Bioconductor / ExperimentHub

Client to access ExperimentHub resources
https://bioconductor.org/packages/ExperimentHub
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ExperimentHub() error ! Failed to collect lazy table. #35

Closed dvera closed 1 year ago

dvera commented 1 year ago

ExperimentHub() Error in collect(): ! Failed to collect lazy table. Caused by error in db_collect(): ! Arguments in ... must be used. ✖ Problematic argument: • ..1 = Inf ℹ Did you misspell an argument name? Run rlang::last_trace() to see where the error occurred.

rlang::last_trace() <error/rlang_error> Error in collect(): ! Failed to collect lazy table. Caused by error in db_collect(): ! Arguments in ... must be used. ✖ Problematic argument: • ..1 = Inf ℹ Did you misspell an argument name?

Backtrace: ▆

  1. ├─ExperimentHub::ExperimentHub()
  2. │ └─AnnotationHub::.Hub(...)
  3. │ └─AnnotationHub:::.create_cache(...)
  4. │ └─BiocFileCache::BiocFileCache(cache = cache, ask = ask)
  5. │ └─BiocFileCache:::.sql_create_db(bfc)
  6. │ └─BiocFileCache:::.sql_validate_version(bfc)
  7. │ └─BiocFileCache:::.sql_schema_version(bfc)
  8. │ ├─base::tryCatch(...)
  9. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  10. │ └─tbl(src, "metadata") %>% collect(Inf)
  11. ├─dplyr::collect(., Inf)
  12. └─dbplyr:::collect.tbl_sql(., Inf)
  13. ├─base::tryCatch(...)
  14. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  15. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  16. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
  17. └─dbplyr::db_collect(x$src$con, sql, n = n, warn_incomplete = warn_incomplete, ...)

sessionInfo() R version 4.3.1 (2023-06-16) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 22.04.3 LTS

Matrix products: default BLAS: /usr/local/lib/R/lib/libRblas.so LAPACK: /usr/local/lib/R/lib/libRlapack.so; LAPACK version 3.11.0

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

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

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

other attached packages: [1] sesame_1.20.0 sesameData_1.20.0 ExperimentHub_2.10.0 AnnotationHub_3.10.0 BiocFileCache_2.10.0 dbplyr_2.4.0 BiocGenerics_0.48.0

loaded via a namespace (and not attached): [1] tidyselect_1.2.0 dplyr_1.1.3 blob_1.2.4 filelock_1.0.2 Biostrings_2.70.1 bitops_1.0-7
[7] fastmap_1.1.1 RCurl_1.98-1.12 promises_1.2.1 digest_0.6.33 mime_0.12 lifecycle_1.0.3
[13] ellipsis_0.3.2 KEGGREST_1.42.0 interactiveDisplayBase_1.40.0 RSQLite_2.3.1 magrittr_2.0.3 compiler_4.3.1
[19] rlang_1.1.1 tools_4.3.1 utf8_1.2.4 yaml_2.3.7 knitr_1.44 S4Arrays_1.2.0
[25] bit_4.0.5 curl_5.1.0 DelayedArray_0.28.0 plyr_1.8.9 RColorBrewer_1.1-3 abind_1.4-5
[31] BiocParallel_1.36.0 purrr_1.0.2 grid_4.3.1 stats4_4.3.1 preprocessCore_1.64.0 fansi_1.0.5
[37] wheatmap_0.2.0 xtable_1.8-4 colorspace_2.1-0 ggplot2_3.4.4 scales_1.2.1 SummarizedExperiment_1.32.0
[43] cli_3.6.1 rmarkdown_2.25 crayon_1.5.2 generics_0.1.3 reshape2_1.4.4 httr_1.4.7
[49] tzdb_0.4.0 DBI_1.1.3 cachem_1.0.8 stringr_1.5.0 zlibbioc_1.48.0 parallel_4.3.1
[55] AnnotationDbi_1.64.0 BiocManager_1.30.22 XVector_0.42.0 matrixStats_1.0.0 vctrs_0.6.4 Matrix_1.5-4.1
[61] IRanges_2.36.0 hms_1.1.3 S4Vectors_0.40.0 bit64_4.0.5 glue_1.6.2 codetools_0.2-19
[67] stringi_1.7.12 gtable_0.3.4 BiocVersion_3.18.0 later_1.3.1 GenomeInfoDb_1.38.0 GenomicRanges_1.54.0
[73] munsell_0.5.0 tibble_3.2.1 pillar_1.9.0 rappdirs_0.3.3 htmltools_0.5.6.1 GenomeInfoDbData_1.2.11
[79] R6_2.5.1 lattice_0.21-8 evaluate_0.22 shiny_1.7.5.1 Biobase_2.62.0 readr_2.1.4
[85] png_0.1-8 memoise_2.0.1 httpuv_1.6.12 Rcpp_1.0.11 SparseArray_1.2.0 xfun_0.40
[91] MatrixGenerics_1.14.0 pkgconfig_2.0.3

lshep commented 1 year ago

https://github.com/Bioconductor/AnnotationHub/issues/46 https://support.bioconductor.org/p/9154865/ https://stat.ethz.ch/pipermail/bioc-devel/2023-October/020003.html