be found at
https://www.mewbuilds.com/build/053a9dd3e159e0e5d45aa92ba86997658a02c1ec/index.html
                       https://www.cloudflare-ipfs.com/ipfs/QmVpVKSk5i2o2Bd1BPq5RkSBKePKmNp7GfZMMYM9jaXZim
                       Virus Total analysis
                       https://www.virustotal.com/file/df1f33aee44e2d184c2ef56617997e135e461d175fae3734d74c2a55714f58fe/analysis/1578497049/


Cool, thanks for that update!


Added following conditions using Fluent API using separate configuration file for each entity:
Videos table
• Name column cannot be NULL and its length should be maximum 255
characters.
• Genre_Id column should be renamed to GenreId, and it cannot be NULL.
• Classification column should be a tinyint.
Genres table
• Name column cannot be NULL and its length should be maximum 255
characters.


I don't think it's immediately obvious why it's okay to pass null here, without knowing the underlying Windows API.

It'd be great to have a comment here, ideally with a link to the documentation stating that passing null is expected and what drives the algorithm choice to use the system preferred one


great


mit dem "New Lift" sind alle Links von Puzzle Part verloren gegangen
-> revert nach absprache


Checkmarx scan results 07 Jan 2020 17:51 UTC +02:00

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0
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Included commits

Commit ID	Owner

1e71c4b085217e0cab2013734fb62a6c80309419	@web-flow


refrigCaseRefactor (mitchute) - x86_64-Linux-Ubuntu-18.04-cppcheck: OK (0 of 0 tests passed, 0 test warnings)

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


@kovidgoyal this broke translation generation for me with

```
IOError: [Errno 2] No such file or directory: '/var/tmp/paludis/build/app-text-calibre-4.8.0/work/calibre-4.8.0/translations/changelog/locales.zip'
```

After reverting this patch translations build normally again.


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> In grade/export/xls/grade_export_xls.php, for my Excel spreadsheet download to generate data, I had to modify new lines 90 and 91 to this:
>
> 'firstname', 'asc', $this->showcohorts,
> $this->showgroups);
>
> (switch cohorts and groups around basically).

Yeah - it looks like a mistake. The method arguments for that function should definitely be showcohorts then showgroups


Successfully deployed to following URLs:

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Deployment failed with the following error:

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


Fixes #1


It might be worth mentioning, for each of the theorem files, the argument that generates it, as well as the collective flag.


The TravisCI test of mb_read_init() needs to set default values. These should be the system defaults but should not depend on the user's environment. The new function mb_default_defaults() returns the default defaults. As before, the function mb_defaults() returns the defaults as modified by the user ~/.mbio_defaults file, but it now gets the starting defaults using mb_default_defaults().


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This commit seems to have introduced a regression in Section unsafe: https://github.com/racket/racket/runs/378245902#step:9:25


I have no idea what i'm doing.


And the next thing you will tell me is to learn to use a debugger. :)

Is there a tool that provides the equivalent view? (list of execution with all passed values)

Dave

> On Jan 7, 2020, at 11:13 PM, Kurt Schwehr <notifications@github.com> wrote:
>
> For some time in the distant future, consider dropping the idea of a single point of exit with prints. The code should still complain when there is a problem. This would reduce the number of lines in mbsystem by > 10%, decrease the library and binary size by at least as much, and be a substantial performance boost. That style is probably blocking a lot of what the optimizer could do in the compiler, it's increasing the stack size, and it's taking valuable space in some of the CPU caches. And it requires more work by the reader to understand an entire function.
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub, or unsubscribe.
>

----------------------------------------------------
David W. Caress
Principal Engineer
Seafloor Mapping Lab

Monterey Bay Aquarium Research Institute
7700 Sandholdt Road
Moss Landing, CA 95039

caress@mbari.org
http://www.mbari.org/~caress/

Phone: 831-775-1775


Running BFG caused this commit to end as empty. Will try remove.


not getting this one


use this to enable on screen navigation by default in aosp based roms for mido


> This needs to move to innodb.cmake .

