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This page was generated on 2023-10-25 11:41:36 -0400 (Wed, 25 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4727
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4465
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4476
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4464
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

Package 1038/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IntOMICS 1.2.0  (landing page)
Pacinkova Anna
Snapshot Date: 2023-10-24 14:05:06 -0400 (Tue, 24 Oct 2023)
git_url: https://git.bioconductor.org/packages/IntOMICS
git_branch: RELEASE_3_18
git_last_commit: df55330
git_last_commit_date: 2023-10-24 11:45:59 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    WARNINGS  YES
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  YES
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    WARNINGS    OK  YES
kjohnson1macOS 13.3.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for IntOMICS on kunpeng2


To the developers/maintainers of the IntOMICS package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IntOMICS.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: IntOMICS
Version: 1.2.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:IntOMICS.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings IntOMICS_1.2.0.tar.gz
StartedAt: 2023-10-25 12:25:33 -0000 (Wed, 25 Oct 2023)
EndedAt: 2023-10-25 12:32:46 -0000 (Wed, 25 Oct 2023)
EllapsedTime: 432.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: IntOMICS.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:IntOMICS.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings IntOMICS_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/IntOMICS.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘IntOMICS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IntOMICS’ version ‘1.2.0’
* 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 ‘IntOMICS’ 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 loading without being on the library search path ... 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 ... WARNING
  Warning: package needs dependence on R (>= 2.10)
* 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 ...
  ‘IntOMICS_vignette.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/IntOMICS.Rcheck/00check.log’
for details.



Installation output

IntOMICS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL IntOMICS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘IntOMICS’ ...
** 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 (IntOMICS)

Tests output

IntOMICS.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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(IntOMICS)
> 
> test_check("IntOMICS")
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 23 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_bn_module.R:1:1'

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 23 ]
> 
> proc.time()
   user  system elapsed 
 20.287   1.167  21.484 

Example timings

IntOMICS.Rcheck/IntOMICS-Ex.timings

nameusersystemelapsed
B_prior_mat_weighted0.0010.0000.000
CPDAGs_sim1000
CPDAGs_sim2000
MCMC_sapling_res000
beta_tuning0.0010.0000.000
bn_module000
dens_edge_weights3.7330.1483.888
edge_weights1.3950.0321.429
emp_b_heatmap3.2660.0753.348
estimated_beta000
estimated_len000
ggraph_weighted_net000
omics_module1.7000.0681.776
rms000
trace_plots000
weighted_net2.1400.0282.171