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CHECK report for rsemmed on merida1

This page was generated on 2021-05-06 12:36:35 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the rsemmed package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1584/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rsemmed 1.0.0  (landing page)
Leslie Myint
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/rsemmed
Branch: RELEASE_3_12
Last Commit: a0d8916
Last Changed Date: 2020-10-27 12:00:59 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: rsemmed
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rsemmed.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rsemmed_1.0.0.tar.gz
StartedAt: 2021-05-06 05:42:53 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 05:43:44 -0400 (Thu, 06 May 2021)
EllapsedTime: 51.7 seconds
RetCode: 0
Status:   OK  
CheckDir: rsemmed.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rsemmed.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rsemmed_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/rsemmed.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rsemmed/DESCRIPTION’ ... OK
* this is package ‘rsemmed’ version ‘1.0.0’
* 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 for sufficient/correct file permissions ... 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


Installation output

rsemmed.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rsemmed
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘rsemmed’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** 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 (rsemmed)

Tests output

rsemmed.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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,pa… Stress           PREDISP… Stress Disorder… dsyn,mobd       
2 dsyn,mobd          Stress Disorder… AFFECTS  Stress           comd,dsyn,fndg,…

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 
  2.505   0.179   2.667 

Example timings

rsemmed.Rcheck/rsemmed-Ex.timings

nameusersystemelapsed
find_nodes0.0690.0120.082
find_paths0.0080.0010.010
get_edge_features0.0340.0030.036
get_middle_nodes0.0730.0040.076
grow_nodes0.0050.0020.007
make_edge_weights0.0220.0010.024
plot_path0.0730.0030.076
summarize_predicates0.1040.0030.107
summarize_semtypes0.3050.0050.311
text_path0.0900.0020.092