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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:oppti.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings oppti_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/oppti.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘oppti/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘oppti’ version ‘1.20.0’
* 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 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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/oppti.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL oppti
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘oppti’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (oppti)

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 
> proc.time()
   user  system elapsed 
   0.13    0.04    0.16