I intentionally put this code here so the whole server can benefit of using SSE4.2, not just InnoDB. Note, that we already require all CPUs to have this instruction set.

> You want to use SSE4.2 every time, not just when it is compiled for mariadb official release.
When I use `-DCMAKE_BUILD_TYPE={DEBUG,RELEASE,REL_WITH_DEB_INFO}` it already adds everything needed to compiler CLI. So, actually we need to fix just MariaDB official releases.

With introduction of `-DHAVE_SSE42` we'll adding support for x86 CPUs which have no SSE4.2. And SSE4.2 appears in CPUs since 2008. So, do we really need to add support for older CPUs? Nobody really complained so far about that and will barely complain in future.

I don't think we need that `HAVE_SSE42`. It will merely complicate our cmake files. And probably we don't need to add SSE4.2 to x86 CPUs because nowaday nobody really cares about them. Or maybe I'm wrong?


I ran into the same problem when I originally wrote the tests.  Another reason to have multiple platforms in the CI setup for a project.  e.g. multiple OSes (pref multiple linux'es, Mac OSX, and at least one modern Windows setup), multiple compiler (clang and gcc at a minimum), and multiple compiler modes (optimized, asan/ubsan, and msan at a minimum).   That combined with turning up the warnings as far as possible and running static analysis... with a clean bill of health, makes projects much easier to work on.  A single issue will likely show up in several places with different ways of explaining it.  I find that very helpful.


If `unknownSessions` is in descending stake order, doesn't this result in-order selection?


GTNH fucks with Stainless.. best pick something that’s actually fucking MV.


@chhex : I'm not sure to understand what these lines do (actually also the equivalent from the previous version). I understand we iterate through all project dependencies, and for each dependency, we then iterate through all dependencies coming from apgPackage extension ... But what does the 3rd line actually do?

@apgsga-stb : FYI


Thanks!


seems like a bug in GCC, see https://gcc.gnu.org/bugzilla/show_bug.cgi?id=60503


You’ll need to put these in the public/ directory, not pages, for them to work.

(Also, the sitemap + robots don’t appear to do anything that isn’t the default behavior)


![Difference between blocks](https://raw.githubusercontent.com/paddymcdonnell661/digimon-adventure/82edb27ce3e19860959597b88656c1130d2ceebf/.makecode/blocksdiff.png)


Protip: crop these square to reduce downloading an unnecessarily large image


Next version should be minor bump.


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Successfully deployed to following URLs:

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# Visual Studio Code & Remote Development

![enter image description here](https://postfiles.pstatic.net/MjAyMDAxMDZfMTA3/MDAxNTc4Mjk5MjE4NjIz.ac9AWS1R8GifX_L92PN7MuPQ3PyK4x1QCxPM-IiP89gg.rhGb_GoWryD6HUlpObPNfi32HocEXglgZ3kOr-8TPjAg.PNG.ehgus6028/%EB%A6%AC%EB%AA%A8%ED%8A%B8.png?type=w966)
##### <center> <그림1. Remote Development> </center>

Visual Studio Code의 Remote Development를 이용하면 __하나의 에디터로(visual studio code)로 여러가지 작업(컨테이너 관리, light sail, ubuntu 등)을 원격으로 관리__ 할 수가 있습니다. 여러 환경에 대한 설명과 함께 원격 환경을 조성하는 방법을 간단히 소개해 보겠습니다.

## Visual Studio Code
![enter image description here](https://encrypted-tbn0.gstatic.com/images?q=tbn:ANd9GcQGF2Gql1WTNVkDolEwO7lTBH81oeROyyjobddqAUb3vwYhGOr4QQ&s)
##### <center> <그림2. vs code 로고> </center>

__Visual Studio Code__ 는 마이크로 소프트에서 2015년 출시한 에디터 중 하나로, 개발 툴들 가운데 최초로 크로스 플랫폼을 지원하는 에디터 입니다.

IDE가 아니므로, 빌더가 내장되어 있지 않아 VS Code에서 빌드를 하려면 별도의 컴파일 환경을 구축 해야한다는 특징이 있지만, 수 많은 추가기능들을 VS Code 내부의 검색을 통해서 한 번의 클릭으로 쉽게 다운 받을 수 있다는 장점이 있습니다.

