[R-pkg-team] Bug#1070843: r-bioc-s4vectors: autopkgtest regression with r-base 4.4.0

[Dirk Eddelbuettel]

On 10 May 2024 at 11:04, Graham Inggs wrote:
| Source: r-bioc-s4vectors
| Version: 0.40.2+dfsg-1
| Severity: serious
| X-Debbugs-Cc: Dirk Eddelbuettel <edd at debian.org>
| User: debian-ci at lists.debian.org
| Usertags: regression
| 
| Hi Maintainer
| 
| r-bioc-s4vectors' autopkgtest regresses when tested with r-base 4.4.0
| [1].  I've copied what I hope is the relevant part of the log below.

FYI, I am not the maintainer of r-bioc-s4vectors.

As you likely know, BioConductor aligns its releases with R releases and is
now at release 3.19 (matching R 4.4.0) for which this package is now at
version 0.42.0.

I suggest the maintainer look into upgrading BioConductor to 3.19.

Dirk

| 
| Regards
| Graham
| 
| 
| [1] https://ci.debian.net/packages/r/r-bioc-s4vectors/testing/amd64/
| 
| 
| 125s > S4Vectors:::.test()
| 129s Timing stopped at: 0.009 0 0.009
| 129s Error in var(x) : is.atomic(y) is not TRUE
| 129s In addition: Warning messages:
| 129s 1: In combineUniqueCols(X, Y, Z, use.names = FALSE) :
| 129s different values in multiple instances of column 'dup', ignoring this
| 129s column in DFrame 2
| 129s 2: In combineUniqueCols(X, Y, Z) :
| 129s different values for shared rows in multiple instances of column 'dup',
| 129s ignoring this column in DFrame 2
| 129s 3: In combineUniqueCols(x, y2) :
| 129s different values for shared rows in multiple instances of column 'X',
| 129s ignoring this column in DFrame 2
| 130s Loading required package: GenomeInfoDb
| 132s
| 132s
| 132s RUNIT TEST PROTOCOL -- Thu May 9 22:12:10 2024
| 132s ***********************************************
| 132s Number of test functions: 74
| 132s Number of errors: 1
| 132s Number of failures: 0
| 132s
| 132s
| 132s 1 Test Suite :
| 132s S4Vectors RUnit Tests - 74 test functions, 1 error, 0 failures
| 132s ERROR in test_Rle_numerical: Error in var(x) : is.atomic(y) is not TRUE
| 132s
| 132s Test files with failing tests
| 132s
| 132s test_Rle-utils.R
| 132s test_Rle_numerical
| 132s
| 132s
| 132s Error in BiocGenerics:::testPackage("S4Vectors") :
| 132s unit tests failed for package S4Vectors
| 132s Calls: <Anonymous> -> <Anonymous>
| 132s Execution halted

-- 
dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org