unused argument error

[nsheff]

Just running the first 2 lines of the vignette on a new install, I see this:

> library("bedbaser")
> api <- BEDbase()
Error in Service(service = "bedbase", host = "api.bedbase.org", api_reference_version = .BEDBASE_API_REFERENCE_VERSION,  : 
  unused argument (api_reference_version = .BEDBASE_API_REFERENCE_VERSION)

Here's my session info

sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0

locale:
[1] C

time zone: Etc/UTC
tzcode source: system (glibc)

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

other attached packages:
[1] bedbaser_0.99.2

loaded via a namespace (and not attached):
 [1] tidyselect_1.2.1            dplyr_1.1.4                
 [3] blob_1.2.4                  filelock_1.0.3             
 [5] R.utils_2.12.3              Biostrings_2.72.1          
 [7] bitops_1.0-9                fastmap_1.2.0              
 [9] RCurl_1.98-1.16             BiocFileCache_2.12.0       
[11] GenomicAlignments_1.40.0    promises_1.3.0             
[13] XML_3.99-0.17               digest_0.6.37              
[15] mime_0.12                   lifecycle_1.0.4            
[17] RSQLite_2.3.7               magrittr_2.0.3             
[19] compiler_4.4.1              rlang_1.1.4                
[21] tools_4.4.1                 utf8_1.2.4                 
[23] yaml_2.3.10                 rtracklayer_1.64.0         
[25] lambda.r_1.2.4              S4Arrays_1.4.1             
[27] htmlwidgets_1.6.4           bit_4.5.0                  
[29] curl_5.2.3                  DelayedArray_0.30.1        
[31] abind_1.4-8                 BiocParallel_1.38.0        
[33] miniUI_0.1.1.1              purrr_1.0.2                
[35] BiocGenerics_0.50.0         R.oo_1.26.0                
[37] grid_4.4.1                  stats4_4.4.1               
[39] fansi_1.0.6                 xtable_1.8-4               
[41] rapiclient_0.1.8            SummarizedExperiment_1.34.0
[43] cli_3.6.3                   crayon_1.5.3               
[45] generics_0.1.3              httr_1.4.7                 
[47] rjson_0.2.23                DBI_1.2.3                  
[49] cachem_1.1.0                stringr_1.5.1              
[51] zlibbioc_1.50.0             parallel_4.4.1             
[53] formatR_1.14                XVector_0.44.0             
[55] restfulr_0.0.15             matrixStats_1.4.1          
[57] vctrs_0.6.5                 Matrix_1.7-0               
[59] jsonlite_1.8.9              IRanges_2.38.1             
[61] S4Vectors_0.42.1            bit64_4.5.2                
[63] tidyr_1.3.1                 glue_1.8.0                 
[65] codetools_0.2-20            DT_0.33                    
[67] stringi_1.8.4               futile.logger_1.4.3        
[69] later_1.3.2                 GenomeInfoDb_1.40.1        
[71] GenomicRanges_1.56.1        BiocIO_1.14.0              
[73] UCSC.utils_1.0.0            tibble_3.2.1               
[75] pillar_1.9.0                htmltools_0.5.8.1          
[77] AnVIL_1.14.2                GenomeInfoDbData_1.2.12    
[79] R6_2.5.1                    dbplyr_2.5.0               
[81] shiny_1.9.1                 Biobase_2.64.0             
[83] lattice_0.22-6              futile.options_1.0.1       
[85] R.methodsS3_1.8.2           Rsamtools_2.20.0           
[87] memoise_2.0.1               httpuv_1.6.15              
[89] Rcpp_1.0.13                 SparseArray_1.4.8          
[91] MatrixGenerics_1.16.0       pkgconfig_2.0.3            
> 

[jwokaty]

How did you install bedbaser? I wonder if this is because we have different versions of AnVIL. I am using AnVIL_1.17.14.

[nsheff]

I used install_github("waldronlab/bedbaser")

[nsheff]

Updating anvil solved it. so maybe you need a minimum version in the reqs?

[sanghoonio]

It also doesn't seem to install required dependencies either, installing from source kept failing because I was missing bioconductor packages like BiocStyle, liftOver, BiocBaseUtils

Edit: disregard, apparently R CMD build/install doesn't install dependencies for you unlike install.packages() or BiocManager::install()