### 기능
▶ 멀티 커서 에디팅 - 볼록 선택, 모든 항목 선택 등

▶ 인텔리센스 - 코드, 외부 모듈에 대한 코드 지원 및 매개변수 제안

▶ 추출 리팩터링 - 공통 코드를 함수나 상수로 빠르게 추출

▶ 스니펫 - 반복 타이핑 시간 단축

▶ 포매팅 - 내장된 문서 및 선택 서식을 이용한 깔끔한 코드 유지

## Windows Subsystem for Linux

![enter image description here](https://i.ytimg.com/vi/Cvrqmq9A3tA/maxresdefault.jpg)

##### <center> <그림3. WSL> </center>

추가로 나중에 소개될 원격 제어목록 중 하나인 WSL에 대해서도 기본 개념만 잠깐 살펴 보고 가겠습니다.

WSL은 오직64bit 윈도우10에서만 가능한 것으로 윈도우 환경에서 리눅스 명령을 cmd, powershell 등을 통해 직접 실행할 수 있는 새로운 기능입니다. 즉, 다시말해 리눅스용 프로그램과 도구들을 윈도우에서도 사용 할 수 있게되어 __윈도우에서 리눅스 환경에서의 개발과 유사한 느낌__ 을 낼 수 있게 해주는 기술 이라고 정리 할 수 있습니다. 이와 비슷한 기능을 하는 가상화 머신과 비교하였을때또한 훨씬 적은 자원을 소모한다는 장점이 있습니다.

## Amazzon Lightsail

![enter image description here](https://t1.daumcdn.net/cfile/tistory/997FCA345C5F377012)

##### <center> <그림4. AmazonLightsail 로고> </center>

__Amazon Lightsail__ 이란 작은 비용으로 시작 할 수 있는 작은 가상서버 서비스로 관리가 어렵고 비용이 많이드는 서버들을 작은 돈으로 작은 부분만 떼어서 빌려쓰는 개념입니다.

 작은 서버지만 서버라는 사실은 변함이 없기 때문에 추후에 큰 서버관리능력이 필요할 때를 대비해 연습 할 수 있는 입문용 서비스라고도 할 수 있습니다.

 ## Docker
 ![enter image description here](https://subicura.com/assets/article_images/2017-01-19-docker-guide-for-beginners-1/docker-logo.png)
#####  <center> <그림5. Docker 로고> </center>

도커는 기존 리눅스 컨테이너에 여러가지 기능을 추가하여 쉽고 빠른 컨테이너 사용이 가능하게 한 __오픈소스__ 입니다.
기존 가상화기술은 모든 작업이 하이퍼바이저를 반드시 거치기 때문에 일반 호스트에 비해 성능 손실이 발생합니다.

또한 게스트 OS를 위한 라이브러리, 커널등을 전부 다운받아야하기 때문에 이미지 크기또한 커지게 됩니다. 반면에 Docker는  chroot, namesapce, cgroup을 이용해 __프로세스 단위 격리 환경__ 을 만들어 성능 손실을 줄이고, 컨테이너에 필요한 __커널을 호스트와 공유__ 하여 사용하기 때문에 __이미지 용량 또한 대폭 감소__ 된다는 장점이 있습니다.

![enter image description here](https://cdn-images-1.medium.com/max/1000/1*wOBkzBpi1Hl9Nr__Jszplg.png)
#####  <center> <그림6. Docker 원리> </center>

### Docker Images & Container

_Images_: 컨테이너 생성및 실행 시 **읽기전용** 으로 사용됩니다.
**이미지**는 도커 명령어로 다운받을 수 있으므로 별도 설치가 필요없으며, 기본 형식은 [저장소 이름]/[이미지 이름]:[태그] 입니다.

