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This page was generated on 2022-01-17 13:05:25 -0500 (Mon, 17 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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 netOmics on nebbiolo2


To the developers/maintainers of the netOmics package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/netOmics.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 1286/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
netOmics 1.0.0  (landing page)
Antoine Bodein
Snapshot Date: 2022-01-16 01:55:05 -0500 (Sun, 16 Jan 2022)
git_url: https://git.bioconductor.org/packages/netOmics
git_branch: RELEASE_3_14
git_last_commit: 00eaf6b
git_last_commit_date: 2021-10-26 13:13:58 -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: netOmics
Version: 1.0.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:netOmics.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings netOmics_1.0.0.tar.gz
StartedAt: 2022-01-16 08:54:32 -0500 (Sun, 16 Jan 2022)
EndedAt: 2022-01-16 08:57:39 -0500 (Sun, 16 Jan 2022)
EllapsedTime: 186.7 seconds
RetCode: 0
Status:   OK  
CheckDir: netOmics.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:netOmics.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings netOmics_1.0.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/netOmics.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘netOmics/DESCRIPTION’ ... OK
* this is package ‘netOmics’ 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 ‘netOmics’ 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 ... NOTE
.interaction_from_dataframe: no visible binding for global variable ‘.’
.rwr_find_closest: no visible binding for global variable ‘SeedName’
.rwr_find_closest: no visible binding for global variable ‘NodeNames’
.rwr_find_closest: no visible binding for global variable ‘Score’
.rwr_find_closest: no visible binding for global variable ‘attribute’
.rwr_find_closest: no visible binding for global variable ‘value’
combine_layers: no visible binding for global variable ‘.’
get_grn: no visible binding for global variable ‘.’
get_interaction_from_ORA: no visible binding for global variable
  ‘significant’
get_interaction_from_ORA: no visible binding for global variable
  ‘term_id’
get_interaction_from_ORA: no visible binding for global variable
  ‘target’
get_interaction_from_ORA: no visible binding for global variable
  ‘input’
plot_rwr_subnetwork: no visible binding for global variable ‘rwr’
plot_rwr_subnetwork: no visible binding for global variable ‘type’
plot_rwr_subnetwork: no visible binding for global variable ‘N’
plot_rwr_subnetwork: no visible global function definition for ‘title’
plot_rwr_subnetwork: no visible binding for global variable ‘name’
rwr_top_k_graph: no visible binding for global variable ‘SeedName’
rwr_top_k_graph: no visible binding for global variable ‘Score’
rwr_top_k_graph: no visible binding for global variable ‘NodeNames’
summary_plot_rwr_attributes: no visible binding for global variable
  ‘seed’
summary_plot_rwr_attributes: no visible binding for global variable ‘N’
summary_plot_rwr_attributes: no visible binding for global variable
  ‘type’
Undefined global functions or variables:
  . N NodeNames Score SeedName attribute input name rwr seed
  significant target term_id title type value
Consider adding
  importFrom("graphics", "title")
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 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
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
get_interaction_from_ORA 0.319  0.043  10.073
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/netOmics.Rcheck/00check.log’
for details.



Installation output

netOmics.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL netOmics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘netOmics’ ...
** 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 (netOmics)

Tests output

netOmics.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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(netOmics)

> 
> test_check("netOmics")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 140 ]
> 
> proc.time()
   user  system elapsed 
 18.183   1.010  46.943 

Example timings

netOmics.Rcheck/netOmics-Ex.timings

nameusersystemelapsed
combine_layers0.0370.0000.038
get_graph_stats0.0230.0040.027
get_grn3.2360.0673.308
get_interaction_from_ORA 0.319 0.04310.073
get_interaction_from_correlation0.0150.0000.015
get_interaction_from_database0.0180.0000.018
plot_rwr_subnetwork0.4350.0240.460
random_walk_restart0.2790.0560.334
rwr_find_closest_type0.4410.0840.524
rwr_find_seeds_between_attributes0.3570.0000.358
summary_plot_rwr_attributes1.6850.1201.804