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This page was generated on 2022-10-19 13:23:25 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for oppti on merida1


To the developers/maintainers of the oppti package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/oppti.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1381/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
oppti 1.10.0  (landing page)
Abdulkadir Elmas
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/oppti
git_branch: RELEASE_3_15
git_last_commit: 574b338
git_last_commit_date: 2022-04-26 12:00:51 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: oppti
Version: 1.10.0
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_1.10.0.tar.gz
StartedAt: 2022-10-19 05:45:41 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 05:47:27 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 106.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: oppti.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/oppti.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘oppti/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘oppti’ version ‘1.10.0’
* 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 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 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 documentation object 'markOut':
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 documentation object 'oppti':
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
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
markOut 7.687  0.134   7.854
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-3.15-bioc/meat/oppti.Rcheck/00check.log’
for details.



Installation output

oppti.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL oppti
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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)

Tests output

oppti.Rcheck/tests/test.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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 
  0.333   0.075   0.384 

Example timings

oppti.Rcheck/oppti-Ex.timings

nameusersystemelapsed
artImpute0.0700.0170.076
clusterData0.0790.0040.082
dropMarkers0.0100.0010.010
dysReg0.3930.0130.394
markOut7.6870.1347.854
oppti0.7900.0170.904
outScores0.0260.0010.026
plotDen0.0840.0040.090
rankPerOut0.4620.0170.508
statTest0.0750.0020.088