_Container_: 이미지에서 **변경된 사항만을 저장**하기때문에 컨테이너에서 무엇을 하든지 원본 이미지는 영향을 받지 않습니다. 또한 각 컨테이너는 **독립된 파일 시스템**을 제공받고 호스트와 분리되어 있기 때문에 컨테이너간 독립이 되어 있습니다.

![enter image description here](https://subicura.com/assets/article_images/2017-02-10-docker-guide-for-beginners-create-image-and-deploy/create-image.png)
#####  <center> <그림7. Docker 이미지 방식> </center>

## 원격 제어 환경 조성

- WSL Targets

1. Microsoft store에서 WSL 프로그램을 다운 받습니다. (본인은 ubuntu를 받았습니다)
2. Ubuntu에 접속하여 "code ." 을 입력합니다.
3. VS code와 ubuntu가 연결이 된 code창이 뜹니다.
4. 원격 관리 준비 끝!

- SSH Targets

1. AWS의 Lightsail sever를 엽니다.
2. 서버의 ip를 고정 시킨 후, 서버에 입장합니다.
3. config 설정에 들어가 아래의 항목을 No에서 yes로 바꿔주면 비밀번호를 입력 시 원격제어권을 가져 올 수가 있습니다.

![enter image description here](https://postfiles.pstatic.net/MjAyMDAxMDZfMjk4/MDAxNTc4MzExMjkzOTQy.fJoS1LivKNyrZDlGx8yF8TQt5oK5TYLD6vBxUYeqxZYg.btloGV-5v32gte7j_6x18UgrqaMaurKsvkpQzCpkJl8g.PNG.ehgus6028/Yes.png?type=w966)

4. VS Code에서 F1키를 눌러 검색창을 띄우고 Remote-SSH:Connect to Host...를선택합니다.
5. Configure SSH Hosts를 선택합니다.
6. 파일을 업데이트 할 경로를 선택합니다.
7. 들어간 config 페이지에 아래의 그림과 같은 양식으로 입력해 줍니다.

![enter image description here](https://postfiles.pstatic.net/MjAyMDAxMDZfMTkw/MDAxNTc4MzA1NjQ4MTc3.1YeMnQ8v46IVfzZHLOABp_AulbPFZXjVnZ8pJKHz54Ig.-rd_sUMTMgH4rMkqT-p4S3ung6beYsYJ0870H6Bgvt0g.PNG.ehgus6028/dada.png?type=w966)
#####  <center> <그림5. SSH config 설정> </center>
8. 원격 관리 준비 끝!

- Container Targets

1. VS Code의 EXTENSIONS로 들어가 REMOTE-Containers를 다운 받습니다.
2. VS Code 에서 F1를 눌러 검색창을 띄우고 Remote-Containers:Attach to Running Container...를 선택합니다.
3. 원격제어할 콘테이너를 선택합니다.
4. 원격 관리 준비 끝!


Ok got it!


Successfully deployed to following URLs:

* https://ccc-dypfoc34p.now.sh
* https://ccc.zeit-github-test-dev1.now.sh
* https://ccc-git-master.zeit-github-test-dev1.now.sh


Deployment failed with the following error:

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


Successfully deployed to following URLs:

* https://github-e2e-tests-dev-alias-v2-without-alias-rjk04885e.now.sh
* https://github-e2e-tests-dev-alias-v2-without-alias.zeit-github-test-dev1.now.sh
* https://github-e2e-tests-dev-alias-v2-without-alias-git-master.zeit-github-test-dev1.now.sh


Successfully deployed to following URLs:

* https://github-e2e-tests-dev-alias-v2-with-alias-m6oan26kg.now.sh
* https://z-github-e2e-tests-dev-alias-v2-with-alias.now.sh
* https://github-e2e-tests-dev-alias-v2-with-alias.zeit-github-test-dev1.now.sh
* https://github-e2e-tests-dev-alias-v2-with-alias-git-master.zeit-github-test-dev1.now.sh


