Hi,

I'm using biovizBase::getIdeogram to retrieve the cytobands of different genomes from UCSC.

For some genomes such as hg38 it works and returns the expected results but produces warnings:

Warning messages:
1: In .local(x, ...) :
  'track' parameter is deprecated now you go by the 'table' instead
                Use ucscTables(genome, track) to retrieve the list of tables for a track
2: In curlSetOpt(..., .opts = .opts, curl = h, .encoding = .encoding) :
  Error setting the option for # 3 (status = 43) (enum = 81) (value = 0x558419645b70): A libcurl function was given a bad argument CURLOPT_SSL_VERIFYHOST no longer supports 1 as value!

but for other genomes it errors and produces no output

> biovizBase::getIdeogram("hg19", cytobands=TRUE, )
[1] "hg19"
Loading ideogram...
Loading ranges...
Error in .normarg_seqlengths(value, seqnames(x)) : 
  the names on the supplied 'seqlengths' vector must be identical to the seqnames
In addition: Warning messages:
1: In .local(x, ...) :
  'track' parameter is deprecated now you go by the 'table' instead
                Use ucscTables(genome, track) to retrieve the list of tables for a track
2: In curlSetOpt(..., .opts = .opts, curl = h, .encoding = .encoding) :
  Error setting the option for # 3 (status = 43) (enum = 81) (value = 0x5584175a7560): A libcurl function was given a bad argument CURLOPT_SSL_VERIFYHOST no longer supports 1 as value!

Could it be a bug in the code or some changes in UCSC that prevent the code from working or it's me doing something wrong?

Thanks a lot

Bernat

sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 10 (buster)

Matrix products: default
BLAS:   /software/debian-10/general/R-4.3.0-bioc-3.17/lib/R/lib/libRblas.so 
LAPACK: /software/debian-10/general/R-4.3.0-bioc-3.17/lib/R/lib/libRlapack.so;  LAPACK version 3.11.0

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

time zone: Europe/Madrid
tzcode source: system (glibc)

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

other attached packages:
[1] rtracklayer_1.60.0   GenomicRanges_1.52.0 GenomeInfoDb_1.36.0  IRanges_2.34.0       S4Vectors_0.38.1     BiocGenerics_0.46.0 
[7] biovizBase_1.48.0   

loaded via a namespace (and not attached):
  [1] DBI_1.1.3                   bitops_1.0-7                gridExtra_2.3               biomaRt_2.56.1              rlang_1.1.1                
  [6] magrittr_2.0.3              matrixStats_1.0.0           compiler_4.3.0              RSQLite_2.3.1               GenomicFeatures_1.52.0     
 [11] png_0.1-8                   vctrs_0.6.3                 ProtGenerics_1.32.0         stringr_1.5.0               pkgconfig_2.0.3            
 [16] crayon_1.5.2                fastmap_1.1.1               backports_1.4.1             dbplyr_2.3.2                XVector_0.40.0             
 [21] utf8_1.2.3                  Rsamtools_2.16.0            rmarkdown_2.22              bit_4.0.5                   xfun_0.39                  
 [26] zlibbioc_1.46.0             cachem_1.0.8                progress_1.2.2              blob_1.2.4                  DelayedArray_0.26.3        
 [31] BiocParallel_1.34.2         parallel_4.3.0              prettyunits_1.1.1           cluster_2.1.4               VariantAnnotation_1.46.0   
 [36] R6_2.5.1                    stringi_1.7.12              RColorBrewer_1.1-3          rpart_4.1.19                SummarizedExperiment_1.30.2
 [41] knitr_1.43                  base64enc_0.1-3             Matrix_1.5-4.1              nnet_7.3-19                 tidyselect_1.2.0           
 [46] yaml_2.3.7                  rstudioapi_0.14             dichromat_2.0-0.1           codetools_0.2-19            curl_5.0.1                 
 [51] lattice_0.21-8              tibble_3.2.1                Biobase_2.60.0              KEGGREST_1.40.0             evaluate_0.21              
 [56] foreign_0.8-84              BiocFileCache_2.8.0         xml2_1.3.4                  Biostrings_2.68.1           pillar_1.9.0               
 [61] filelock_1.0.2              MatrixGenerics_1.12.2       checkmate_2.2.0             generics_0.1.3              RCurl_1.98-1.12            
 [66] ensembldb_2.24.0            hms_1.1.3                   ggplot2_3.4.2               munsell_0.5.0               scales_1.2.1               
 [71] glue_1.6.2                  Hmisc_5.1-0                 lazyeval_0.2.2              tools_4.3.0                 BiocIO_1.10.0              
 [76] data.table_1.14.8           BSgenome_1.68.0             GenomicAlignments_1.36.0    XML_3.99-0.14               grid_4.3.0                 
 [81] AnnotationDbi_1.62.1        colorspace_2.1-0            GenomeInfoDbData_1.2.10     restfulr_0.0.15             htmlTable_2.4.1            
 [86] Formula_1.2-5               cli_3.6.1                   rappdirs_0.3.3              fansi_1.0.4                 S4Arrays_1.0.4             
 [91] dplyr_1.1.2                 AnnotationFilter_1.24.0     gtable_0.3.3                digest_0.6.31               rjson_0.2.21               
 [96] htmlwidgets_1.6.2           memoise_2.0.1               htmltools_0.5.5             lifecycle_1.0.3             httr_1.4.6                 
[101] bit64_4.0.5

It is unfortunately not uncommon for UCSC to change table structure or contents and end up breaking things on our end. The error comes from some error checking within getIdeogram that you might not need. You are really just querying the cytoBand table.

> library(rtracklayer)
> session <- browserSession()
> genome(session) <- "hg19"
> query <- ucscTableQuery(session, "cytoBand")
Warning message:
In .local(x, ...) :
  'track' parameter is deprecated now you go by the 'table' instead
                Use ucscTables(genome, track) to retrieve the list of tables for a track

> df <- getTable(query)
> gr <- with(df, GRanges(chrom, IRanges(chromStart, chromEnd), name = factor(name), gieStain = factor(gieStain)))
> gr <- keepStandardChromosomes(gr, pruning.mode = "coarse")
> library(ggbio)
> autoplot(gr, layout = "karyotype", cytobands = TRUE)

OR alternatively just note that you already have these data!

> data(ideoCyto)
> autoplot(ideoCyto$hg19, layout = "karyotype", cytobands = TRUE)