I tested it with R 4.2.0 on Windows system and got the same error. I stopped the test and looked rankingBootstrapped1 and rankingBootstrapped2. Here are the screenshots:

Warning messages when there are missing values in the data were reviewed as below:

Hey everyone,

Hey everyone,

I added tests in current future branch for checking class of “algorithm” column in challenge object.

I have added object[[algorithm]] <- as.factor(object[[algorithm]]) to challengeR.R as you suggested. Now everything works without any problem. No need of stating stringsAsFactors anymore during CSV read.

Hi again :)

Hi again,

Finally, I could find the source of the bug. 😊 It is caused by changed output type of unique() function in R:Base from R-3 to R-4.

Update: I go deeper with debugging and some reverse engineering. The source of the problem is the miss-ranking of the algorithms. When we use testThenRank and rankThenAggregate methods, the ranking of the algorithms seems wrong, as it is seen on the screenshot (marked with red rectangular). There is no problem with aggregateThenRank method so far.

In T29167#238218, @wiesenfa wrote:

From the change log for R 4.2.0

GRAPHICS:

• The graphics engine version, R_GE_version, has been bumped to 15 and so packages that provide graphics devices should be reinstalled.

Maybe just reinstalling the package helps?

I have detected the same problem with R 4.2.0. It seems, it is caused by major version change of R. We need to go deeper and find the source of this change.

I am sharing my current test code with artificial data. Since there can be 4-5 blob plots in the report (depending on data, task number), I need to prepare a new test code for only blob plots. Until that, you may use the code I am sharing.

I have tried this approach. I just needed to remove minor_breaks=NULL, line since there is no such a config in R/scale-discrete-.r

I have tried many configurations just to force ggplot2 to start y-axis labels from "1" when choosing automatic scaling. However, it was not possible :/

Let's try the automatic config of ggplot :)

I agree with you. On the other hand, putting breaks according to a defined integer can be tricky. For example, let's assume that we have decided to define breaks on every 5th element. The y-axis will be a 1,5,10,15,18 for a challenge with 18 algorithms. The last portion of the sequence will have a different period. Therefore, I offer including all integer breaks for the [1, #algorithms] range. I am putting some examples here:

I have tried suggested codes but they did not fix the problem. Besides, there caused additional issues. :)

The problem is almost fixed by giving na.treat parameter in both as.challenge and ranking methods (except rankThenAggregate). Now we can generate reports for all ranking methods.

scale_y_continuous functions inside ./R/Stability.R file were modified. The problem seems solved. You can test it feature/T28966-YaxisOfBlobPlotsAlwaysScaledTo5 branch via the file at the attachment. (You can run it root folder of the challengeR code)

Current status of the issue:

visart@dkfz-heidelberg.de mail list has been configured by ITCF. The mails that sent to this address will be forwarded to people on the list.

Configuration summary on report generation page has been added. Users can check their preferences just before report generation.

For upload process, dash-uploader library is used. This library offers built-in progress bar support. Users can see the uploading stage.

It seems there is no practical way to handle this. Dash offers loading_state property for each component. This is useable (callable) via CSS or JS codes.

Descriptions for each ranking method were added.

Deployment configurations were completed. A user guide was added to the Readme file in the root folder.

The reason for the problem is that the server is configured to accept connections from only authorized users. ITFC added Ali Emre Kavur and Fabian Isensee as authorized users.

After contacting Marco Pascale, it is decided to format the server to a new version of CentOS or Ubuntu. Still waiting response from IT side.

Following operations has been done: