"object of type 'closure' is not subsettable" errors

hpages commented 3 years ago

Running BiocCheck() on the MatrixQCvis package (https://github.com/tnaake/MatrixQCvis) produces "object of type 'closure' is not subsettable" errors:

> library(BiocCheck)
Bioconductor version 3.13 (BiocManager 1.30.12), ?BiocManager::install for help
> BiocCheck("MatrixQCvis_0.99.3.tar.gz")
This is BiocCheck version 1.27.13. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
...
* Checking for library/require of MatrixQCvis...
* Checking coding practice...
Warning in readLines(infile) :
  incomplete final line found on '/tmp/Rtmpl5Xsls/file11165226d774f/MatrixQCvis/tests/testthat.R'
Error in params$missingValue : 
  object of type 'closure' is not subsettable
Error in params$missingValue : 
  object of type 'closure' is not subsettable
Error in params$missingValue : 
  object of type 'closure' is not subsettable
Error in params$missingValue : 
  object of type 'closure' is not subsettable
Error in params$missingValue : 
  object of type 'closure' is not subsettable
Error in params$missingValue : 
  object of type 'closure' is not subsettable
Error in params$missingValue : 
  object of type 'closure' is not subsettable
Error in params$missingValue : 
  object of type 'closure' is not subsettable
* Checking parsed R code in R directory, examples, vignettes...
...

sessionInfo():

R Under development (unstable) (2021-03-08 r80083)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.10

Matrix products: default
BLAS:   /home/hpages/R/R-4.1.r80083/lib/libRblas.so
LAPACK: /home/hpages/R/R-4.1.r80083/lib/libRlapack.so

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=en_US.UTF-8          
 [9] LC_ADDRESS=en_US.UTF-8        LC_TELEPHONE=en_US.UTF-8     
[11] LC_MEASUREMENT=en_US.UTF-8    LC_IDENTIFICATION=en_US.UTF-8

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

other attached packages:
 [1] MatrixQCvis_0.99.3          shiny_1.6.0                
 [3] plotly_4.9.3                ggplot2_3.3.3              
 [5] SummarizedExperiment_1.21.3 Biobase_2.51.0             
 [7] GenomicRanges_1.43.4        GenomeInfoDb_1.27.11       
 [9] IRanges_2.25.9              S4Vectors_0.29.12          
[11] BiocGenerics_0.37.2         MatrixGenerics_1.3.1       
[13] matrixStats_0.58.0          BiocCheck_1.27.13          

