Missing dependency: statmod

[HenrikBengtsson]

Hi, while running reverse dependency checks on matrixStats, I spotted what looks like a missing dependency in muscat causing the package tests to fail. Adding statmod to Suggests: should fix this. (BTW, adding also TCGAbiolinks will fix that Rd NOTE.)

* 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 ‘muscat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘muscat’ version ‘1.6.0’
* 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 ‘muscat’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    5.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
Running the tests in ‘tests/testthat.R’ failed.
Last 50 lines of output:
  > library(testthat)
  > library(muscat)
  > 
  > test_check("muscat")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-mmDS.R:70:9): mmDS-utils; .mm_vst ───────────────────────────────
  Error: statmod package required but is not installed
  Backtrace:
      █
   1. ├─base::suppressWarnings(get(fun)(x[gs, cs], verbose = FALSE)) test-mmDS.R:70:8
   2. │ └─base::withCallingHandlers(...)
   3. └─get(fun)(x[gs, cs], verbose = FALSE)
   4.   └─muscat:::.mm_eBayes(fits, coef)
   5.     └─limma::eBayes(res, trend = trended, robust = TRUE)
   6.       └─limma:::.ebayes(...)
   7.         └─limma::squeezeVar(...)
   8.           └─limma::fitFDistRobustly(...)
  ── Error (test-pbDS.R:34:9): defaults - pbDS.limma-trend ───────────────────────
  Error: statmod package required but is not installed
  Backtrace:
       █
    1. └─muscat::pbDS(pb, method = method, filter = "none", verbose = FALSE) test-pbDS.R:34:8
    2.   ├─BiocParallel::bplapply(...)
    3.   └─BiocParallel::bplapply(...)
    4.     └─base::lapply(X, FUN_, ...)
    5.       └─BiocParallel:::FUN(X[[i]], ...)
    6.         └─BiocParallel:::FUN(...)
    7.           ├─base::withCallingHandlers(...)
    8.           └─base::tryCatch(...)
    9.             └─base:::tryCatchList(expr, classes, parentenv, handlers)
   10.               └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   11.                 └─value[[3L]](cond)
  ── Error (test-pbDS.R:52:13): pbDS.limma-trend ─────────────────────────────────
  Error: statmod package required but is not installed
  Backtrace:
       █
    1. └─muscat::pbDS(...) test-pbDS.R:52:12
    2.   ├─BiocParallel::bplapply(...)
    3.   └─BiocParallel::bplapply(...)
    4.     └─base::lapply(X, FUN_, ...)
    5.       └─BiocParallel:::FUN(X[[i]], ...)
    6.         └─BiocParallel:::FUN(...)
    7.           ├─base::withCallingHandlers(...)
    8.           └─base::tryCatch(...)
    9.             └─base:::tryCatchList(expr, classes, parentenv, handlers)
   10.               └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   11.                 └─value[[3L]](cond)

  [ FAIL 3 | WARN 1 | SKIP 0 | PASS 536 ]
  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
  ‘analysis.Rmd’ using ‘UTF-8’... OK
  ‘simulation.Rmd’ using ‘UTF-8’... OK
* checking re-building of vignette outputs ... SKIPPED
* DONE
Status: 2 ERRORs, 1 NOTE

[HelenaLC]

Thanks Henrik for pointing this out. I added statmod to Suggests: which resolved this for me, however, I could not see a different with/outTCGAbiolinks; which .Rd note are you referring to? Or, could you explain why this should be added to Suggests:? It's hard for me to grasp how I'd know to add this.

[HenrikBengtsson]

Hi, I think you should see it if you run with:

R CMD check --as-cran ...