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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')"

Hello,

I tried to use R package of parsemsf.

I have no idea of this kinds of error.

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
software error
• 4,838 views • link
updated by Biostar Biostar • written by yueli7 yueli7

R version 3.6.1, dplyr_0.8.2, parsemsf_0.1.1, dbplyr_1.3.0

> library(parsemsf)
> area_table <- make_area_table(parsemsf_example("test_db.msf"))
> knitr::kable(head(area_table))


| peptide_id| spectrum_id|protein_desc |sequence        |     area|     mass|      m_z| charge| intensity| first_scan|
|----------:|-----------:|:------------|:---------------|--------:|--------:|--------:|------:|---------:|----------:|
|      27146|       15646|NP_041997.1  |AALTDQVALGK     | 55120084| 1086.616| 544.0622|      2|  634147.8|      17577|
|      27177|       15663|NP_041997.1  |AALTDQVALGK     | 55120084| 1086.615| 544.0622|      2|  721063.0|      17595|
|      35484|       20122|NP_041997.1  |ANFQADQIIAK     | 37046635| 1218.648| 610.5803|      2|  152654.2|      22420|
|      35511|       20136|NP_041997.1  |ANFQADQIIAK     | 37046635| 1218.648| 610.5803|      2|  169355.0|      22436|
|      37869|       21360|NP_041997.1  |TQAAYLAPGENLDDK |       NA| 1605.775|       NA|      2|  382864.4|      23744|
|      37913|       21384|NP_041997.1  |TQAAYLAPGENLDDK |       NA| 1605.775|       NA|      2|  282891.8|      23769|


> sessionInfo()
R version 3.6.1 (2019-07-05)
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              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] dplyr_0.8.2    ggplot2_3.3.2  parsemsf_0.1.1

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5       knitr_1.30       magrittr_2.0.1   munsell_0.5.0   
 [5] tidyselect_1.1.0 bit_4.0.4        colorspace_2.0-0 R6_2.5.0        
 [9] rlang_0.4.9      highr_0.8        stringr_1.4.0    blob_1.2.1      
[13] tools_3.6.1      grid_3.6.1       gtable_0.3.0     xfun_0.19       
[17] DBI_1.1.0        withr_2.3.0      dbplyr_1.3.0     ellipsis_0.3.1  
[21] bit64_4.0.5      lazyeval_0.2.2   assertthat_0.2.1 digest_0.6.27   
[25] tibble_3.0.4     lifecycle_0.2.0  crayon_1.3.4     farver_2.0.3    
[29] purrr_0.3.4      tidyr_1.1.2      vctrs_0.3.5      memoise_1.1.0   
[33] glue_1.4.2       RSQLite_2.2.1    labeling_0.4.2   stringi_1.5.3   
[37] compiler_3.6.1   pillar_1.4.7     scales_1.1.1     pkgconfig_2.0.3
• 0 views • link
written by yueli7 yueli7

So, your solution was to downgrade R and according packages?

• 0 views • link
written by e.rempel e.rempel

Hello e.rempel,

Thank you for your comments!

I think It also can work on R version 3.6.3, dplyr_0.8.2 , dbplyr_1.3.0 .

Thank you again!

> library(parsemsf)
> area_table <- make_area_table(parsemsf_example("test_db.msf"))

> knitr::kable(head(area_table))


| peptide_id| spectrum_id|protein_desc |sequence        |     area|     mass|      m_z| charge| intensity| first_scan|
|----------:|-----------:|:------------|:---------------|--------:|--------:|--------:|------:|---------:|----------:|
|      27146|       15646|NP_041997.1  |AALTDQVALGK     | 55120084| 1086.616| 544.0622|      2|  634147.8|      17577|
|      27177|       15663|NP_041997.1  |AALTDQVALGK     | 55120084| 1086.615| 544.0622|      2|  721063.0|      17595|
|      35484|       20122|NP_041997.1  |ANFQADQIIAK     | 37046635| 1218.648| 610.5803|      2|  152654.2|      22420|
|      35511|       20136|NP_041997.1  |ANFQADQIIAK     | 37046635| 1218.648| 610.5803|      2|  169355.0|      22436|
|      37869|       21360|NP_041997.1  |TQAAYLAPGENLDDK |       NA| 1605.775|       NA|      2|  382864.4|      23744|



> 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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] parsemsf_0.1.1 limma_3.42.2  

loaded via a namespace (and not attached):
 [1] Biobase_2.46.0              tidyr_1.1.2                 bit64_4.0.5                 splines_3.6.3               Formula_1.2-4               assertthat_0.2.1           
 [7] highr_0.8                   stats4_3.6.3                latticeExtra_0.6-29         blob_1.2.1                  GenomeInfoDbData_1.2.2      pillar_1.4.7               
[13] RSQLite_2.2.1               backports_1.2.0             lattice_0.20-41             glue_1.4.2                  digest_0.6.27               GenomicRanges_1.38.0       
[19] RColorBrewer_1.1-2          XVector_0.26.0              checkmate_2.0.0             colorspace_2.0-0            htmltools_0.5.0             Matrix_1.2-18              
[25] DESeq2_1.26.0               XML_3.99-0.3                pkgconfig_2.0.3             genefilter_1.68.0           zlibbioc_1.32.0             purrr_0.3.4                
[31] xtable_1.8-4                scales_1.1.1                jpeg_0.1-8.1                BiocParallel_1.20.1         htmlTable_2.1.0             tibble_3.0.4               
[37] annotate_1.64.0             IRanges_2.20.2              ggplot2_3.3.2               ellipsis_0.3.1              SummarizedExperiment_1.16.1 lazyeval_0.2.2             
[43] nnet_7.3-14                 BiocGenerics_0.32.0         cli_2.2.0                   survival_3.2-7              magrittr_2.0.1              crayon_1.3.4               
[49] memoise_1.1.0               fansi_0.4.1                 foreign_0.8-76              tools_3.6.3                 data.table_1.13.2           lifecycle_0.2.0            
[55] matrixStats_0.57.0          stringr_1.4.0               S4Vectors_0.24.4            locfit_1.5-9.4              munsell_0.5.0               cluster_2.1.0              
[61] DelayedArray_0.12.3         AnnotationDbi_1.48.0        compiler_3.6.3              GenomeInfoDb_1.22.1         rlang_0.4.9                 grid_3.6.3                 
 [67] RCurl_1.98-1.2              rstudioapi_0.13             htmlwidgets_1.5.2           bitops_1.0-6                base64enc_0.1-3             gtable_0.3.0               
 [73] DBI_1.1.0                   R6_2.5.0                    gridExtra_2.3               knitr_1.30                  dplyr_0.8.2                 bit_4.0.4                  
 [79] Hmisc_4.4-2                 stringi_1.5.3               parallel_3.6.3              Rcpp_1.0.5                  vctrs_0.3.5                 geneplotter_1.64.0         
 [85] rpart_4.1-15                png_0.1-7                   dbplyr_1.3.0                tidyselect_1.1.0            xfun_0.19                  





> library(parsemsf)

Warning message:
package ‘parsemsf’ was built under R version 3.6.3

```

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written by yueli7 yueli7

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