loaded via a namespace (and not attached):
  [1] backports_1.2.1        circlize_0.4.12        Hmisc_4.5-0           
  [4] proDA_1.5.0            plyr_1.8.6             gmm_1.6-6             
  [7] lazyeval_0.2.2         shinydashboard_0.7.1   splines_4.1.0         
 [10] digest_0.6.27          foreach_1.5.1          htmltools_0.5.1.1     
 [13] fansi_0.4.2            magrittr_2.0.1         checkmate_2.0.0       
 [16] xlsx_0.6.5             cluster_2.1.2          doParallel_1.0.16     
 [19] limma_3.47.12          ComplexHeatmap_2.7.9   imputeLCMD_2.0        
 [22] sandwich_3.0-0         askpass_1.1            jpeg_0.1-8.1          
 [25] colorspace_2.0-0       xfun_0.22              dplyr_1.0.5           
 [28] crayon_1.4.1           RCurl_1.98-1.3         jsonlite_1.7.2        
 [31] graph_1.69.0           impute_1.65.0          survival_3.2-10       
 [34] zoo_1.8-9              iterators_1.0.13       ape_5.4-1             
 [37] glue_1.4.2             gtable_0.3.0           zlibbioc_1.37.0       
 [40] XVector_0.31.1         UpSetR_1.4.0           GetoptLong_1.0.5      
 [43] DelayedArray_0.17.10   shape_1.4.5            scales_1.1.1          
 [46] vsn_3.59.1             mvtnorm_1.1-1          DBI_1.1.1             
 [49] Rcpp_1.0.6             viridisLite_0.4.0      xtable_1.8-4          
 [52] htmlTable_2.1.0        clue_0.3-59            reticulate_1.18       
 [55] foreign_0.8-81         preprocessCore_1.53.2  Formula_1.2-4         
 [58] MsCoreUtils_1.3.3      umap_0.2.7.0           htmlwidgets_1.5.3     
 [61] httr_1.4.2             getopt_1.20.3          RColorBrewer_1.1-2    
 [64] ellipsis_0.3.1         rJava_0.9-13           pkgconfig_2.0.3       
 [67] XML_3.99-0.6           nnet_7.3-15            utf8_1.2.1            
 [70] tidyselect_1.1.0       shinyhelper_0.3.2      rlang_0.4.10          
 [73] later_1.1.0.1          munsell_0.5.0          biocViews_1.59.3      
 [76] tools_4.1.0            generics_0.1.0         evaluate_0.14         
 [79] stringr_1.4.0          fastmap_1.1.0          yaml_2.2.1            
 [82] knitr_1.32             purrr_0.3.4            RBGL_1.67.0           
 [85] nlme_3.1-152           mime_0.10              compiler_4.1.0        
 [88] rstudioapi_0.13        curl_4.3               png_0.1-7             
 [91] affyio_1.61.0          tibble_3.1.1           stringi_1.5.3         
 [94] RSpectra_0.16-0        lattice_0.20-41        Matrix_1.3-2          
 [97] permute_0.9-5          shinyjs_2.0.0          vegan_2.5-7           
[100] tmvtnorm_1.4-10        vctrs_0.3.7            stringdist_0.9.6.3    
[103] pillar_1.6.0           norm_1.0-9.5           lifecycle_1.0.0       
[106] RUnit_0.4.32           optparse_1.6.6         BiocManager_1.30.12   
[109] GlobalOptions_0.1.2    data.table_1.14.0      bitops_1.0-6          
[112] httpuv_1.5.5           affy_1.69.1            R6_2.5.0              
[115] latticeExtra_0.6-29    pcaMethods_1.83.0      promises_1.2.0.1      
[118] gridExtra_2.3          codetools_0.2-18       MASS_7.3-53.1         
[121] assertthat_0.2.1       xlsxjars_0.6.1         openssl_1.4.3         
[124] rjson_0.2.20           withr_2.4.2            GenomeInfoDbData_1.2.4
[127] mgcv_1.8-35            grid_4.1.0             rpart_4.1-15          
[130] tidyr_1.1.3            rmarkdown_2.7          Cairo_1.5-12.2        
[133] Rtsne_0.15             base64enc_0.1-3

lshep commented 3 years ago

I can't reproduce this.

> library(BiocCheck)
> BiocCheck("MatrixQCvis_0.99.3.tar.gz")
This is BiocCheck version 1.27.13. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Registered S3 method overwritten by 'dendextend':
  method     from 
  rev.hclust vegan
Registered S3 method overwritten by 'seriation':
  method         from 
  reorder.hclust vegan
* Checking if other packages can import this one...
    * ERROR: Packages providing 1 object(s) used in this package should
      be imported in the NAMESPACE file, otherwise packages importing
      this package may fail.

      package::object in function()
        plotly::partial_bundle in distServer ()

* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
    Package version 0.99.3; pre-release
* Checking R Version dependency...
* Checking package size...
* Checking individual file sizes...
    * WARNING: The following files are over 5MB in size:
      'inst/doc/MatrixQCvis.html'
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
    Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
    * NOTE: Consider adding these automatically suggested biocViews:
      Sequencing, Coverage
See http://bioconductor.org/developers/how-to/biocViews/
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
    * NOTE: License 'GPL (>= 3)' unknown; licenses cannot restrict use
* Checking DESCRIPTION/NAMESPACE consistency...
    * WARNING: Import ComplexHeatmap in DESCRIPTION as well as
      NAMESPACE.
* Checking .Rbuildignore...
* Checking vignette directory...
    This is a software package
* Checking library calls...
* Checking for library/require of MatrixQCvis...
* Checking coding practice...
Warning in readLines(infile) :
  incomplete final line found on '/tmp/RtmpPg9nMI/file448052c7e334/MatrixQCvis/tests/testthat.R'
Error in params$missingValue : 
  object of type 'closure' is not subsettable
Error in params$missingValue : 
  object of type 'closure' is not subsettable
Error in params$missingValue : 
  object of type 'closure' is not subsettable
Error in params$missingValue : 
  object of type 'closure' is not subsettable
Error in params$missingValue : 
  object of type 'closure' is not subsettable
Error in params$missingValue : 
  object of type 'closure' is not subsettable
Error in params$missingValue : 
  object of type 'closure' is not subsettable
Error in params$missingValue : 
  object of type 'closure' is not subsettable
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths.......................................................
    * NOTE: Recommended function length <= 50 lines.
      There are 25 functions > 50 lines.
      The longest 5 functions are:
        .initialize_server() (R/shinyQC.R, line 218): 527 lines
        maServer() (R/module_values.R, line 757): 158 lines
        _anonymous_.762() (R/module_values.R, line 762): 151 lines
        shinyQC() (R/shinyQC.R, line 68): 124 lines
        maxQuant() (R/conversion.R, line 112): 93 lines
* Checking man page documentation...
    * NOTE: Usage of dontrun{} / donttest{} found in man page examples.
      8% of man pages use one of these cases.
      Found in the following files:
        biocrates.Rd
        maxQuant.Rd
        shinyQC.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 32 lines (0%) are > 80 characters
      long.
    First 6 lines:
      R/conversion.R:156         rD$Unique_razor_sequence_coverage <- xls[, "...
      R/module_global.R:121         condition = "input.tabs == 'Dimension Red...
      R/module_global.R:172     conditionalPanel("output.missingVals == 'TRUE...
      R/shinyQC.R:134                     $(".main-sidebar .sidebar").css({"p...
      R/shinyQC.R:379                 "It seems you have applied a batch corr...
      R/shinyQC.R:380                 "Please make sure to assess the existen...
    * NOTE: Consider multiples of 4 spaces for line indents, 95
      lines(1%) are not.
    First 6 lines:
      R/module_values.R:76                      selected = "boxplot")),
      man/create_boxplot.Rd:8   se,
      man/create_boxplot.Rd:9   orderCategory = colnames(colData(se)),
      man/create_boxplot.Rd:10   title = "",
      man/create_boxplot.Rd:11   log2 = TRUE,
      man/create_boxplot.Rd:12   violin = FALSE
    See http://bioconductor.org/developers/how-to/coding-style/
    See styler package: https://cran.r-project.org/package=styler as
      described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking for bioc-devel mailing list subscription...
    * NOTE: Cannot determine whether maintainer is subscribed to the
      bioc-devel mailing list (requires admin credentials).  Subscribe
      here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
    Maintainer is registered at support site.
    * ERROR: Maintainer must add package name to Watched Tags on the
      support site; Edit your Support Site User Profile to add Watched
      Tags.

Summary:
ERROR count: 2
WARNING count: 2
NOTE count: 7
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.13/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheck FAILED.
$error
[1] "Packages providing 1 object(s) used in this package should be imported in the NAMESPACE file, otherwise packages importing this package may fail."
[2] "Maintainer must add package name to Watched Tags on the support site; Edit your Support Site User Profile to add Watched Tags."                   

$warning
[1] "The following files are over 5MB in size: 'inst/doc/MatrixQCvis.html'"
[2] "Import ComplexHeatmap in DESCRIPTION as well as NAMESPACE."           

