parsemsf uses old dplyr style with dbplyr

[hadley]

    > make_area_table(parsemsf_example("test_db.msf"))
    Error in UseMethod("select_") : 
      no applicable method for 'select_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
    Calls: make_area_table ... _fseq -> freduce -> withVisible -> <Anonymous> -> select_
    Execution halted

I'd recommend updating to use tidyeval, since these methods are likely to be removed in the next version of dbplyr.

[yueli8]

@hadley

Thank you so much for your comments!

I have the same error. How can I fix it?

Thank you in advance for your great help!

Best,

Yue

> library(parsemsf)
> area_table <- make_area_table(parsemsf_example("test_db.msf"))
Error in UseMethod("select_") : no applicable method for 'select_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"


 > sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

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       

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

other attached packages:
[1] parsemsf_0.1.1          dplyr_1.0.2             AnnotationHub_2.18.0    BiocFileCache_1.10.2    dbplyr_2.0.0            ensembldb_2.10.2        AnnotationFilter_1.10.0
[8] GenomicFeatures_1.38.2  AnnotationDbi_1.48.0    Biobase_2.46.0          GenomicRanges_1.38.0    GenomeInfoDb_1.22.1     IRanges_2.20.2          S4Vectors_0.24.4       
[15] BiocGenerics_0.32.0     limma_3.42.2           

loaded via a namespace (and not attached):
[1] colorspace_2.0-0              ellipsis_0.3.1                htmlTable_2.1.0               XVector_0.26.0                base64enc_0.1-3              
[6] rstudioapi_0.13               bit64_4.0.5                   interactiveDisplayBase_1.24.0 splines_3.6.3                 geneplotter_1.64.0           
[11] knitr_1.30                    Formula_1.2-4                 Rsamtools_2.2.3               annotate_1.64.0               cluster_2.1.0                
[16] png_0.1-7                     shiny_1.5.0                   BiocManager_1.30.10           compiler_3.6.3                httr_1.4.2                   
[21] backports_1.2.0               assertthat_0.2.1              Matrix_1.2-18                 fastmap_1.0.1                 lazyeval_0.2.2               
[26] later_1.1.0.1                 htmltools_0.5.0               prettyunits_1.1.1             tools_3.6.3                   gtable_0.3.0                 
[31] glue_1.4.2                    GenomeInfoDbData_1.2.2        rappdirs_0.3.1                Rcpp_1.0.5                    vctrs_0.3.5                  
[36] Biostrings_2.54.0             rtracklayer_1.46.0            xfun_0.19                     stringr_1.4.0                 mime_0.9                     
[41] lifecycle_0.2.0               XML_3.99-0.3                  zlibbioc_1.32.0               scales_1.1.1                  hms_0.5.3                    
[46] promises_1.1.1                ProtGenerics_1.18.0           SummarizedExperiment_1.16.1   RColorBrewer_1.1-2            yaml_2.2.1                   
[51] curl_4.3                      memoise_1.1.0                 gridExtra_2.3                 ggplot2_3.3.2                 biomaRt_2.42.1               
[56] rpart_4.1-15                  latticeExtra_0.6-29           stringi_1.5.3                 RSQLite_2.2.1                 BiocVersion_3.10.1           
[61] genefilter_1.68.0             checkmate_2.0.0               BiocParallel_1.20.1           rlang_0.4.9                   pkgconfig_2.0.3              
[66] matrixStats_0.57.0            bitops_1.0-6                  lattice_0.20-41               purrr_0.3.4                   GenomicAlignments_1.22.1     
[71] htmlwidgets_1.5.2             bit_4.0.4                     tidyselect_1.1.0              magrittr_2.0.1                DESeq2_1.26.0                
[76] R6_2.5.0                      generics_0.1.0                Hmisc_4.4-2                   DelayedArray_0.12.3           DBI_1.1.0                    
[81] pillar_1.4.7                  foreign_0.8-76                survival_3.2-7                RCurl_1.98-1.2                nnet_7.3-14                  
[86] tibble_3.0.4                  crayon_1.3.4                  jpeg_0.1-8.1                  progress_1.2.2                locfit_1.5-9.4               
[91] grid_3.6.3                    data.table_1.13.2             blob_1.2.1                    digest_0.6.27                 xtable_1.8-4                 
[96] tidyr_1.1.2                   httpuv_1.5.4                  openssl_1.4.3                 munsell_0.5.0                 askpass_1.1