Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-14 13:06:34 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
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

CHECK results for IHW on tokay2


To the developers/maintainers of the IHW package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 918/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IHW 1.22.0  (landing page)
Nikos Ignatiadis
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/IHW
git_branch: RELEASE_3_14
git_last_commit: 0d30505
git_last_commit_date: 2021-10-26 12:25:00 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: IHW
Version: 1.22.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IHW.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings IHW_1.22.0.tar.gz
StartedAt: 2022-01-13 21:05:40 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 21:08:14 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 154.2 seconds
RetCode: 0
Status:   OK  
CheckDir: IHW.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IHW.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings IHW_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/IHW.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IHW/DESCRIPTION' ... OK
* this is package 'IHW' version '1.22.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
ihw.default 5.98   0.11     6.4
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
ihw.default    7    0.1   27.57
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/IHW.Rcheck/00check.log'
for details.



Installation output

IHW.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/IHW_1.22.0.tar.gz && rm -rf IHW.buildbin-libdir && mkdir IHW.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IHW.buildbin-libdir IHW_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL IHW_1.22.0.zip && rm IHW_1.22.0.tar.gz IHW_1.22.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 34526  100 34526    0     0   407k      0 --:--:-- --:--:-- --:--:--  411k

install for i386

* 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
  converting help for package 'IHW'
    finding HTML links ... done
    get_bh_threshold                        html  
    groups_by_filter                        html  
    ihw.DESeqResults                        html  
    ihw.default                             html  
    ihwResult-class                         html  
    plot-ihwResult-method                   html  
** 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

install for x64

* installing *source* package 'IHW' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'IHW' as IHW_1.22.0.zip
* DONE (IHW)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'IHW' successfully unpacked and MD5 sums checked

Tests output

IHW.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
  17.39    0.43   18.31 

IHW.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
  17.42    0.29   27.96 

Example timings

IHW.Rcheck/examples_i386/IHW-Ex.timings

nameusersystemelapsed
get_bh_threshold000
groups_by_filter000
ihw.DESeqResults000
ihw.default5.980.116.40
ihwResult-class3.420.053.46
plot-ihwResult-method4.190.074.27

IHW.Rcheck/examples_x64/IHW-Ex.timings

nameusersystemelapsed
get_bh_threshold000
groups_by_filter000
ihw.DESeqResults000
ihw.default 7.00 0.1027.57
ihwResult-class3.080.003.07
plot-ihwResult-method3.670.033.71