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CHECK report for IHW on malbec2

This page was generated on 2020-10-17 11:54:58 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE IHW PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 863/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IHW 1.16.0
Nikos Ignatiadis
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/IHW
Branch: RELEASE_3_11
Last Commit: d5a05b9
Last Changed Date: 2020-04-27 14:54:10 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: IHW
Version: 1.16.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:IHW.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings IHW_1.16.0.tar.gz
StartedAt: 2020-10-17 02:18:49 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:19:41 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 52.2 seconds
RetCode: 0
Status:  OK 
CheckDir: IHW.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:IHW.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings IHW_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/IHW.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IHW/DESCRIPTION’ ... OK
* this is package ‘IHW’ version ‘1.16.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘IHW’ 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 ... NOTE
filter_pvals_for_optim: no visible global function definition for
  ‘p.adjust’
groups_by_filter: no visible global function definition for ‘runif’
ihw.DESeqResults: no visible global function definition for ‘mcols’
ihw.DESeqResults: no visible global function definition for ‘mcols<-’
ihw.DESeqResults: no visible global function definition for ‘metadata’
ihw.DESeqResults: no visible global function definition for
  ‘metadata<-’
ihw.default: no visible global function definition for ‘runif’
ihw.default: no visible global function definition for ‘p.adjust’
ihw_convex: no visible global function definition for ‘gurobi’
ihw_internal: no visible global function definition for ‘p.adjust’
ihw_milp: no visible global function definition for ‘str’
ihw_milp: no visible global function definition for ‘gurobi’
plot_decisionboundary: no visible binding for global variable ‘stratum’
plot_decisionboundary: no visible binding for global variable
  ‘covariate’
plot_decisionboundary: no visible binding for global variable ‘pvalue’
plot_decisionboundary: no visible binding for global variable ‘fold’
rand_cbum: no visible global function definition for ‘rbinom’
rand_cbum: no visible global function definition for ‘runif’
rand_cbum: no visible global function definition for ‘qbeta’
rand_cbum: no visible global function definition for ‘pbeta’
thresholds_ihwResult: no visible global function definition for
  ‘na.exclude’
thresholds,ihwResult: no visible global function definition for
  ‘na.exclude’
Undefined global functions or variables:
  covariate fold gurobi mcols mcols<- metadata metadata<- na.exclude
  p.adjust pbeta pvalue qbeta rbinom runif str stratum
Consider adding
  importFrom("stats", "na.exclude", "p.adjust", "pbeta", "qbeta",
             "rbinom", "runif")
  importFrom("utils", "str")
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 ... OK
* 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 ‘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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/IHW.Rcheck/00check.log’
for details.



Installation output

IHW.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL IHW
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘IHW’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘IHW’
** 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 (IHW)

Tests output

IHW.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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("IHW")
> 
> test_check("IHW")
List of 3
 $ solution: num [1:2000] 0 0 0 0 0 0 0 0 0 0 ...
 $ objval  : num 70
 $ status  : Named int 0
  ..- attr(*, "names")= chr "TM_OPTIMAL_SOLUTION_FOUND"
NULL
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 34 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 12.217   0.127  12.436 

Example timings

IHW.Rcheck/IHW-Ex.timings

nameusersystemelapsed
get_bh_threshold0.0030.0000.002
groups_by_filter0.0020.0000.002
ihw.DESeqResults000
ihw.default3.6460.0413.750
ihwResult-class2.0050.0002.006
plot-ihwResult-ANY-method2.9980.0203.017