$note
[1] "Consider adding these automatically suggested biocViews: Sequencing, Coverage"                                                                                                     
[2] "License 'GPL (>= 3)' unknown; licenses cannot restrict use"                                                                                                                        
[3] "Recommended function length <= 50 lines."                                                                                                                                          
[4] "Usage of dontrun{} / donttest{} found in man page examples."                                                                                                                       
[5] "Consider shorter lines; 32 lines (0%) are > 80 characters long."                                                                                                                   
[6] "Consider multiples of 4 spaces for line indents, 95 lines(1%) are not."                                                                                                            
[7] "Cannot determine whether maintainer is subscribed to the bioc-devel\nmailing list (requires admin credentials).  Subscribe here:\nhttps://stat.ethz.ch/mailman/listinfo/bioc-devel"

> sessionInfo()
R Under development (unstable) (2021-04-09 r80152)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS:   /home/shepherd/R-Installs/bin/R-devel/lib/libRblas.so
LAPACK: /home/shepherd/R-Installs/bin/R-devel/lib/libRlapack.so

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=en_US.UTF-8          
 [9] LC_ADDRESS=en_US.UTF-8        LC_TELEPHONE=en_US.UTF-8     
[11] LC_MEASUREMENT=en_US.UTF-8    LC_IDENTIFICATION=en_US.UTF-8

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

other attached packages:
 [1] MatrixQCvis_0.99.3          shiny_1.6.0                
 [3] plotly_4.9.3                ggplot2_3.3.3              
 [5] SummarizedExperiment_1.21.3 Biobase_2.51.0             
 [7] GenomicRanges_1.43.4        GenomeInfoDb_1.27.11       
 [9] IRanges_2.25.9              S4Vectors_0.29.15          
[11] BiocGenerics_0.37.2         MatrixGenerics_1.3.1       
[13] matrixStats_0.58.0          BiocCheck_1.27.13          
[15] praise_1.0.0                BiocManager_1.30.12        

loaded via a namespace (and not attached):
  [1] backports_1.2.1        circlize_0.4.12        Hmisc_4.5-0           
  [4] proDA_1.5.0            plyr_1.8.6             gmm_1.6-6             
  [7] lazyeval_0.2.2         shinydashboard_0.7.1   splines_4.1.0         
 [10] digest_0.6.27          foreach_1.5.1          htmltools_0.5.1.1     
 [13] viridis_0.6.0          fansi_0.4.2            magrittr_2.0.1        
 [16] checkmate_2.0.0        xlsx_0.6.5             cluster_2.1.2         
 [19] doParallel_1.0.16      limma_3.47.12          ComplexHeatmap_2.7.9  
 [22] imputeLCMD_2.0         sandwich_3.0-0         askpass_1.1           
 [25] jpeg_0.1-8.1           colorspace_2.0-0       xfun_0.22             
 [28] dplyr_1.0.5            crayon_1.4.1           RCurl_1.98-1.3        
 [31] jsonlite_1.7.2         graph_1.69.0           impute_1.65.0         
 [34] survival_3.2-10        zoo_1.8-9              iterators_1.0.13      
 [37] ape_5.4-1              glue_1.4.2             registry_0.5-1        
 [40] gtable_0.3.0           zlibbioc_1.37.0        XVector_0.31.1        
 [43] webshot_0.5.2          UpSetR_1.4.0           GetoptLong_1.0.5      
 [46] DelayedArray_0.17.10   shape_1.4.5            scales_1.1.1          
 [49] vsn_3.59.1             mvtnorm_1.1-1          DBI_1.1.1             
 [52] Rcpp_1.0.6             viridisLite_0.4.0      xtable_1.8-4          
 [55] htmlTable_2.1.0        clue_0.3-59            reticulate_1.18       
 [58] foreign_0.8-81         preprocessCore_1.53.2  Formula_1.2-4         
 [61] MsCoreUtils_1.3.3      umap_0.2.7.0           htmlwidgets_1.5.3     
 [64] httr_1.4.2             getopt_1.20.3          RColorBrewer_1.1-2    
 [67] ellipsis_0.3.1         rJava_0.9-13           pkgconfig_2.0.3       
 [70] XML_3.99-0.6           nnet_7.3-15            utf8_1.2.1            
 [73] tidyselect_1.1.0       shinyhelper_0.3.2      rlang_0.4.10          
 [76] later_1.1.0.1          munsell_0.5.0          biocViews_1.59.3      
 [79] tools_4.1.0            generics_0.1.0         evaluate_0.14         
 [82] stringr_1.4.0          fastmap_1.1.0          yaml_2.2.1            
 [85] heatmaply_1.2.1        knitr_1.32             purrr_0.3.4           
 [88] dendextend_1.14.0      RBGL_1.67.0            nlme_3.1-152          
 [91] mime_0.10              compiler_4.1.0         rstudioapi_0.13       
 [94] curl_4.3               png_0.1-7              affyio_1.61.0         
 [97] tibble_3.1.1           stringi_1.5.3          RSpectra_0.16-0       
[100] lattice_0.20-41        Matrix_1.3-2           permute_0.9-5         
[103] shinyjs_2.0.0          vegan_2.5-7            tmvtnorm_1.4-10       
[106] vctrs_0.3.7            stringdist_0.9.6.3     pillar_1.6.0          
[109] norm_1.0-9.5           lifecycle_1.0.0        RUnit_0.4.32          
[112] optparse_1.6.6         GlobalOptions_0.1.2    data.table_1.14.0     
[115] bitops_1.0-6           seriation_1.2-9        httpuv_1.5.5          
[118] affy_1.69.1            R6_2.5.0               latticeExtra_0.6-29   
[121] pcaMethods_1.83.0      TSP_1.1-10             promises_1.2.0.1      
[124] gridExtra_2.3          codetools_0.2-18       MASS_7.3-53.1         
[127] assertthat_0.2.1       xlsxjars_0.6.1         openssl_1.4.3         
[130] rjson_0.2.20           withr_2.4.2            GenomeInfoDbData_1.2.4
[133] mgcv_1.8-35            grid_4.1.0             rpart_4.1-15          
[136] tidyr_1.1.3            rmarkdown_2.7          Cairo_1.5-12.2        
[139] Rtsne_0.15             base64enc_0.1-3       
>

