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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:findIPs.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings findIPs_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/findIPs.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 ‘findIPs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘findIPs’ version ‘1.2.0’
* 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 ‘findIPs’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
findIPs          28.711  0.173  28.881
getdrop1ranks    22.054  0.448  22.503
plotRankScatters 21.424  0.911  22.335
sumRanks         20.977  0.027  21.003
plotIPs          20.281  0.390  20.671
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: OK

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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL findIPs
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘findIPs’ ...
** using staged installation
** R
** data
** 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 (findIPs)

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.

> library(testthat)
> library(findIPs)
> 
> # get data
> data(miller05)
> X <- miller05$X
> y <- miller05$y
> surv <- miller05$surv
> 
> # save expected results
> 
> # obj <- getdrop1ranks(X, y,
> #                      fun = "t.test",
> #                      decreasing = FALSE,
> #                      topN = 100)
> #
> # expected.t.adaptive <- sumRanks(origRank = obj$origRank,
> #                                 drop1Rank = obj$drop1Rank,
> #                                 topN = 100,
> #                                 method = "adaptive")
> #
> # expected.t.unweighted <- sumRanks(origRank = obj$origRank,
> #                                   drop1Rank = obj$drop1Rank,
> #                                   topN = 100,
> #                                   method = "unweighted")
> #
> # expected.t.weighted <- sumRanks(origRank = obj$origRank,
> #                                 drop1Rank = obj$drop1Rank,
> #                                 topN = 100,
> #                                 method = "weightedSpearman")
> #
> # expected.t.adaptive.ipsr <- findIPs(X, y,
> #                                     fun = "t.test",
> #                                     decreasing = FALSE,
> #                                     topN = 100,
> #                                     method = "adaptive")
> #
> # expected.cox.adaptive.ipsr <- findIPs(X, surv,
> #                                       fun = "cox",
> #                                       decreasing = FALSE,
> #                                       topN = 100,
> #                                       method = "adaptive")
> #
> # save(list = c("expected.t.adaptive", "expected.t.unweighted",
> #               "expected.t.weighted", "expected.t.adaptive.ipsr",
> #               "expected.cox.adaptive.ipsr"),
> #      file = "./expectedResults/expectedResults.RData")
> 
> # get observed results
> 
> load("./expectedResults/expectedResults.RData")
> 
> obj <- getdrop1ranks(X, y,
+                      fun = "t.test",
+                      decreasing = FALSE,
+                      topN = 100)
> 
> observed.t.adaptive <- sumRanks(origRank = obj$origRank,
+                                 drop1Rank = obj$drop1Rank,
+                                 topN = 100,
+                                 method = "adaptive")
> 
> observed.t.unweighted <- sumRanks(origRank = obj$origRank,
+                                   drop1Rank = obj$drop1Rank,
+                                   topN = 100,
+                                   method = "unweighted")
> 
> observed.t.weighted <- sumRanks(origRank = obj$origRank,
+                                 drop1Rank = obj$drop1Rank,
+                                 topN = 100,
+                                 method = "weightedSpearman")
> 
> observed.t.adaptive.ipsr <- findIPs(X, y,
+                                     fun = "t.test",
+                                     decreasing = FALSE,
+                                     topN = 100,
+                                     method = "adaptive")
> 
> observed.cox.adaptive.ipsr <- findIPs(X, surv,
+                                       fun = "cox",
+                                       decreasing = FALSE,
+                                       topN = 100,
+                                       method = "adaptive")
> 
> test_that("test getdrop1ranks and sumRanks",{
+     expect_equal(expected.t.adaptive, observed.t.adaptive)
+     expect_equal(expected.t.unweighted, observed.t.unweighted)
+     expect_equal(expected.t.weighted, expected.t.weighted)
+ })
Test passed 😀
> 
> test_that("stepwise(getdrop1ranks and sumRanks) and one-step procedure",{
+     expect_equal(observed.t.adaptive.ipsr, observed.t.adaptive)
+ })
Test passed 😸
> 
> test_that("test ipsr",{
+     expect_equal(expected.t.adaptive.ipsr, observed.t.adaptive.ipsr)
+ })
Test passed 🎊
> 
> test_that("test ipsr for survival outcomes (ranked by univariate cox)",{
+     expect_equal(expected.cox.adaptive.ipsr, observed.cox.adaptive.ipsr)
+ })
Test passed 🥇
> 
> 
> 
> 
> 
> proc.time()
   user  system elapsed 
120.679   2.113 122.782