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This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
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

Package 700/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
findIPs 1.1.0  (landing page)
Shuo Wang
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/findIPs
git_branch: devel
git_last_commit: fda12ef
git_last_commit_date: 2024-04-30 11:56:32 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  


CHECK results for findIPs on palomino6

To the developers/maintainers of the findIPs package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/findIPs.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: findIPs
Version: 1.1.0
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:findIPs.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings findIPs_1.1.0.tar.gz
StartedAt: 2024-07-16 00:03:05 -0400 (Tue, 16 Jul 2024)
EndedAt: 2024-07-16 00:09:14 -0400 (Tue, 16 Jul 2024)
EllapsedTime: 368.8 seconds
RetCode: 0
Status:   OK  
CheckDir: findIPs.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:findIPs.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings findIPs_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/findIPs.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'findIPs/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'findIPs' version '1.1.0'
* 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 '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 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          27.24   1.15   28.65
sumRanks         20.41   0.86   21.88
plotIPs          19.16   1.27   20.45
plotRankScatters 19.62   0.75   20.39
getdrop1ranks    19.16   0.64   19.84
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

findIPs.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL findIPs
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/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)

Tests output

findIPs.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
 117.90    3.62  122.46 

Example timings

findIPs.Rcheck/findIPs-Ex.timings

nameusersystemelapsed
findIPs27.24 1.1528.65
getdrop1ranks19.16 0.6419.84
miller050.010.000.02
plotAdaptiveWeights000
plotIPs19.16 1.2720.45
plotRankScatters19.62 0.7520.39
sumRanks20.41 0.8621.88