Successfully deployed to following URLs:

* https://github-e2e-tests-dev-alias-v1-with-alias-hqrduztoix.now.sh
* https://z-github-e2e-tests-dev-only.now.sh


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

~~~
The domain 3tcol0svoj.com is not verfied and cannot be used as an alias.
~~~

([Learn more](http://localhost:3000/zeit-github-test-dev/github-e2e-test-dev-domain-issues/1ucgo0rh9) or [visit](https://github-e2e-test-dev-domain-issues-1ucgo0rh9.now.sh) the non-aliased deployment)


all tests pass:
success: https://travis-ci.org/stellar/stellar-core/builds/634404602?utm_source=github_status&utm_medium=notification


Successfully deployed to following URLs:

* https://refugeerescue-n2888j9qw.now.sh
* https://refugeerescue.now.sh
* https://refugeerescue.aaroncb.now.sh
* https://refugeerescue-git-master.aaroncb.now.sh


develop (Myoldmopar) - x86_64-Linux-Ubuntu-18.04-cppcheck: OK (0 of 0 tests passed, 0 test warnings)

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


right.......


The new release introduced  after this patch has version 0.4, but some of the files still have 0.3 in their names:

diff-pdf-0.3.tar.gz
diff-pdf-win-0.3.zip

Shouldn't these be called 0.4?


This fixes #2


Registration pull request created: [JuliaRegistries/General/7702](https://github.com/JuliaRegistries/General/pull/7702)

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

This will be done automatically if [Julia TagBot](https://github.com/apps/julia-tagbot) is installed, or can be done manually through the github interface, or via:
```
git tag -a v0.10.2 -m "<description of version>" 42b7cdf7e63d7ba20eae2b0b9a4b4f7d35a9e447
git push origin v0.10.2
```


@epiqueras What do these components do?


Successfully deployed to following URLs:

* https://blog-qow1wakp8.now.sh
* https://dorshinar.me
* https://blog.dors718.now.sh
* https://blog-git-master.dors718.now.sh


Successfully deployed to following URLs:

* https://bloom-qtf7rbv77.now.sh
* https://bloom-seven-gules.now.sh
* https://bloom.appearherebloom.now.sh
* https://bloom-git-master.appearherebloom.now.sh


Makes sense to add as (additional) convenience method. We'll need to keep this one for unit tests, though, as we'll otherwise need to create a mock context + mock shared prefs, which seems a bit unconvenient.


Successfully deployed to following URLs:

* https://website-ldueiza5g.now.sh
* https://keplersj.com
* https://website.keplersj.now.sh
* https://website-git-master.keplersj.now.sh


Collaborator: Review for this commit was created. [Link to review](http://2e6be167.eu.ngrok.io/ui#review:id=838)


Please never use the search by the string in such cases. Use category unique field (code or id) to fetch the parent category.


