##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:oppti.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings oppti_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/oppti.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘oppti/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘oppti’ version ‘1.21.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘oppti’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
  MIT
* 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 ... 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 whether startup messages can be suppressed ... 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 ... NOTE
gqplot: no visible binding for global variable ‘variable2’
gqplot: no visible binding for global variable ‘variable1’
gqplot: no visible binding for global variable ‘cupper’
gqplot: no visible binding for global variable ‘clower’
markOut: no visible binding for global variable ‘data’
per.test: no visible binding for global variable ‘oppti.result’
per.test: no visible binding for global variable ‘weight’
per.test: no visible binding for global variable ‘..density..’
Undefined global functions or variables:
  ..density.. clower cupper data oppti.result variable1 variable2
  weight
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'markOut.Rd':
markOut
  Code: function(dat, dat.imp, dat.imp.test, dat.dys, dys.sig.thr.upp,
                 marker.proc.list = NULL, dataset = "", num.omit.fit =
                 NULL, draw.sc = TRUE, draw.vi = TRUE, conf.int = 0.95,
                 ylab = "Observed", xlab = "Inferred", cohort.name =
                 NULL)
  Docs: function(dat, dat.imp, dat.imp.test, dat.dys, dys.sig.thr.upp,
                 marker.proc.list = NULL, dataset = "", num.omit.fit =
                 NULL, draw.sc = TRUE, draw.vi = TRUE, conf.int = 0.95,
                 ylab = "Observed", xlab = "Inferred")
  Argument names in code not in docs:
    cohort.name

Codoc mismatches from Rd file 'oppti.Rd':
oppti
  Code: function(data, mad.norm = FALSE, cohort.names = NULL, panel =
                 "global", panel.markers = NULL, tol.nas = 20, ku = 6,
                 miss.pstat = 0.4, demo.panels = FALSE, save.data =
                 FALSE, draw.sc.plots = FALSE, draw.vi.plots = FALSE,
                 draw.sc.markers = NULL, draw.ou.plots = FALSE,
                 draw.ou.markers = NULL, permutation.tests = TRUE,
                 n.per.test = 10, draw.per.test = FALSE,
                 plot.set.per.test = list(BRCA = c("ERBB2"), CCRCC =
                 c("ERBB2", "TP53")), verbose = FALSE)
  Docs: function(data, mad.norm = FALSE, cohort.names = NULL, panel =
                 "global", panel.markers = NULL, tol.nas = 20, ku = 6,
                 miss.pstat = 0.4, demo.panels = FALSE, save.data =
                 FALSE, draw.sc.plots = FALSE, draw.vi.plots = FALSE,
                 draw.sc.markers = NULL, draw.ou.plots = FALSE,
                 draw.ou.markers = NULL, verbose = FALSE)
  Argument names in code not in docs:
    permutation.tests n.per.test draw.per.test plot.set.per.test
  Mismatches in argument names:
    Position: 16 Code: permutation.tests Docs: verbose

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/oppti.Rcheck/00check.log’
for details.