Axelle Loriot
| Snapshot Date: 2024-12-08 13:40 -0500 (Sun, 08 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/CTexploreR |
| git_branch: devel |
| git_last_commit: b8dffc6 |
| git_last_commit_date: 2024-10-29 11:26:00 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-09 11:46 -0500 (Mon, 09 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4749 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4461 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4411 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4366 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4241 |
| 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 466/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CTexploreR 1.3.0 (landing page) Axelle Loriot
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | TIMEOUT | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the CTexploreR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]: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: 1.3.0 |
| 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_1.3.0.tar.gz |
| StartedAt: 2024-12-09 04:57:59 -0000 (Mon, 09 Dec 2024) |
| EndedAt: 2024-12-09 05:26:37 -0000 (Mon, 09 Dec 2024) |
| EllapsedTime: 1718.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CTexploreR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running 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_1.3.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/CTexploreR.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (conda-forge gcc 14.2.0-1) 14.2.0
GNU Fortran (conda-forge gcc 14.2.0-1) 14.2.0
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CTexploreR/DESCRIPTION’ ... OK
* this is package ‘CTexploreR’ version ‘1.3.0’
* 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 ‘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 14.278 0.526 21.423
embryos_mean_methylation 14.343 0.438 19.168
normal_tissues_methylation 11.555 0.651 14.630
fetal_germcells_mean_methylation 10.317 0.331 14.455
normal_tissues_mean_methylation 9.758 0.233 15.701
GTEX_expression 7.216 1.102 12.889
HPA_cell_type_expression 6.404 0.299 10.585
normal_tissue_expression_multimapping 5.447 0.154 9.405
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* 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: OK
CTexploreR.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD INSTALL CTexploreR
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘CTexploreR’ ...
** 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 Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 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
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see ?CTdata and browseVignettes('CTdata') for documentation
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see ?CTdata and browseVignettes('CTdata') for documentation
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see ?CTdata and browseVignettes('CTdata') for documentation
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see ?CTdata and browseVignettes('CTdata') for documentation
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see ?CTdata and browseVignettes('CTdata') for documentation
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see ?CTdata and browseVignettes('CTdata') for documentation
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[ FAIL 0 | WARN 0 | SKIP 0 | PASS 135 ]
Deleting unused snapshots:
• GTEX_expression/gtex-expression-on-mage.svg
>
> proc.time()
user system elapsed
1133.182 35.507 1310.984
CTexploreR.Rcheck/CTexploreR-Ex.timings
| name | user | system | elapsed | |
| CCLE_expression | 0 | 0 | 0 | |
| CT_correlated_genes | 0.000 | 0.000 | 0.001 | |
| CT_genes | 0.072 | 0.004 | 0.077 | |
| DAC_induction | 14.278 | 0.526 | 21.423 | |
| GTEX_expression | 7.216 | 1.102 | 12.889 | |
| HPA_cell_type_expression | 6.404 | 0.299 | 10.585 | |
| TCGA_expression | 0 | 0 | 0 | |
| TCGA_methylation_expression_correlation | 0 | 0 | 0 | |
| all_genes | 0.049 | 0.004 | 0.053 | |
| check_names | 0 | 0 | 0 | |
| embryo_expression | 0 | 0 | 0 | |
| embryos_mean_methylation | 14.343 | 0.438 | 19.168 | |
| fetal_germcells_expression | 0.001 | 0.000 | 0.000 | |
| fetal_germcells_mean_methylation | 10.317 | 0.331 | 14.455 | |
| hESC_expression | 0 | 0 | 0 | |
| hESC_mean_methylation | 0.000 | 0.000 | 0.001 | |
| normal_tissue_expression_multimapping | 5.447 | 0.154 | 9.405 | |
| normal_tissues_mean_methylation | 9.758 | 0.233 | 15.701 | |
| normal_tissues_methylation | 11.555 | 0.651 | 14.630 | |
| oocytes_expression | 0 | 0 | 0 | |
| prepare_TCGA_methylation_expression | 0 | 0 | 0 | |
| set_fontsize | 0 | 0 | 0 | |
| subset_database | 2.619 | 0.083 | 4.575 | |
| testis_expression | 0 | 0 | 0 | |