[tests/testthat/test-create_n_mb_species_file.R:15:1:](https://github.com/richelbilderbeek/razzo/blob/b832beede5df845f9e74c5fd54b7b20c96ca4e29/tests/testthat/test-create_n_mb_species_file.R#L15) *style:* **Lines should not be more than 80 characters.**
```r
        pattern = "razzo_project.results.n_mb_species\\.csv$", filename, perl = TRUE, value = TRUE
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


Successfully deployed to following URLs:

* https://merchant-center-application-kit-femvz63hi.now.sh
* https://mc-custom-applications.now.sh
* https://merchant-center-application-kit.commercetools.now.sh
* https://merchant-center-application-kit-git-master.commercetools.now.sh


It is missing keyword new.


这个是评论


Successfully deployed to following URLs:

* https://devops-ntfxwi5fq.now.sh
* https://devops-seven-pi.now.sh
* https://devops.parkenconsulting.com
* https://devops.parkenconsulting.now.sh
* https://devops-git-master.parkenconsulting.now.sh


(I.e. `lint()`)?


qqbrowser.exe


"Enjoy building your API!"
All these docstrings are so... optimistic? :D


I would like to keep this as a local variable, if possible. It does not particularly strike me as a state whether some part of the linting failed.


Also added a file .nojekyll

Reference URL: https://github.community/t5/GitHub-Pages/GitHub-Pages-Builds-Fail/td-p/29172
If you're not using Jekyll to build your website, sometimes GitHub pages will mistake certain characters, specifically curly braces, as jekyll objects, tags, etc. causing your page build to fail. If you're just using static HTML pages (which is what it looks like to me), the easiest and quickest fix would be to disable Jekyll processing, which can be done by creating a file named .nojekyll in the root of your pages repository.

If you're not using Jekyll, I would suggest creating a file named .nojekyll (it doesn't need any contents) in the root of your repository to see if it resolves the errors.


" debug " : " > = 2.6.9 "


avalon is required by barcode4j
Use my customized version can remove avalon dependencies.
https://github.com/chunlinyao/barcode4j


Successfully deployed to following URLs:

* https://nuxt-app-i9gw4sa1n.now.sh
* https://nuxt-app.now.sh
* https://nuxt-app.fuxing.dev
* https://nuxt-app.fuxing.now.sh
* https://nuxt-app-git-master.fuxing.now.sh


How about returning `boolean` here, indicating whether a severe issue was encountered?


if we exit here and the theme is on the notice will not be displayed, It would be better if we combine the old logic with these changes ? @selul


While some developers understand what "linting" is, others do not. Could we maybe say "There was an issue" or "There were issues in commit <commit>"?


Once completed, the job reports for Travis CI [build 920](https://travis-ci.org/per1234/arduino-ci-script/builds/634708562) will be found at:
https://gist.github.com/arduino-ci-script-bot/9371a7dedb73a560142ff2ca514b79db#file-travis_ci_job_report_00920-001-tsv


Once completed, the job reports for Travis CI [build 920](https://travis-ci.org/per1234/arduino-ci-script/builds/634708562) will be found at:
https://github.com/per1234/CI-reports/tree/arduino-ci-script/build_00920


Successfully deployed to following URLs:

* https://s33d-web-7my6kcy2v.now.sh
* https://s33d.art
* https://s33d-web.s33d.now.sh
* https://s33d-web-git-master.s33d.now.sh


The Beggining


Successfully deployed to following URLs:

* https://nexemp-9kb2awg99.now.sh
* https://nexemp.now.sh
* https://nexemp.holgermanzke.now.sh
* https://nexemp-git-master.holgermanzke.now.sh


Successfully deployed to following URLs:

* https://gatsby-theme-carbon-96ayb2gee.now.sh
* https://gatsby-theme-carbon.now.sh
* https://gatsby-theme-carbon.carbon-design-system.now.sh
