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This page was generated on 2022-03-18 11:08:13 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
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 riesling1


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? here 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 1352/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
oppti 1.9.0  (landing page)
Abdulkadir Elmas
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/oppti
git_branch: master
git_last_commit: 03be903
git_last_commit_date: 2021-10-26 12:55:45 -0400 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
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: 1.9.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:oppti.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings oppti_1.9.0.tar.gz
StartedAt: 2022-03-17 19:46:52 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 19:48:06 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 73.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: oppti.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:oppti.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings oppti_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/oppti.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'oppti/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'oppti' version '1.9.0'
* 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 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
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/oppti.Rcheck/00check.log'
for details.



Installation output

oppti.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL oppti
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'oppti' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'oppti'
    finding HTML links ... done
    artImpute                               html  
    clusterData                             html  
    dropMarkers                             html  
    dysReg                                  html  
    markOut                                 html  
    oppti                                   html  
    outScores                               html  
    plotDen                                 html  
    rankPerOut                              html  
    statTest                                html  
** 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)
Making 'packages.html' ... done

Tests output

oppti.Rcheck/tests/test.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
   0.09    0.06    0.14 

Example timings

oppti.Rcheck/oppti-Ex.timings

nameusersystemelapsed
artImpute0.030.020.04
clusterData0.110.000.11
dropMarkers0.010.000.01
dysReg0.220.000.22
markOut4.010.044.06
oppti0.330.000.33
outScores0.020.000.01
plotDen0.050.000.05
rankPerOut0.210.000.22
statTest0.040.000.03