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This page was generated on 2024-07-16 17:41 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4742
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4484
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4513
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4462
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 1022/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IHW 1.32.0  (landing page)
Nikos Ignatiadis
Snapshot Date: 2024-07-14 14:00 -0400 (Sun, 14 Jul 2024)
git_url: https://git.bioconductor.org/packages/IHW
git_branch: RELEASE_3_19
git_last_commit: af19127
git_last_commit_date: 2024-04-30 10:47:54 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for IHW on merida1

To the developers/maintainers of the IHW package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IHW.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: IHW
Version: 1.32.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:IHW.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings IHW_1.32.0.tar.gz
StartedAt: 2024-07-15 06:07:51 -0400 (Mon, 15 Jul 2024)
EndedAt: 2024-07-15 06:10:41 -0400 (Mon, 15 Jul 2024)
EllapsedTime: 169.4 seconds
RetCode: 0
Status:   OK  
CheckDir: IHW.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:IHW.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings IHW_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/IHW.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IHW/DESCRIPTION’ ... OK
* this is package ‘IHW’ version ‘1.32.0’
* 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 ... OK
* 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 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 ... 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’
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 pvalue runif str stratum
Consider adding
  importFrom("stats", "na.exclude", "p.adjust", "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
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
ihw.default           15.096  0.405  18.447
plot-ihwResult-method 11.513  0.206  14.304
ihwResult-class        9.428  0.164  11.878
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/IHW.Rcheck/00check.log’
for details.


Installation output

IHW.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL IHW
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 34 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
 46.334   0.944  54.652 

Example timings

IHW.Rcheck/IHW-Ex.timings

nameusersystemelapsed
get_bh_threshold0.0050.0010.007
groups_by_filter0.0020.0010.004
ihw.DESeqResults0.0000.0010.001
ihw.default15.096 0.40518.447
ihwResult-class 9.428 0.16411.878
plot-ihwResult-method11.513 0.20614.304