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CHECK report for adaptest on malbec2

This page was generated on 2019-04-09 11:50:18 -0400 (Tue, 09 Apr 2019).

Package 17/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
adaptest 1.3.0
Weixin Cai
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/adaptest
Branch: master
Last Commit: 156e9d8
Last Changed Date: 2018-10-30 11:54:39 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  ERROR  OK 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: adaptest
Version: 1.3.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:adaptest.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings adaptest_1.3.0.tar.gz
StartedAt: 2019-04-08 22:37:47 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 22:43:29 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 341.9 seconds
RetCode: 0
Status:  OK 
CheckDir: adaptest.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:adaptest.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings adaptest_1.3.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/adaptest.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘adaptest/DESCRIPTION’ ... OK
* this is package ‘adaptest’ version ‘1.3.0’
* 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 ‘adaptest’ 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 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 ... 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 or elapsed time > 5s
                 user system elapsed
get_composition 5.374  0.004   5.379
adaptest        4.942  0.088   5.035
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: OK


Installation output

adaptest.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL adaptest
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘adaptest’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (adaptest)

Tests output

adaptest.Rcheck/tests/testthat.Rout


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.

> library(testthat)
> library(adaptest)
adaptest v1.3.0: Data-Adaptive Statistics for High-Dimensional Multiple Testing
> 
> Sys.setenv(R_TESTS = "")
> test_check("adaptest")
[1] "Fold: 1"
[1] "Fold: 2"
[1] "Fold: 3"
[1] "Fold: 4"
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 12 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
286.490   5.530 181.262 

Example timings

adaptest.Rcheck/adaptest-Ex.timings

nameusersystemelapsed
adapTMLE-class3.1710.0523.228
adaptest4.9420.0885.035
bioadaptest2.6790.0242.703
get_composition5.3740.0045.379
get_significant_biomarker3.7320.0043.736
rank_DE1.0490.0001.052
rank_ttest0.3000.0040.304