* using log directory ‘/srv/hornik/tmp/CRAN/oncoPredict.Rcheck’
* using R Under development (unstable) (2024-04-02 r86304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 17.0.6 (5)
    Debian flang-new version 17.0.6 (5)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘oncoPredict/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘oncoPredict’ version ‘1.2’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/4s] NOTE
Maintainer: ‘Robert Gruener <rgruener@umn.edu>’

New maintainer:
  Robert Gruener <rgruener@umn.edu>
Old maintainer(s):
  Danielle Maeser <maese005@umn.edu>

Possibly misspelled words in DESCRIPTION:
  CNV (20:121)
  GLDS (19:5)
  IDWAS (20:5)
  Unniversity (16:225)
  calcPhenotype (18:5, 20:37)

Author field should be Authors@R.  Current value is:
  Authors@R: 
      c(person(given = "Danielle",
             family = "Maeser",
             role = c("aut", "cre"),
             email = "maese005@umn.edu",
             comment = c(ORCID = "0000-0002-3890-887X")),
        person(given = 'Robert',
             family = 'Gruener',
             role = 'aut',
             email = 'rgruener@umn.edu'))
* 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 ‘oncoPredict’ can be installed ... [27s/27s] OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] OK
* checking loading without being on the library search path ... [8s/8s] OK
* checking use of S3 registration ... 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 ... [37s/37s] NOTE
Found if() conditions comparing class() to string:
File ‘oncoPredict/R/IDWAS.R’: if (class(drug_prediction) != "data.frame") ...
File ‘oncoPredict/R/IDWAS.R’: if (class(data) != "data.frame") ...
Use inherits() (or maybe is()) instead.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'calcPhenotype.Rd'
  ‘folder’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... NONE
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [67s/67s] OK
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 WARNING, 3 NOTEs