trackNames() stopped working on a UCSCSession, possibly due to change on UCSC's side

[hpages]

trackNames() is expected to return a named character vector where the vector elements are table names and the names on the vector the corresponding track names. However, recently it started to return a character vector where the names are missing (all but one name are set to NA):

library(rtracklayer)
session <- browserSession()

genome(session) <- "hg38"
genome_tracknames <- trackNames(session)
head(genome_tracknames)
#      Base Position                <NA>                <NA>                <NA> 
#            "ruler" "fixSeqLiftOverPsl" "altSeqLiftOverPsl"              "gold" 
#               <NA>                <NA> 
#      "centromeres"          "cytoBand" 

genome(session) <- "mm10"
genome_tracknames <- trackNames(session)
head(genome_tracknames)
#      Base Position                <NA>                <NA>                <NA> 
#            "ruler" "fixSeqLiftOverPsl" "altSeqLiftOverPsl"              "gold" 
#               <NA>                <NA> 
#         "cytoBand"     "cloneEndSuper" 

genome(session) <- "sacCer3"
genome_tracknames <- trackNames(session)
genome_tracknames
#      Base Position                <NA>                <NA>                <NA> 
#            "ruler"          "sgdClone"              "gold"         "gc5BaseBw" 
#               <NA>                <NA>                <NA>                <NA> 
#          "cutters"        "oligoMatch"   "refSeqComposite"           "sgdGene" 
#               <NA>                <NA>                <NA>                <NA> 
#         "sgdOther"      "augustusGene"            "crispr"           "ensGene" 
#               <NA>                <NA>                <NA>                <NA> 
#      "blastHg18KG"       "xenoRefGene"           "uniprot"               "est" 
#               <NA>                <NA>                <NA>                <NA> 
#             "mrna"         "intronEst"      "transRegCode" "transRegCodeProbe" 
#               <NA>                <NA>                <NA>                <NA> 
#         "oreganno"  "esRegGeneToMotif"          "cons7way"          "microsat" 
#               <NA> 
#     "simpleRepeat" 

I get this on all platforms, in release (BioC 3.17) and devel (BioC 3.18), and for all the genomes I tried.

FWIW this breaks GenomicFeatures::makeTxDbFromUCSC() on all platforms in release and devel:

• https://bioconductor.org/checkResults/3.17/bioc-LATEST/GenomicFeatures/
• https://bioconductor.org/checkResults/3.18/bioc-LATEST/GenomicFeatures/

Thanks, H.

sessionInfo():

R version 4.3.0 Patched (2023-05-31 r84481)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 23.04

Matrix products: default
BLAS:   /home/hpages/R/R-4.3.r84481/lib/libRblas.so 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: America/Los_Angeles
tzcode source: system (glibc)

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] rtracklayer_1.60.0   GenomicRanges_1.52.0 GenomeInfoDb_1.36.1 
[4] IRanges_2.34.1       S4Vectors_0.38.1     BiocGenerics_0.46.0 

loaded via a namespace (and not attached):
 [1] crayon_1.5.2                DelayedArray_0.26.7        
 [3] SummarizedExperiment_1.30.2 GenomicAlignments_1.36.0   
 [5] rjson_0.2.21                RCurl_1.98-1.12            
 [7] Biostrings_2.68.1           XML_3.99-0.14              
 [9] MatrixGenerics_1.12.3       Biobase_2.60.0             
[11] grid_4.3.0                  restfulr_0.0.15            
[13] abind_1.4-5                 bitops_1.0-7               
[15] yaml_2.3.7                  compiler_4.3.0             
[17] codetools_0.2-19            XVector_0.40.0             
[19] BiocParallel_1.34.2         lattice_0.21-8             
[21] BiocIO_1.10.0               parallel_4.3.0             
[23] GenomeInfoDbData_1.2.10     Matrix_1.6-0               
[25] tools_4.3.0                 matrixStats_1.0.0          
[27] Rsamtools_2.16.0            zlibbioc_1.46.0            
[29] S4Arrays_1.0.6             

[sanchit-saini]

Thanks for reporting it. I will look into it.

[MurliNair]

I see this issue has been closed. Do you reinstall GenomicFeatures? Thanks ../Murli

[hpages]

@lawremi @sanchit-saini Thanks for the PR. Can you please push to git.bioconductor.org, apply the fix to the RELEASE_3_17 branch (release), and bump the package version in both branches (release and devel). Thanks again!

[hpages]

@MurliNair Some steps are missing for the fix to actually propagate to Bioconductor (see above for the details). Once they are completed, it will take between 24 and 48 hrs before the new version of rtracklayer becomes available for installation via BiocManager::install().

[MurliNair]

Thanks for your kind reply and for your efforts in resolving the error. I tried installing using BiocManager::install() and it still give the same error I reported earlier. I presume the issue is still not resolved. Just keeping you posted about it.