hpages commented 3 years ago

I see it in your output ;-)

LiNk-NY commented 3 years ago

This error happens because the old code was checking every folder including inst/ (there's bad code in the inst folder but I'm not sure if that is something we want to check). I've updated the code to only look at R files and vignettes.

packageVersion("BiocCheck")
#> [1] '1.29.14'
BiocCheck::BiocCheck("~/gh/MatrixQCvis")
This is BiocCheck version 1.29.14. BiocCheck is a work in progress. Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking version number validity...
* Checking R Version dependency...
* Checking package size...
        Skipped... only checked on source tarball
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
    Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
    * NOTE: Consider adding these automatically suggested biocViews: Sequencing, Coverage
See http://bioconductor.org/developers/how-to/biocViews/
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
    * NOTE: License 'GPL (>= 3)' unknown; licenses cannot restrict use
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking package installation calls in R code...
* Checking for library/require of MatrixQCvis...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
        suppressWarnings() in R/tab_values.R (line 203, column 9)
        suppressWarnings() in R/tab_values.R (line 815, column 9)
        suppressWarnings() in R/tab_values.R (line 1066, column 14)
* Checking function lengths........................................................
    * NOTE: Recommended function length <= 50 lines.
      There are 26 functions > 50 lines.
      The longest 5 functions are:
        .initialize_server() (R/shinyQC.R, line 216): 536 lines
        maServer() (R/module_values.R, line 821): 170 lines
        _anonymous_.826() (R/module_values.R, line 826): 163 lines
        shinyQC() (R/shinyQC.R, line 63): 123 lines
        maxQuant() (R/conversion.R, line 115): 94 lines
* Checking man page documentation...
    * NOTE: Usage of dontrun{} / donttest{} found in man page examples.
      10% of man pages use one of these cases.
      Found in the following files:
        biocrates.Rd
        maxQuant.Rd
        shinyQC.Rd
        volcanoPlot.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and vignette source...
    * NOTE: Consider shorter lines; 44 lines (0%) are > 80 characters long.
    First 6 lines:
      R/conversion.R:90 #' function from the `openxlsx` package (e.g. specifying the sheet name or index 
      R/conversion.R:159         rD$Unique_razor_sequence_coverage <- xls[, "Unique...razor.sequence.coverage...."]
      R/landingPage.R:60                 shiny::showNotification("invalid SummarizedExperiment supplied", 
      R/module_dimensionreduction.R:78                 plotly::plotlyOutput(outputId = ns("plot"), height = "auto") %>% 
      R/module_dimensionreduction.R:200                 plotly::plotlyOutput(outputId = ns("plot"), height = "auto") %>% 
      R/module_dimensionreduction.R:258                 plotly::plotlyOutput(outputId = ns("plot"), height = "auto") %>% 
    * NOTE: Consider multiples of 4 spaces for line indents, 81 lines(1%) are not.
    First 6 lines:
      R/module_values.R:85                      selected = "boxplot")),
      man/batchCorrectionAssay.Rd:9   se,
      man/batchCorrectionAssay.Rd:10   method = c("none", "removeBatchEffect (limma)"),
      man/batchCorrectionAssay.Rd:11   batchColumn = colnames(colData(se))
      man/create_boxplot.Rd:8   se,
      man/create_boxplot.Rd:9   orderCategory = colnames(colData(se)),
    See http://bioconductor.org/developers/how-to/coding-style/
    See styler package: https://cran.r-project.org/package=styler as described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking for bioc-devel mailing list subscription...
    * NOTE: Cannot determine whether maintainer is subscribed to the bioc-devel mailing list (requires admin credentials).  Subscribe here:
      https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
    Maintainer is registered at support site.
    Package name is in support site watched tags.

Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 8
For detailed information about these checks, see the BiocCheck vignette, available at
https://bioconductor.org/packages/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
$error
character(0)

$warning
character(0)

$note
[1] "Consider adding these automatically suggested biocViews: Sequencing, Coverage"                                                                                                    
[2] "License 'GPL (>= 3)' unknown; licenses cannot restrict use"                                                                                                                       
[3] "Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)"                                                                                                                 
[4] "Recommended function length <= 50 lines."                                                                                                                                         
[5] "Usage of dontrun{} / donttest{} found in man page examples."                                                                                                                      
[6] "Consider shorter lines; 44 lines (0%) are > 80 characters long."                                                                                                                  
[7] "Consider multiples of 4 spaces for line indents, 81 lines(1%) are not."                                                                                                           
[8] "Cannot determine whether maintainer is subscribed to the bioc-devel mailing list (requires admin credentials).  Subscribe here:\nhttps://stat.ethz.ch/mailman/listinfo/bioc-devel"

^{Created on 2021-08-13 by the reprex package (v2.0.1)}

Session info

``` r sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.1.0 (2021-05-18) #> os Ubuntu 20.04.2 LTS #> system x86_64, linux-gnu #> ui X11 #> language (EN) #> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz Etc/UTC #> date 2021-08-13 #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> ! package * version date lib source #> affy 1.71.0 2021-05-19 [1] Bioconductor #> affyio 1.63.1 2021-05-30 [1] Bioconductor #> askpass 1.1 2019-01-13 [2] RSPM (R 4.1.0) #> assertthat 0.2.1 2019-03-21 [1] RSPM (R 4.1.0) #> backports 1.2.1 2020-12-09 [1] RSPM (R 4.1.0) #> base64enc 0.1-3 2015-07-28 [4] RSPM (R 4.1.0) #> Biobase * 2.53.0 2021-05-19 [1] Bioconductor #> BiocCheck 1.29.14 2021-08-13 [1] Bioconductor #> BiocGenerics * 0.39.1 2021-06-08 [1] Bioconductor #> BiocManager 1.30.16 2021-06-15 [1] RSPM (R 4.1.0) #> biocViews 1.61.1 2021-07-30 [1] Bioconductor #> bitops 1.0-7 