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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rsemmed.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings rsemmed_1.5.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/rsemmed.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rsemmed/DESCRIPTION' ... OK
* this is package 'rsemmed' version '1.5.0'
* 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 whether package 'rsemmed' 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
* 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

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###
### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL rsemmed
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'rsemmed' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'rsemmed'
    finding HTML links ... done
    find_nodes                              html  
    find_paths                              html  
    g_mini                                  html  
    g_small                                 html  
    get_edge_features                       html  
    get_middle_nodes                        html  
    grow_nodes                              html  
    make_edge_weights                       html  
    plot_path                               html  
    summarize_predicates                    html  
    summarize_semtypes                      html  
    text_path                               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
* DONE (rsemmed)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'BiocFileCache' is missing or broken
 done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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(rsemmed)
Loading required package: igraph

Attaching package: 'igraph'

The following object is masked from 'package:testthat':

    compare

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

> 
> test_check("rsemmed")
Serum cortisol --- Mood :
# A tibble: 1 x 5
  from_semtype from           via      to    to_semtype    
  <chr>        <chr>          <chr>    <chr> <chr>         
1 horm,strd    Serum cortisol AUGMENTS Mood  aapp,gngm,menp

Serum cortisol --- Stress :
# A tibble: 1 x 5
  from_semtype from           via      to     to_semtype              
  <chr>        <chr>          <chr>    <chr>  <chr>                   
1 horm,strd    Serum cortisol DISRUPTS Stress comd,dsyn,fndg,patf,sosy

Stress --- Stress Disorders, Traumatic :
# A tibble: 2 x 5
  from_semtype             from                        via      to    to_semtype
  <chr>                    <chr>                       <chr>    <chr> <chr>     
1 comd,dsyn,fndg,patf,sosy Stress                      PREDISP~ Stre~ dsyn,mobd 
2 dsyn,mobd                Stress Disorders, Traumatic AFFECTS  Stre~ comd,dsyn~

Serum cortisol ----------> Chronic Stress 
.
PREDISPOSES    DISRUPTS         ISA      TREATS 
          3           1           1           1 

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 67 ]
> 
> proc.time()
   user  system elapsed 
   1.68    0.20    1.87