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This page was generated on 2025-06-19 12:06 -0400 (Thu, 19 Jun 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4810
palomino8Windows Server 2022 Datacenterx644.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" 4548
kjohnson3macOS 13.7.1 Venturaarm644.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" 4528
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4493
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 2144/2309HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TENET 1.1.90  (landing page)
Rhie Lab at the University of Southern California
Snapshot Date: 2025-06-18 13:25 -0400 (Wed, 18 Jun 2025)
git_url: https://git.bioconductor.org/packages/TENET
git_branch: devel
git_last_commit: d7c49fe
git_last_commit_date: 2025-05-30 05:45:13 -0400 (Fri, 30 May 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for TENET on taishan

To the developers/maintainers of the TENET package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TENET.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: TENET
Version: 1.1.90
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:TENET.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings TENET_1.1.90.tar.gz
StartedAt: 2025-06-17 12:33:12 -0000 (Tue, 17 Jun 2025)
EndedAt: 2025-06-17 12:38:03 -0000 (Tue, 17 Jun 2025)
EllapsedTime: 290.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: TENET.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:TENET.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings TENET_1.1.90.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/TENET.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TENET/DESCRIPTION’ ... OK
* this is package ‘TENET’ version ‘1.1.90’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘TENET’ 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 code 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 ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘TENET-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TENETCacheAllData
> ### Title: Cache all online datasets required by TENET examples and
> ###   optional features
> ### Aliases: TENETCacheAllData
> 
> ### ** Examples
> 
> TENETCacheAllData()
Caching sesameData datasets if needed
Caching TENET.ExperimentHub metadata (N=1)
Caching TENET.ExperimentHub datasets (1/1): Example TENET step2GetDifferentiallyMethylatedSites purity SummarizedExperiment (EH9590)
Error: Failed to cache TENET.ExperimentHub datasets. Please ensure you have internet access and the latest versions of R, TENET, Bioconductor, and ExperimentHub.
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/TENET.Rcheck/00check.log’
for details.


Installation output

TENET.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL TENET
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘TENET’ ...
** this is package ‘TENET’ version ‘1.1.90’
** 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 (TENET)

Tests output


Example timings

TENET.Rcheck/TENET-Ex.timings

nameusersystemelapsed
TCGADownloader0.0000.0010.001