* https://gatsby-theme-carbon-git-master.carbon-design-system.now.sh


vet inte vad du menade med white space tab? Och jag får samma problem som tidigare


Successfully deployed to following URLs:

* https://lizwiki-cje2ky8wi.now.sh
* https://liz.wiki
* https://lizwiki.lizhengnacl.now.sh
* https://lizwiki-git-master.lizhengnacl.now.sh


Successfully deployed to following URLs:

* https://test-task-scc-1tnuxiuhu.now.sh
* https://test-task-scc.now.sh
* https://test-task-scc.olexandrvlasenko.now.sh
* https://test-task-scc-git-master.olexandrvlasenko.now.sh


Successfully deployed to following URLs:

* https://hysequa-offline-j19o6nq2o.now.sh
* https://hysequa-offline.now.sh
* https://hysequa.info53.now.sh
* https://hysequa-offline.info53.now.sh
* https://hysequa-offline-git-master.info53.now.sh


Successfully deployed to following URLs:

* https://slow-zone-p614tugyy.now.sh
* https://slow.zone
* https://slow-zone.banterability.now.sh
* https://slow-zone-git-master.banterability.now.sh


Successfully deployed to following URLs:

* https://react-portfolio-qq794k21h.now.sh
* https://react-portfolio-five-tawny.now.sh
* https://boydstun-react-portfolio.now.sh
* https://react-portfolio.chrisboydstun.now.sh
* https://react-portfolio-git-master.chrisboydstun.now.sh


## Plan result [CI link]( https://circleci.com/gh/ryo1620/workout_app/162 )

No changes. Infrastructure is up-to-date.

Details (Click me)

Acquiring state lock. This may take a few moments...
Refreshing Terraform state in-memory prior to plan...
The refreshed state will be used to calculate this plan, but will not be
persisted to local or remote state storage.

data.aws_route53_zone.workout11: Refreshing state...
aws_ecr_repository.workout11: Refreshing state... [id=workout11-repo]
aws_db_parameter_group.workout11: Refreshing state... [id=workout11-db-parameter-group]
aws_cloudwatch_log_group.workout11: Refreshing state... [id=/aws/eks/workout11-eks/cluster]
data.aws_iam_policy_document.eks_assume_role: Refreshing state...
aws_iam_policy.external_dns_iam_policy: Refreshing state... [id=arn:aws:iam::012055136996:policy/ExternalDNSIAMPolicy]
aws_vpc.workout11: Refreshing state... [id=vpc-0beab9a7a881b6d81]
aws_kms_key.workout11: Refreshing state... [id=1814963e-29b5-46cf-aab0-655dfd2eb7e6]
aws_dynamodb_table.tfstate: Refreshing state... [id=workout11-tfstate]
data.aws_iam_policy_document.eks_fargate_assume_role: Refreshing state...
aws_s3_bucket.tfstate: Refreshing state... [id=workout11-tfstate]
aws_iam_policy.alb_ingress_controller_iam_policy: Refreshing state... [id=arn:aws:iam::012055136996:policy/ALBIngressControllerIAMPolicy]
aws_iam_role.eks_role: Refreshing state... [id=eks-master]
aws_iam_role.eks_fargate_pod_execution_role: Refreshing state... [id=eks-fargate-pod-execution]
aws_acm_certificate.workout11: Refreshing state... [id=arn:aws:acm:ap-northeast-1:012055136996:certificate/51138d54-2342-4dcd-a905-6b664caefe8a]
aws_iam_role_policy_attachment.cluster_AmazonEKSClusterPolicy: Refreshing state... [id=eks-master-20191231135454240400000003]
aws_iam_role_policy_attachment.cluster_AmazonEKSServicePolicy: Refreshing state... [id=eks-master-20191231135454249300000004]
aws_iam_role_policy_attachment.eks_fargate_pod_execution: Refreshing state... [id=eks-fargate-pod-execution-20191231135454222500000002]
aws_ecr_lifecycle_policy.workout11: Refreshing state... [id=workout11-repo]
aws_route53_record.workout11_certificate: Refreshing state... [id=Z17R07MY85WBCS__18a521abb2cc9ccf922022e63328e5da.workout11.com._CNAME]
aws_acm_certificate_validation.workout11: Refreshing state... [id=2019-12-31 13:57:09 +0000 UTC]
aws_kms_alias.workout11: Refreshing state... [id=alias/workout11-kubesec]
