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This page was generated on 2022-10-19 13:20:49 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 rsemmed on nebbiolo1


To the developers/maintainers of the rsemmed package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rsemmed.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1709/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rsemmed 1.6.0  (landing page)
Leslie Myint
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/rsemmed
git_branch: RELEASE_3_15
git_last_commit: 6525cb6
git_last_commit_date: 2022-04-26 12:08:26 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: rsemmed
Version: 1.6.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:rsemmed.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings rsemmed_1.6.0.tar.gz
StartedAt: 2022-10-18 21:36:15 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 21:36:51 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 36.1 seconds
RetCode: 0
Status:   OK  
CheckDir: rsemmed.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:rsemmed.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings rsemmed_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/rsemmed.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rsemmed/DESCRIPTION’ ... OK
* this is package ‘rsemmed’ version ‘1.6.0’
* 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:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL rsemmed
###
##############################################################################
##############################################################################


* installing to library ‘/home/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
** 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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 × 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 × 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 × 5
  from_semtype             from                        via         to    to_se…¹
  <chr>                    <chr>                       <chr>       <chr> <chr>  
1 comd,dsyn,fndg,patf,sosy Stress                      PREDISPOSES Stre… dsyn,m…
2 dsyn,mobd                Stress Disorders, Traumatic AFFECTS     Stre… comd,d…
# … with abbreviated variable name ¹​to_semtype

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 
  1.951   0.119   2.058 

Example timings

rsemmed.Rcheck/rsemmed-Ex.timings

nameusersystemelapsed
find_nodes0.0430.0010.043
find_paths0.0030.0000.004
get_edge_features0.0290.0000.029
get_middle_nodes0.1160.0040.119
grow_nodes0.0040.0000.004
make_edge_weights0.0140.0000.013
plot_path0.0490.0000.049
summarize_predicates0.1270.0000.127
summarize_semtypes0.4030.0000.403
text_path0.2640.0200.283