Are certain Bioconductor packages out of date?

[rcannood]

I've been getting some issues with using bioconductor packages related to images that should have already been solved in Bioconductor 3.17.

Looking at https://r2u.stat.illinois.edu/ubuntu/pool/dists/jammy/main/ it seems (for example) that DelayedArray was last updated on June 12th when it was updated to v0.26.3-1:

r-bioc-csaw_1.34.0-1.ca2004.2_amd64.deb            28-Apr-2023 05:30             1116136
r-bioc-decipher_2.28.0-1.ca2004.2_amd64.deb        28-Apr-2023 05:19            16072628
r-bioc-delayedarray_0.26.3-1.ca2004.1_amd64.deb    12-Jun-2023 15:25             1931432 <--
r-bioc-delayedmatrixstats_1.22.0-1.ca2004.2_all..> 28-Apr-2023 04:38              672268
r-bioc-deseq2_1.40.2-1.ca2004.1_amd64.deb          14-Jul-2023 19:57             2578212
r-bioc-diffbind_3.10.0-1.ca2004.2_amd64.deb        28-Apr-2023 13:05             7175872

However, the latest release of DelayedArray on Bioconductor 3.17 is 0.26.7 (link). This is also the version available in the posit package manager (link).

The only solution I found for now is installing DelayedArray from source, which misses the entire point of r2u.

Could it be that something is wrong with the procedure for updating the r2u apt repository, or is this intended behaviour?

Thank you for taking the time to look into this issue.

[eddelbuettel]

Could be -- help welcome! Could you cook up and run available.packages() and compare?

"By design" we run against CRAN and pull in BioC as needed. That leaves the door open for something from BioConductor to be stale. We do bulk update to new BioC releases, in between ... may need an additional call we need to fill in. Help from experienced BioC users appreciated!

[eddelbuettel]

I think I have a handle on it. It is simply not an update run I have done, but should do. Maybe weekend-ish. Current subset among those already built:

> ap[newpkgs,.(Package, Version),on="pkgver"]
               Package Version
                <char>  <char>
 1:               affy  1.78.2
 2:    AnnotationForge  1.42.2
 3:             apeglm  1.22.1
 4:             CelliD   1.8.1
 5:           cliqueMS  1.14.1
 6:    clusterProfiler   4.8.3
 7:       DelayedArray  0.26.7
 8: DelayedMatrixStats  1.22.6
 9:           DiffBind  3.10.1
10:               DOSE  3.26.1
11:             gdsfmt  1.36.1
12:         genefilter  1.82.1
13:        GeneticsPed  1.62.1
14:       GenomeInfoDb  1.36.2
15:    GenomicFeatures  1.52.2
16:             ggtree   3.8.2
17:       GreyListChIP  1.32.1
18:               Gviz  1.44.1
19:          HDF5Array  1.28.1
20:              HIBAG  1.36.2
21:         HiCcompare  1.22.1
22:     InteractionSet  1.28.1
23:             lefser  1.10.1
24:                lfa  2.0.11
25:     MatrixGenerics  1.12.3
26:    multiHiCcompare  1.18.1
27:                mzR  2.34.1
28:            qpgraph  2.34.2
29:   RaggedExperiment  1.24.2
30:               RCy3  2.20.1
31:              RedeR   2.4.3
32:       rhdf5filters  1.12.1
33:        rtracklayer  1.60.1
34:           S4Arrays   1.0.6
35:               safe  3.40.1
36:       ScaledMatrix   1.8.1
37:             scater  1.28.0
38:              scran  1.28.2
39:            scuttle  1.10.2
40:           SeqArray  1.40.1
41:  sparseMatrixStats  1.12.2
42:           STRINGdb  2.12.1
43:        systemPipeR   2.6.3
44:        trackViewer  1.36.2
45:             treeio  1.24.3
46:          tweeDEseq  1.46.2
47:     universalmotif  1.18.1
               Package Version
> 

[eddelbuettel]

Done for jammy, will do focal next.

Thanks for the heads-up, this was an oversight and is something that clearly improves the overall experience!

[eddelbuettel]

Now also taken care of for focal. Thanks again.