In this case we solved it by upgrading BiocManager. Probably the previous version did not know about the later version of "graph".
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Mar 3 2021
Mar 3 2021
The package "graph" was moved from CRAN to Bioconductor:
https://cran.r-project.org/web/packages/graph/index.html
Jan 28 2021
Jan 28 2021
eisenman closed T28194: drop restriction at least 3 algorithms required for bootstrapping as Resolved.
Jan 27 2021
Jan 27 2021
Merge tag 'v1.0.1' into develop
eisenman committed rCHALLENGER9446685d5425: Merge branch 'release/T28227-v1.0.1' (authored by eisenman).
Merge branch 'release/T28227-v1.0.1'
Add change notes
Bump version number
eisenman added a comment to T28194: drop restriction at least 3 algorithms required for bootstrapping.
This issue will be fixed in v1.0.1.
eisenman moved T28210: update citation of paper to scientific reports from In Progress to Done on the challengeR board.
eisenman committed rCHALLENGER59053e5b0b24: Merge branch 'feature/T28210-UpdateCitation' into develop (authored by eisenman).
Merge branch 'feature/T28210-UpdateCitation' into develop
Update citation
An update is also required in report.Rmd, visualizations.Rmd and CITATION.
This issue will be fixed in v1.0.1.
eisenman moved T28202: Error in stabilityByAlgorithm if only one case is used from In Progress to Done on the challengeR board.
This issue will be fixed in v1.0.1.
Seems fine!
eisenman moved T28193: bug in stabilityByAlgorithm.bootstrap.list from In Progress to Done on the challengeR board.
This issue will be fixed in v1.0.1.
eisenman committed rCHALLENGER06191a233e37: Merge branch 'feature/T28193-UnitTestsMoreTasksThanAlgorithms' into develop (authored by eisenman).
Merge branch 'feature/T28193-UnitTestsMoreTasksThanAlgorithms' into develop
Jan 26 2021
Jan 26 2021
The unit tests can be found here: feature/T28193-UnitTestsMoreTasksThanAlgorithms
eisenman committed rCHALLENGER88533dcc2c22: Test that stacked frequency plot for visualizing ranking stability by algorithm… (authored by eisenman).
Test that stacked frequency plot for visualizing ranking stability by algorithm…
eisenman committed rCHALLENGERe1cfc864d52c: Test that PDF report for multi-task data set with bootstrapping is created… (authored by eisenman).
Test that PDF report for multi-task data set with bootstrapping is created…
eisenman committed rCHALLENGEReea8960f2cd0: Test that stacked bar plot for visualizing ranking stability by algorithm… (authored by eisenman).
Test that stacked bar plot for visualizing ranking stability by algorithm…
eisenman committed rCHALLENGERecd51e31c4e3: Test that stacked frequency plot for visualizing ranking stability by algorithm… (authored by eisenman).
Test that stacked frequency plot for visualizing ranking stability by algorithm…
eisenman committed rCHALLENGER28b8d1693b58: Test that stacked bar plot for visualizing ranking stability by algorithm… (authored by eisenman).
Test that stacked bar plot for visualizing ranking stability by algorithm…
eisenman committed rCHALLENGERc2b0873eb0f3: Test that blob plot for visualizing ranking stability by algorithm returns one… (authored by eisenman).
Test that blob plot for visualizing ranking stability by algorithm returns one…
eisenman committed rCHALLENGER8d0b5eeeee9b: Test that blob plot for visualizing ranking stability by algorithm returns one… (authored by eisenman).
Test that blob plot for visualizing ranking stability by algorithm returns one…
eisenman moved T28193: bug in stabilityByAlgorithm.bootstrap.list from Done to In Progress on the challengeR board.
I will extend the unit tests to show that this issue is solved.
eisenman edited projects for T27867: report corrections, added: challengeR (v1.0); removed challengeR.
eisenman edited projects for T27832: Complete troublshooting, added: challengeR (v1.0); removed challengeR.
eisenman moved T28201: Avoid blank pages in report from In Progress to Done on the challengeR board.
eisenman committed rCHALLENGERd5de45f65829: Merge branch 'feature/T28201-FixPageBreak' into develop (authored by eisenman).
Merge branch 'feature/T28201-FixPageBreak' into develop
Fix page break
eisenman moved T28201: Avoid blank pages in report from Backlog to In Progress on the challengeR board.
Jan 25 2021
Jan 25 2021
What exactly is the error? What are the steps to reproduce this? Runtime error or wrong content in report?
Jan 22 2021
Jan 22 2021
Files that cannot be read by a CSV reader should be deleted immediately to avoid that potentially malicious resources are hosted on this public server. A simple check for file extension is not enough. Arbitrary files can be uploaded by just adding the extension *.csv.
Dec 20 2020
Dec 20 2020
eisenman moved T28125: challangeR Release v1.0.0 from In Progress to Done on the challengeR (v1.0) board.
eisenman closed T27410: Correct description of variability of achieved rankings across tasks as Resolved.
eisenman closed T27407: Warnings are shown in multi-task challenge report for violin plot as Resolved.
eisenman closed T27769: Top x performing algorithms are not mentioned in the reports anymore as Resolved.
eisenman closed T27294: add multiple figure output formats in report with option clean=TRUE as Resolved.