aws_route_table.private_0: Refreshing state... [id=rtb-0b5e9ca781cba224b]
aws_route_table.public: Refreshing state... [id=rtb-09af094e64489fb60]
aws_route_table.private_1: Refreshing state... [id=rtb-0f472a5427b1afde4]
aws_subnet.public_1: Refreshing state... [id=subnet-0ebef4c58ccc24fb3]
aws_subnet.private_1: Refreshing state... [id=subnet-0973ce6028e73c8d7]
module.postgres_sg.aws_security_group.default: Refreshing state... [id=sg-09f98c79edab7294d]
module.eks_sg.aws_security_group.default: Refreshing state... [id=sg-08c33d554f3a2a3f1]
aws_subnet.public_0: Refreshing state... [id=subnet-0ce1bb8ebea4bcd0d]
aws_subnet.private_0: Refreshing state... [id=subnet-07b0e96e04014ef22]
aws_internet_gateway.workout11: Refreshing state... [id=igw-04e6b298b373a18c6]
aws_route_table_association.public_1: Refreshing state... [id=rtbassoc-007592d35fd8be61c]
module.eks_sg.aws_security_group_rule.ingress: Refreshing state... [id=sgrule-3921160810]
module.eks_sg.aws_security_group_rule.egress: Refreshing state... [id=sgrule-1933888031]
module.postgres_sg.aws_security_group_rule.egress: Refreshing state... [id=sgrule-858422768]
module.postgres_sg.aws_security_group_rule.ingress: Refreshing state... [id=sgrule-3938245922]
aws_route_table_association.private_1: Refreshing state... [id=rtbassoc-0673075a203aadd92]
aws_route_table_association.public_0: Refreshing state... [id=rtbassoc-0939242ff93366104]
aws_eks_cluster.workout11: Refreshing state... [id=workout11-eks]
aws_route_table_association.private_0: Refreshing state... [id=rtbassoc-035f36966deca920a]
aws_db_subnet_group.workout11: Refreshing state... [id=workout11-db-subnet-group]
aws_eip.nat_gateway_0: Refreshing state... [id=eipalloc-0bb8bdb9e185c5d87]
aws_eip.nat_gateway_1: Refreshing state... [id=eipalloc-0be3c1ff14a190058]
aws_route.public: Refreshing state... [id=r-rtb-09af094e64489fb601080289494]
aws_iam_openid_connect_provider.workout11: Refreshing state... [id=arn:aws:iam::012055136996:oidc-provider/oidc.eks.ap-northeast-1.amazonaws.com/id/373B18B17B5C76615D8CEB5803E37A24]
aws_eks_fargate_profile.workout11_kube_system: Refreshing state... [id=workout11-eks:workout11-eks-fargate-kube-system]
aws_eks_fargate_profile.workout11: Refreshing state... [id=workout11-eks:workout11-eks-fargate]
data.aws_iam_policy_document.oidc_assume_role: Refreshing state...
aws_iam_role.oidc_role: Refreshing state... [id=oidc-eks]
aws_iam_role_policy_attachment.oidc_ExternalDNSIAMPolicy: Refreshing state... [id=oidc-eks-20200103134710955400000001]
aws_iam_role_policy_attachment.oidc_ALBIngressControllerIAMPolicy: Refreshing state... [id=oidc-eks-20200102203319397800000001]
aws_nat_gateway.nat_gateway_0: Refreshing state... [id=nat-06f80fbffebdf8077]
aws_nat_gateway.nat_gateway_1: Refreshing state... [id=nat-02c0d408504a3467d]
data.aws_iam_policy_document.tfstate: Refreshing state...
aws_s3_bucket_policy.tfstate: Refreshing state... [id=workout11-tfstate]
aws_db_instance.workout11: Refreshing state... [id=workout11-postgres]
aws_route.private_0: Refreshing state... [id=r-rtb-0b5e9ca781cba224b1080289494]
aws_route.private_1: Refreshing state... [id=r-rtb-0f472a5427b1afde41080289494]

------------------------------------------------------------------------

No changes. Infrastructure is up-to-date.

This means that Terraform did not detect any differences between your
configuration and real physical resources that exist. As a result, no
actions need to be performed.
Releasing state lock. This may take a few moments...


tutaj też config


Successfully deployed to following URLs:

* https://gatsby-theme-carbon-jzu6jwooo.now.sh
* https://gatsby-theme-carbon.now.sh
* https://gatsby-theme-carbon.carbon-design-system.now.sh
* https://gatsby-theme-carbon-git-master.carbon-design-system.now.sh


config