Bioconductor BBS: Organism.dplyr / BioC 3.18, 10/27/93

[mtmorgan]

Hi Organism.dplyr maintainer,

According to the Multiple platform build/check report for BioC 3.18,
the Organism.dplyr package has the following problem(s):

o ERROR for 'R CMD build' on nebbiolo2. See the details here:
https://master.bioconductor.org/checkResults/3.18/bioc-LATEST/Organism.dplyr/nebbiolo2-buildsrc.html

Please take the time to address this by committing and pushing
changes to your package at git.bioconductor.org

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[mtmorgan]

This error occurs in the vignette. A reproducible example is

src <- src_organism(dbpath = hg38light())
keytypes(src)
## Error in `tbl_sql()`:
## ! Arguments in `...` must be used.
## ✖ Problematic argument:
## • .load_tbl_only = .load_tbl_only
## ℹ Did you misspell an argument name?
## Run `rlang::last_trace()` to see where the error occurred.

with rlang::last_trace() giving

<error/rlib_error_dots_unused>
Error in `tbl_sql()`:
! Arguments in `...` must be used.
✖ Problematic argument:
• .load_tbl_only = .load_tbl_only
ℹ Did you misspell an argument name?
---
Backtrace:
     ▆
  1. ├─AnnotationDbi::keytypes(src)
  2. └─Organism.dplyr::keytypes(src)
  3.   └─base::lapply(...) at Organism.dplyr/R/select.R:4:4
  4.     └─Organism.dplyr (local) FUN(X[[i]], ...)
  5.       ├─base::colnames(tbl(x, table, .load_tbl_only = TRUE)) at Organism.dplyr/R/select.R:4:34
  6.       │ └─base::is.data.frame(x)
  7.       ├─dplyr::tbl(x, table, .load_tbl_only = TRUE)
  8.       ├─Organism.dplyr:::tbl.src_organism(x, table, .load_tbl_only = TRUE)
  9.       ├─base::NextMethod(src, ...) at Organism.dplyr/R/src.R:485:4
 10.       └─dbplyr:::tbl.src_dbi(x, table, .load_tbl_only = TRUE)
 11.         └─dbplyr::tbl_sql(c(subclass, "dbi"), src = src, from = from, ...)
Run rlang::last_trace(drop = FALSE) to see 5 hidden frames.

The error comes from a change in dbplyr, where only arguments defined in the generic are allowed. See tidyverse/dbplyr#1384.

I believe the dbplyr change is INCORRECT (methods are allowed to add arguments to the generic), and should be reverted. Will return to this in a few days.

> BiocManager::valid()

* sessionInfo()

R Under development (unstable) (2023-10-30 r85438)
Platform: aarch64-apple-darwin21.6.0
Running under: macOS Monterey 12.6.8

Matrix products: default
BLAS:   /Users/ma38727/bin/R-devel/lib/libRblas.dylib
LAPACK: /Users/ma38727/bin/R-devel/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

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

other attached packages:
[1] Organism.dplyr_1.31.0   testthat_3.2.0          AnnotationFilter_1.27.0
[4] dplyr_1.1.3

loaded via a namespace (and not attached):
  [1] DBI_1.1.3                   bitops_1.0-7
  [3] remotes_2.4.2.1             biomaRt_2.59.0
  [5] rlang_1.1.1                 magrittr_2.0.3
  [7] matrixStats_1.0.0           compiler_4.4.0
  [9] RSQLite_2.3.2               GenomicFeatures_1.55.1
 [11] png_0.1-8                   callr_3.7.3
 [13] vctrs_0.6.4                 stringr_1.5.0
 [15] profvis_0.3.8               pkgconfig_2.0.3
 [17] crayon_1.5.2                fastmap_1.1.1
 [19] dbplyr_2.4.0                XVector_0.43.0
 [21] ellipsis_0.3.2              utf8_1.2.4
 [23] Rsamtools_2.19.0            promises_1.2.1
 [25] sessioninfo_1.2.2           ps_1.7.5
 [27] purrr_1.0.2                 bit_4.0.5
 [29] zlibbioc_1.49.0             cachem_1.0.8
 [31] GenomeInfoDb_1.39.0         progress_1.2.2
 [33] blob_1.2.4                  later_1.3.1
 [35] DelayedArray_0.29.0         BiocParallel_1.37.0
 [37] parallel_4.4.0              prettyunits_1.2.0
 [39] R6_2.5.1                    stringi_1.7.12
 [41] rtracklayer_1.63.0          pkgload_1.3.3
 [43] brio_1.1.3                  GenomicRanges_1.55.1
 [45] Rcpp_1.0.11                 SummarizedExperiment_1.33.0
 [47] usethis_2.2.2               IRanges_2.37.0
 [49] httpuv_1.6.12               Matrix_1.6-1.1
 [51] tidyselect_1.2.0            rstudioapi_0.15.0
 [53] abind_1.4-5                 yaml_2.3.7
 [55] codetools_0.2-19            miniUI_0.1.1.1
 [57] curl_5.1.0                  processx_3.8.2
 [59] pkgbuild_1.4.2              lattice_0.22-5
 [61] tibble_3.2.1                Biobase_2.63.0
 [63] shiny_1.7.5.1               withr_2.5.2
 [65] KEGGREST_1.43.0             desc_1.4.2
 [67] urlchecker_1.0.1            BiocFileCache_2.11.1
 [69] xml2_1.3.5                  Biostrings_2.71.1
 [71] BiocManager_1.30.22         pillar_1.9.0
 [73] filelock_1.0.2              MatrixGenerics_1.15.0
 [75] stats4_4.4.0                generics_0.1.3
 [77] rprojroot_2.0.3             RCurl_1.98-1.12
 [79] S4Vectors_0.41.1            hms_1.1.3
 [81] xtable_1.8-4                glue_1.6.2
 [83] lazyeval_0.2.2              tools_4.4.0
 [85] BiocIO_1.13.0               GenomicAlignments_1.39.0
 [87] fs_1.6.3                    XML_3.99-0.14
 [89] grid_4.4.0                  devtools_2.4.5
 [91] AnnotationDbi_1.65.0        GenomeInfoDbData_1.2.11
 [93] restfulr_0.0.15             cli_3.6.1
 [95] rappdirs_0.3.3              fansi_1.0.5
 [97] S4Arrays_1.3.0              digest_0.6.33
 [99] BiocGenerics_0.49.0         SparseArray_1.3.0
[101] rjson_0.2.21                htmlwidgets_1.6.2
[103] memoise_2.0.1               htmltools_0.5.6.1
[105] lifecycle_1.0.3             httr_1.4.7
[107] mime_0.12                   bit64_4.0.5

Bioconductor version '3.19'

  * 1 packages out-of-date
  * 0 packages too new

create a valid installation with

  BiocManager::install("cellxgenedp", update = TRUE, ask = FALSE, force = TRUE)

more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date

Warning message:
1 packages out-of-date; 0 packages too new