[R-pkg-team] Bug#1074528: r-bioc-eir: autopkgtest regression with r-base 4.4.1 (i386)

[Dirk Eddelbuettel]

On 30 June 2024 at 12:13, Graham Inggs wrote:
| Source: r-bioc-eir
| 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-eir's autopkgtest regresses when tested with r-base 4.4.1 [1].
| I've copied what I hope is the relevant part of the log below.

See https://www.bioconductor.org/packages/release/bioc/html/eiR.html -- the
current version of the BioConductor eiR package, listed to work with R
4.4.*. is now version 1.44.0.  With a version skew this big auto-package
tests may not be sensible.

Dirk

| 
| Regards
| Graham
| 
| 
| [1] https://ci.debian.net/packages/r/r-bioc-eir/testing/i386/
| 
| 
| 202s checking descriptors
| 204s [1] "52614449152, 52615498752, 52616546304, 52616546305,
| 52617594880, 52617594881, 52618645504, 52619700224, 52619708416,
| 52620740608, 52620742656, 52621789184, 52621789185, 52622853120,
| 52622853121, 53688190976, 53688190977, 53688192000, 53688192001,
| 53688192002, 53688193024, 53688193025, 53688193026, 53688193027,
| 53688193028, 53688206336, 53688206337, 53688207360, 53689239552,
| 53689239553, 53689239554, 53689239555, 53689239556, 53689239557,
| 53689239558, 53689240576, 53689240577, 53689241600, 53689241601,
| 53689241602, 53689247744, 53689247745, 53689247746, 53689247747,
| 53689247748, 53689255936, 53689255937, 53690288128, 53690288129,
| 53690288130, 53690288131, 53690288132, 53690288133, 53690290176,
| 53690290177, 53690290178, 53690290179, 53690296320, 53690296321,
| 53690303488, 53690303489, 53690303490, 53690303491, 53690304512,
| 53690304513, 53690304514, 53690304515, 53691336704, 53691336705,
| 53691336706, 53691336707, 53691336708, 53691336709, 53691338752,
| 53691338753, 53691338754, 53692385280, 53692385281, 53692385282,
| 53692385283, 53692386304, 53692393472, 53692400640, 53692400641,
| 53692400642, 53692400643, 53692401664, 53693433856, 53693434880,
| 53693434881, 53693435904, 53693449216, 53693449217, 53693449218,
| 53693449219, 53694482432, 53694482433, 53695546368, 53695546369,
| 54764032000, 54765086720, 54765094912, 54766129152, 54768239616,
| 54768239617, 55835682816, 55835682817, 55835691008, 55836725248,
| 55836738560, 55836738561, 55836739584, 55838835712, 55838835713,
| 62279190528, 62280238080, 62280238081, 69797479424, 69797480448,
| 69797480449"
| 204s [1] 0.09880833 -0.50000000 0.50000000 -0.50000000 0.44497142 -0.50000000
| 204s [7] -0.46578560 -0.14094824 -0.50000000 0.50000000 -0.50000000 0.50000000
| 204s [13] 0.32523258 0.50000000 0.50000000 -0.15679727 0.50000000 0.50000000
| 204s [19] -0.14531272 0.50000000 -0.24475611 -0.50000000 -0.50000000 0.50000000
| 204s [25] 0.50000000 -0.50000000 -0.50000000 -0.50000000 0.50000000 -0.50000000
| 204s [31] -0.50000000 0.50000000 -0.02047354 0.50000000 0.42086814 0.49316889
| 204s [37] 0.50000000 0.13759897 -0.50000000 -0.28723564
| 204s [1] 0.067484805 0.035798683 0.222776498 -0.087693802 0.078308303
| 204s [6] 0.014039434 0.145663927 0.146636241 -0.115706962 -0.041990705
| 204s [11] -0.017631332 -0.159832996 0.022971835 0.143518592 0.079955212
| 204s [16] 0.011394956 -0.007657527 -0.038522903 0.040856140 -0.033808531
| 204s [21] -0.182359089 -0.023518567 -0.184551059 -0.014498910 -0.060822373
| 204s [26] 0.050760008 0.091104077 -0.250043683 0.002980295 0.042988884
| 204s [31] -0.195190130 0.002355715 0.224217296 0.298889809 0.014137881
| 204s [36] -0.135371953 -0.288479428 -0.052005737 -0.245504847 0.015318735
| 204s Timing stopped at: 12.97 0.12 25.3
| 204s Error in checkDescriptor(conn, rid, descriptorIndex = i) :
| 204s descriptor mismatch found! db version does not match the just computed one
| 204s In addition: Warning message:
| 204s call dbDisconnect() when finished working with a connection
| 204s eiQuery
| 204s using runId 0
| 204s eiQuery test 1
| 204s Timing stopped at: 0.031 0.004 0.035
| 204s Error in eiQuery(runId, sdfsample[1:2], K = 15, asSimilarity =
| TRUE, dir = test_dir) :
| 204s no information found for 0
| 204s Timing stopped at: 0.007 0 0.006
| 204s Error in eiPerformanceTest(runId, K = 22, dir = test_dir) :
| 204s no information found for 0
| 204s using runId 0
| 204s eiAdd test1
| 204s Timing stopped at: 0.264 0.004 0.267
| 204s Error in eiAdd(runId, examples[1:2], dir = test_dir) :
| 204s no information found for run 0
| 204s Timing stopped at: 0.002 0.004 0.007
| 204s Error in eiCluster(runId, K = numNbrs, minNbrs = minNbrs, cutoff = 1 - :
| 204s no information found for 0
| 204s
| 204s
| 204s RUNIT TEST PROTOCOL -- Sat Jun 29 16:27:30 2024
| 204s ***********************************************
| 204s Number of test functions: 8
| 204s Number of errors: 5
| 204s Number of failures: 0

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