| Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-21 12:07 -0400 (Tue, 21 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4887 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4677 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4622 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4642 |
| 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 488/2353 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CTexploreR 1.5.2 (landing page) Axelle Loriot
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | TIMEOUT | ||||||||||
|
To the developers/maintainers of the CTexploreR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CTexploreR.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. |
| Package: CTexploreR |
| Version: 1.5.2 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:CTexploreR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CTexploreR_1.5.2.tar.gz |
| StartedAt: 2025-10-17 07:46:12 -0000 (Fri, 17 Oct 2025) |
| EndedAt: 2025-10-17 08:26:13 -0000 (Fri, 17 Oct 2025) |
| EllapsedTime: 2400.5 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: CTexploreR.Rcheck |
| Warnings: NA |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD check --install=check:CTexploreR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings CTexploreR_1.5.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/CTexploreR.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 ‘CTexploreR/DESCRIPTION’ ... OK
* this is package ‘CTexploreR’ version ‘1.5.2’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CTexploreR’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
DAC_induction 13.914 0.403 21.016
embryos_mean_methylation 13.879 0.347 18.270
normal_tissues_mean_methylation 9.884 0.275 16.182
fetal_germcells_mean_methylation 9.706 0.239 13.966
normal_tissues_methylation 9.093 0.275 11.866
GTEX_expression 6.671 0.379 11.577
HPA_cell_type_expression 6.430 0.179 10.619
normal_tissue_expression_multimapping 5.315 0.263 9.626
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
CTexploreR.Rcheck/00install.out
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###
### Running command:
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### /home/biocbuild/R/R/bin/R CMD INSTALL CTexploreR
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘CTexploreR’ ...
** this is package ‘CTexploreR’ version ‘1.5.2’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
** 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 (CTexploreR)
CTexploreR.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(CTexploreR)
Loading required package: CTdata
>
> test_check("CTexploreR")
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
see ?CTdata and browseVignettes('CTdata') for documentation
loading from cache
CTexploreR.Rcheck/CTexploreR-Ex.timings
| name | user | system | elapsed | |
| CCLE_expression | 0 | 0 | 0 | |
| CT_correlated_genes | 0.001 | 0.000 | 0.000 | |
| CT_genes | 0.065 | 0.012 | 0.077 | |
| DAC_induction | 13.914 | 0.403 | 21.016 | |
| GTEX_expression | 6.671 | 0.379 | 11.577 | |
| HPA_cell_type_expression | 6.430 | 0.179 | 10.619 | |
| TCGA_expression | 0 | 0 | 0 | |
| TCGA_methylation_expression_correlation | 0 | 0 | 0 | |
| all_genes | 0.052 | 0.000 | 0.051 | |
| embryo_expression | 0 | 0 | 0 | |
| embryos_mean_methylation | 13.879 | 0.347 | 18.270 | |
| fetal_germcells_expression | 0 | 0 | 0 | |
| fetal_germcells_mean_methylation | 9.706 | 0.239 | 13.966 | |
| hESC_expression | 0 | 0 | 0 | |
| hESC_mean_methylation | 0 | 0 | 0 | |
| normal_tissue_expression_multimapping | 5.315 | 0.263 | 9.626 | |
| normal_tissues_mean_methylation | 9.884 | 0.275 | 16.182 | |
| normal_tissues_methylation | 9.093 | 0.275 | 11.866 | |
| oocytes_expression | 0 | 0 | 0 | |
| set_fontsize | 0 | 0 | 0 | |
| testis_expression | 0 | 0 | 0 | |