The package "graph" was moved from CRAN to Bioconductor:
https://cran.r-project.org/web/packages/graph/index.html

This issue will be fixed in v1.0.1.

An update is also required in report.Rmd, visualizations.Rmd and CITATION.

This issue will be fixed in v1.0.1.

This issue will be fixed in v1.0.1.

Seems fine!

This issue will be fixed in v1.0.1.

additional test in test-blobPlotStabilityByAlgorithm for the case "one task out of 3 tasks contains >1 test cases". in this case bootstrap() gives result for this remaining task and stability() only produces plot with this task. @eisenman could you please check and close?

@eisenman yes, should be sufficient
only one case per task covered in bootstrap() now see T28202

bootstrap() now gives error if all tasks only contain 1 test case and a message if some tasks contain only 1 test case (tasks with 1 test case are excluded from bootstrapping)
test-bootstrap.R contains tests. @eisenman could you please check test

The unit tests can be found here: feature/T28193-UnitTestsMoreTasksThanAlgorithms

I will extend the unit tests to show that this issue is solved.

task names ( names(x$matlist) ) had been used for facet titles instead of algorithm names ( stored in "ordering").

What exactly is the error? What are the steps to reproduce this? Runtime error or wrong content in report?

Ok, we can keep them in this release.

Discussed with @wiesenfa that this issue is not critical for release v1.0.

turned off in v1.0, everything else postponed

I also agree!

I agree!

At the meeting on 30/03/2020 we agreed that the messages should be extended to warn the user of that scenario. Since the column containing the tasks is unknown when the parameter "by" is not specified, an automatic detection can only be realized with a lot of effort.

In the meeting on 30/03/2020 we agreed that this issue won't be fixed. Cases can appear more than once per algorithm in bootstrapping and thus the sanity check has to be turned off. Performance reasons were also mentioned.

In the meeting on 30/03/2020 we agreed that this issue won't be fixed. Parameters have to be described properly to raise awareness of this scenario to the user.

The given example is already available as a unit test.

After discussing, the next steps have been decided:

1. @wiesenfa: look into a way to output a the readme.md in another way (probably in another folder)
2. @aguilera: create scripts to extend the code from the readme, in a different folder
3. @aguilera: crete a troubleshooting section

There should be a team section where all of you are acknowledged

in my opinion this is a desirable feature

Make the task visible in the workboard column "Done".