DavisLaboratory / singscore

An R/Bioconductor package that implements a single-sample molecular phenotyping approach
https://davislaboratory.github.io/singscore/
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Missing dependency: hexbin #31

Closed HenrikBengtsson closed 3 years ago

HenrikBengtsson commented 3 years ago

Hi, while running reverse dependency checks on matrixStats, I spotted what looks like a missing dependency in singscore causing the package tests to fail. Adding hexbin to Suggests: should fix this.

* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--no-manual --no-build-vignettes’
* checking for file ‘singscore/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘singscore’ version ‘1.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘singscore’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.9Mb
    doc    1.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... ERROR
  Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(singscore)
  > 
  > test_check("singscore")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-projectScoreLandscape.R:70:2): projectScoreLandscape works for interactive plots ──
  Error: there is no package called 'hexbin'
  Backtrace:
       █
    1. ├─singscore::projectScoreLandscape(...) test-projectScoreLandscape.R:70:8
    2. │ ├─plotly::ggplotly(p1)
    3. │ └─plotly:::ggplotly.ggplot(p1)
    4. │   └─plotly::gg2list(...)
    5. │     └─plotly:::layers2traces(data, prestats_data, layout, plot)
    6. │       ├─plotly::to_basic(...)
    7. │       └─plotly:::to_basic.GeomHex(...)
    8. └─base::loadNamespace(x)
    9.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   10.     └─base:::withOneRestart(expr, restarts[[1L]])
   11.       └─base:::doWithOneRestart(return(expr), restart)

  [ FAIL 1 | WARN 37 | SKIP 0 | PASS 133 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... NONE
  ‘singscore.Rmd’ using ‘UTF-8’... OK
* checking re-building of vignette outputs ... SKIPPED
* DONE
Status: 1 ERROR, 1 NOTE
bhuvad commented 3 years ago

Hi @HenrikBengtsson,

Thanks for pointing this out! I will fix it ASAP.

Cheers, Dharmesh