cbg-ethz / nempi

Nested Effects Models based Perturbation Inference - https://doi.org/10.1093/bioinformatics/btab113 - https://bioconductor.org/packages/nempi
http://bioconductor.org/packages/nempi
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Missing dependency: RUnit #1

Closed HenrikBengtsson closed 3 years ago

HenrikBengtsson commented 3 years ago

Hi, I'm running reverse dependency checks on my matrixStats package and spotted that nempi is missing RUnit under Suggests:. I get:

* 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 ‘nempi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘nempi’ version ‘1.0.0’
* 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 ‘nempi’ can be installed ... OK
* checking installed package size ... OK
* 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 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 ‘runTests.R’
Running the tests in ‘tests/runTests.R’ failed.
Complete output:
  > BiocGenerics:::testPackage("nempi")
  Error in library("RUnit", quietly = TRUE) : 
    there is no package called 'RUnit'
  Calls: <Anonymous> -> library
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... NONE
  ‘nempi.Rmd’ using ‘UTF-8’... OK
* checking re-building of vignette outputs ... SKIPPED
* DONE
Status: 1 ERROR

Adding:

Suggests: RUnit

should fix this.

HenrikBengtsson commented 2 years ago

Just reporting back; I just revdep checked nempi 1.2.0 and this problem is now gone.