2021-04-24 [1] RSPM (R 4.1.0) #> checkmate 2.0.0 2020-02-06 [1] RSPM (R 4.1.0) #> circlize 0.4.13 2021-06-09 [1] RSPM (R 4.1.0) #> cli 2.5.0 2021-04-26 [2] RSPM (R 4.1.0) #> clue 0.3-59 2021-04-16 [1] RSPM (R 4.1.0) #> cluster 2.1.2 2021-04-17 [3] CRAN (R 4.1.0) #> codetools 0.2-18 2020-11-04 [3] CRAN (R 4.1.0) #> colorspace 2.0-2 2021-06-24 [1] RSPM (R 4.1.0) #> ComplexHeatmap 2.9.3 2021-08-02 [1] Bioconductor #> crayon 1.4.1 2021-02-08 [2] RSPM (R 4.1.0) #> data.table 1.14.0 2021-02-21 [1] RSPM (R 4.1.0) #> DBI 1.1.1 2021-01-15 [1] RSPM (R 4.1.0) #> DelayedArray 0.19.1 2021-06-25 [1] Bioconductor #> digest 0.6.27 2020-10-24 [2] RSPM (R 4.1.0) #> doParallel 1.0.16 2020-10-16 [1] RSPM (R 4.1.0) #> dplyr 1.0.7 2021-06-18 [1] RSPM (R 4.1.0) #> ellipsis 0.3.2 2021-04-29 [2] RSPM (R 4.1.0) #> evaluate 0.14 2019-05-28 [2] RSPM (R 4.1.0) #> fansi 0.5.0 2021-05-25 [2] RSPM (R 4.1.0) #> fastmap 1.1.0 2021-01-25 [2] RSPM (R 4.1.0) #> foreach 1.5.1 2020-10-15 [1] RSPM (R 4.1.0) #> foreign 0.8-81 2020-12-22 [3] CRAN (R 4.1.0) #> Formula 1.2-4 2020-10-16 [1] RSPM (R 4.1.0) #> fs 1.5.0 2020-07-31 [2] RSPM (R 4.1.0) #> generics 0.1.0 2020-10-31 [1] RSPM (R 4.1.0) #> GenomeInfoDb * 1.29.3 2021-07-01 [1] Bioconductor #> GenomeInfoDbData 1.2.6 2021-06-11 [1] Bioconductor #> GenomicRanges * 1.45.0 2021-05-19 [1] Bioconductor #> getopt 1.20.3 2019-03-22 [1] RSPM (R 4.1.0) #> GetoptLong 1.0.5 2020-12-15 [1] RSPM (R 4.1.0) #> ggplot2 * 3.3.5 2021-06-25 [1] RSPM (R 4.1.0) #> GlobalOptions 0.1.2 2020-06-10 [1] RSPM (R 4.1.0) #> glue 1.4.2 2020-08-27 [2] RSPM (R 4.1.0) #> gmm 1.6-6 2021-03-05 [1] RSPM (R 4.1.0) #> graph 1.71.2 2021-05-27 [1] Bioconductor #> gridExtra 2.3 2017-09-09 [1] RSPM (R 4.1.0) #> gtable 0.3.0 2019-03-25 [1] RSPM (R 4.1.0) #> highr 0.9 2021-04-16 [2] RSPM (R 4.1.0) #> Hmisc 4.5-0 2021-02-28 [1] RSPM (R 4.1.0) #> htmlTable 2.2.1 2021-05-18 [1] RSPM (R 4.1.0) #> htmltools 0.5.1.1 2021-01-22 [1] RSPM (R 4.1.0) #> htmlwidgets 1.5.3 2020-12-10 [1] RSPM (R 4.1.0) #> 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2021-08-06 [1] RSPM (R 4.1.0) #> XML 3.99-0.6 2021-03-16 [1] RSPM (R 4.1.0) #> xtable 1.8-4 2019-04-21 [1] RSPM (R 4.1.0) #> XVector 0.33.0 2021-05-19 [1] Bioconductor #> yaml 2.2.1 2020-02-01 [2] RSPM (R 4.1.0) #> zip 2.2.0 2021-05-31 [1] RSPM (R 4.1.0) #> zlibbioc 1.39.0 2021-05-19 [1] Bioconductor #> zoo 1.8-9 2021-03-09 [1] RSPM (R 4.1.0) #> #> [1] /usr/local/lib/R/host-site-library #> [2] /usr/local/lib/R/site-library #> [3] /usr/local/lib/R/library #> [4] /home/rstudio/R/x86_64-pc-linux-gnu-library/4.1 #> #> P ── Loaded and on-disk path mismatch. ```

Bioconductor / BiocCheck

"object of type 'closure' is not subsettable" errors #131