Package: IHW

Version: 1.12.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IHW.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings IHW_1.12.0.tar.gz

StartedAt: 2019-10-16 04:32:35 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:34:23 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 108.0 seconds

RetCode: 0

Status:  OK

CheckDir: IHW.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IHW.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings IHW_1.12.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/IHW.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.12.0'
* 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 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'
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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
ihw.default  5.3   0.08    5.47
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
ihw.default 4.55   0.11   13.81
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/IHW.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/IHW_1.12.0.tar.gz && rm -rf IHW.buildbin-libdir && mkdir IHW.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IHW.buildbin-libdir IHW_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL IHW_1.12.0.zip && rm IHW_1.12.0.tar.gz IHW_1.12.0.zip
###
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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-ANY-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_1.12.0.zip
* DONE (IHW)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'IHW' successfully unpacked and MD5 sums checked

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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
== testthat results  ===========================================================
[ OK: 34 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  13.10    0.35   13.45 

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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
== testthat results  ===========================================================
[ OK: 34 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  12.82    0.28   14.26