[R-pkg-devel] DBI namespace not found on check

[Dayne Filer]

Hi,

I am preparing a package for submission and having issues with R CMD check, both using the r-lib GitHub actions and r-hub. I keep getting the warning message:

* checking whether package ‘toxpiR’ can be installed ... WARNING
Found the following significant warnings:
  Warning: namespace ‘DBI’ is not available and has been replaced
See ‘.../00install.out’ for details.

I cannot replicate the warning while checking as-cran on my local machine. Going through the logs it’s clear that DBI is not getting installed, but I also do not know who/what is calling it. I see that knitr lists DBI in imports, so it’s odd to me that it’s not getting installed. I do not directly import or use any DBI functions. The easy solution would be to add DBI to ‘Suggests’ — and that feels more like a bandaid than a good solution.

DBI is also being loaded into the Namespace when loading the package. From a clean session:

> library(toxpiR)
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRlapack.dylib

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

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

other attached packages:
[1] toxpiR_0.1.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.8          knitr_1.37          magrittr_2.0.2      BiocGenerics_0.40.0 tidyselect_1.1.1    R6_2.5.1            rlang_1.0.0        
 [8] fastmap_1.1.0       fansi_1.0.2         stringr_1.4.0       dplyr_1.0.7         tools_4.1.2         grid_4.1.2          xfun_0.29          
[15] utf8_1.2.2          DBI_1.1.2           cli_3.1.1           ellipsis_0.3.2      htmltools_0.5.2     assertthat_0.2.1    yaml_2.2.2         
[22] digest_0.6.29       tibble_3.1.6        lifecycle_1.0.1     crayon_1.4.2        purrr_0.3.4         pryr_0.1.5          tidyr_1.1.4        
[29] vctrs_0.3.8         S4Vectors_0.32.3    codetools_0.2-18    glue_1.6.1          evaluate_0.14       rmarkdown_2.11      stringi_1.7.6      
[36] pillar_1.6.5        compiler_4.1.2      generics_0.1.1      stats4_4.1.2        pkgconfig_2.0.3    

Any help is greatly appreciated!! Below I have linked to the  r-hub results and the pasted the Desc/Namespace. 

Thank you!

Dayne Filer, PhD
UNC School of Medicine
Renaissance Computing Institute 

Links to the r-hub results:

Windows/dev: https://artifacts.r-hub.io/toxpiR_0.1.0.tar.gz-36c4ff0f5ae348e7a5b28c15ca9d761d <https://artifacts.r-hub.io/toxpiR_0.1.0.tar.gz-36c4ff0f5ae348e7a5b28c15ca9d761d>
Linux/release: https://artifacts.r-hub.io/toxpiR_0.1.0.tar.gz-f631ce3fc55d44b98bc328f2886caf6c/ <https://artifacts.r-hub.io/toxpiR_0.1.0.tar.gz-f631ce3fc55d44b98bc328f2886caf6c/>
Linux/dev: https://artifacts.r-hub.io/toxpiR_0.1.0.tar.gz-d64875065b744735bd4991da2d2dc185/ <https://artifacts.r-hub.io/toxpiR_0.1.0.tar.gz-d64875065b744735bd4991da2d2dc185/>

The package DESCRIPTION:

Package: toxpiR
Type: Package
Title: Create ToxPi Prioritization Models
Version: 0.1.0
Authors using R: 
    c(person("Dayne L", "Filer", 
             role = c("aut"), 
             email = "dayne.filer using gmail.com",
             comment = c(ORCID = "0000-0002-3443-5315")),
      person("Dillon T", "Lloyd",
             role = "aut"),
      person("Preethi", "Thunga",
             role = "aut",
             comment = c(ORCID = "0000-0001-5447-0129")),
      person("Skylar W", "Marvel",
             role = "aut"),      
      person("David M", "Reif",
             role = c("aut", "cre"),
             email = "reif.david using gmail.com",
             comment = c(ORCID = "0000-0001-7815-6767")))
Description: 
  Enables users to build ToxPi prioritization models and provides 
  functionality within the grid framework for plotting ToxPi graphs.
  toxpiR allows for more customization than the ToxPi GUI (toxpi.org)
  and integration into existing workflows for greater ease-of-use, 
  reproducibility, and transparency.
  toxpiR package behaves nearly identically to the GUI; the package 
  documentation includes notes about all differences.
Imports: 
    grDevices,
    methods,
    S4Vectors,
    grid,
    rlang,
    stats,
    BiocGenerics,
    pryr,
    tidyr,
    utils
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.2
Roxygen: list(markdown = TRUE)
Depends: 
    R (>= 3.5.0)
Suggests: 
    rmarkdown,
    knitr,
    testthat (>= 3.0.0),
    covr
Config/testthat/edition: 3
Config/testthat/parallel: true
VignetteBuilder: knitr
License: GPL (>= 3)

Package NAMESPACE:

S3method(editDetails,pieGrob)
export(TxpModel)
export(TxpModelList)
export(TxpResultList)
export(TxpSlice)
export(TxpSliceList)
export(TxpTransFunc)
export(TxpTransFuncList)
export(as.TxpModelList)
export(as.TxpResultList)
export(as.TxpSliceList)
export(as.TxpTransFuncList)
export(grid.pieGridGrob)
export(grid.pieGrob)
export(pieGridGrob)
export(pieGrob)
export(txpCalculateScores)
export(txpImportGui)
exportClasses(TxpModel)
exportClasses(TxpModelList)
exportClasses(TxpResult)
exportClasses(TxpResultList)
exportClasses(TxpSlice)
exportClasses(TxpSliceList)
exportClasses(TxpTransFunc)
exportClasses(TxpTransFuncList)
exportMethods("[")
exportMethods("names<-")
exportMethods("txpIDs<-")
exportMethods("txpSlices<-")
exportMethods("txpTransFuncs<-")
exportMethods("txpValueNames<-")
exportMethods("txpWeights<-")
exportMethods(as.data.frame)
exportMethods(duplicated)
exportMethods(length)
exportMethods(merge)
exportMethods(names)
exportMethods(plot)
exportMethods(sort)
exportMethods(txpCalculateScores)
exportMethods(txpIDs)
exportMethods(txpModel)
exportMethods(txpRanks)
exportMethods(txpScores)
exportMethods(txpSliceScores)
exportMethods(txpSlices)
exportMethods(txpTransFuncs)
exportMethods(txpValueNames)
exportMethods(txpWeights)
import(grid)
import(methods)
importClassesFrom(S4Vectors,List)
importClassesFrom(S4Vectors,SimpleList)
importClassesFrom(S4Vectors,character_OR_NULL)
importFrom(BiocGenerics,as.data.frame)
importFrom(BiocGenerics,duplicated)
importFrom(BiocGenerics,sort)
importFrom(BiocGenerics,updateObject)
importFrom(S4Vectors,List)
importFrom(S4Vectors,classNameForDisplay)
importFrom(S4Vectors,coolcat)
importFrom(S4Vectors,new2)
importFrom(S4Vectors,setValidity2)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,extendrange)
importFrom(pryr,make_function)
importFrom(pryr,substitute_q)
importFrom(rlang,is_integerish)
importFrom(rlang,is_named)
importFrom(rlang,is_scalar_character)
importFrom(rlang,is_scalar_integerish)
importFrom(rlang,is_scalar_logical)
importFrom(stats,sd)
importFrom(tidyr,separate)
importFrom(utils,data)
importFrom(utils,read.csv)
importFrom(utils,type.convert)


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