Angelo Velle
| Snapshot Date: 2024-11-27 13:40 -0500 (Wed, 27 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/gINTomics |
| git_branch: devel |
| git_last_commit: 3ba788e |
| git_last_commit_date: 2024-10-29 11:30:48 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-28 12:17 -0500 (Thu, 28 Nov 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" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
| 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 858/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gINTomics 1.3.0 (landing page) Angelo Velle
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the gINTomics package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gINTomics.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. |
| Package: gINTomics |
| Version: 1.3.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gINTomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gINTomics_1.3.0.tar.gz |
| StartedAt: 2024-11-27 22:28:14 -0500 (Wed, 27 Nov 2024) |
| EndedAt: 2024-11-27 22:38:52 -0500 (Wed, 27 Nov 2024) |
| EllapsedTime: 638.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: gINTomics.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gINTomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gINTomics_1.3.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/gINTomics.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gINTomics/DESCRIPTION’ ... OK
* this is package ‘gINTomics’ version ‘1.3.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
INFO
Imports includes 40 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 ‘gINTomics’ 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 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
[2024-11-27 22:34:30] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-27 22:34:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-27 22:34:30] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-27 22:34:30] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-11-27 22:34:30] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-27 22:34:30] [TRACE] [OmnipathR] Contains 1 files.
[2024-11-27 22:34:30] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-11-27 22:34:30] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-27 22:34:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-27 22:34:30] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-27 22:34:30] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-11-27 22:34:30] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-27 22:34:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-27 22:34:30] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-27 22:34:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-27 22:34:30] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-27 22:34:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-27 22:34:30] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-27 22:34:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-27 22:34:30] [TRACE] [OmnipathR] Cache locked: FALSE
.build_histo: no visible binding for global variable ‘chr_cov’
.build_histo: no visible binding for global variable ‘significance’
.build_ridge: no visible binding for global variable ‘coef’
.build_ridge: no visible binding for global variable ‘significance’
.circos_preprocess: no visible binding for global variable ‘cnv_met’
.prepare_cnv_heatmap: no visible binding for global variable ‘cnv’
.prepare_gen_heatmap: no visible binding for global variable ‘met’
.prepare_gen_heatmap: no visible binding for global variable ‘cnv’
.prepare_met_heatmap: no visible binding for global variable ‘met’
.prepare_mirna_heatmap: no visible binding for global variable
‘mirna_cnv’
.prepare_network: no visible binding for global variable ‘omics’
.prepare_reactive_histo_tf: no visible binding for global variable
‘Freq’
.prepare_reactive_venn: no visible binding for global variable
‘cnv_met’
.prepare_reactive_venn: no visible binding for global variable ‘pval’
.shiny_preprocess: no visible binding for global variable ‘cov’
plot_tf_distribution: no visible binding for global variable ‘Freq’
Undefined global functions or variables:
Freq chr_cov cnv cnv_met coef cov met mirna_cnv omics pval
significance
Consider adding
importFrom("stats", "coef", "cov")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
mmultiassay_ov.Rd: MultiAssayExperiment-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_volcano 9.789 0.642 23.232
extract_model_res 8.683 0.456 9.171
plot_ridge 6.035 0.336 6.391
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/gINTomics.Rcheck/00check.log’
for details.
gINTomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gINTomics ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘gINTomics’ ... ** using staged installation ** R [2024-11-27 15:36:19] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-27 15:36:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-27 15:36:19] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-11-27 15:36:19] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-11-27 15:36:19] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-11-27 15:36:19] [TRACE] [OmnipathR] Contains 1 files. [2024-11-27 15:36:19] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-11-27 15:36:19] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-27 15:36:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-27 15:36:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-11-27 15:36:19] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-11-27 15:36:19] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-11-27 15:36:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-27 15:36:19] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-11-27 15:36:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-27 15:36:19] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-11-27 15:36:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-27 15:36:19] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-11-27 15:36:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-27 15:36:19] [TRACE] [OmnipathR] Cache locked: FALSE ** data ** inst ** byte-compile and prepare package for lazy loading [2024-11-27 15:36:43] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-27 15:36:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-27 15:36:43] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-11-27 15:36:43] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-11-27 15:36:43] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-11-27 15:36:43] [TRACE] [OmnipathR] Contains 1 files. [2024-11-27 15:36:43] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-11-27 15:36:43] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-27 15:36:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-27 15:36:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-11-27 15:36:43] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-11-27 15:36:43] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-11-27 15:36:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-27 15:36:43] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-11-27 15:36:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-27 15:36:43] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-11-27 15:36:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-27 15:36:43] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-11-27 15:36:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-27 15:36:43] [TRACE] [OmnipathR] Cache locked: FALSE ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2024-11-27 15:37:13] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-27 15:37:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-27 15:37:13] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-11-27 15:37:13] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-11-27 15:37:13] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-11-27 15:37:13] [TRACE] [OmnipathR] Contains 1 files. [2024-11-27 15:37:13] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-11-27 15:37:13] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-27 15:37:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-27 15:37:13] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-11-27 15:37:13] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-11-27 15:37:13] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-11-27 15:37:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-27 15:37:14] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-11-27 15:37:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-27 15:37:14] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-11-27 15:37:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-27 15:37:14] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-11-27 15:37:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-27 15:37:14] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-11-27 15:37:37] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-27 15:37:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-27 15:37:37] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-11-27 15:37:37] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-11-27 15:37:37] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-11-27 15:37:37] [TRACE] [OmnipathR] Contains 1 files. [2024-11-27 15:37:37] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-11-27 15:37:37] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-27 15:37:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-27 15:37:37] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-11-27 15:37:37] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-11-27 15:37:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-11-27 15:37:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-27 15:37:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-11-27 15:37:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-27 15:37:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-11-27 15:37:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-27 15:37:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-11-27 15:37:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-27 15:37:37] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (gINTomics)
gINTomics.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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(gINTomics)
[2024-11-27 22:37:38] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-27 22:37:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-27 22:37:38] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-27 22:37:38] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-11-27 22:37:38] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-27 22:37:38] [TRACE] [OmnipathR] Contains 6 files.
[2024-11-27 22:37:38] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-11-27 22:37:38] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-27 22:37:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-27 22:37:38] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-27 22:37:39] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-11-27 22:37:39] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-27 22:37:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-27 22:37:39] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-27 22:37:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-27 22:37:39] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-27 22:37:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-27 22:37:39] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-27 22:37:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-27 22:37:39] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check("gINTomics")
[2024-11-27 22:37:42] [TRACE] [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions,datasets=mirnatarget]
[2024-11-27 22:37:42] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-11-27 22:37:42] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-27 22:37:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-27 22:37:42] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-11-27 22:37:42] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-27 22:37:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-27 22:37:42] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-11-27 22:37:42] [TRACE] [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-11-27 22:37:42] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-11-27 22:37:42] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-11-27 22:37:43] [TRACE] [OmnipathR] HTTP 200
[2024-11-27 22:37:43] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2024-11-27 22:37:43] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-27 22:37:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-27 22:37:43] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2024-11-27 22:37:43] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-11-27 22:37:43] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2024-11-27 22:37:43] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2024-11-27 22:37:43] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-27 22:37:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-27 22:37:43] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-27 22:37:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-27 22:37:43] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2024-11-27 22:37:43] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-11-27 22:37:43] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2024-11-27 22:37:43] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2024-11-27 22:37:44] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-11-27 22:37:44] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2024-11-27 22:37:44] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-27 22:37:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-27 22:37:44] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2024-11-27 22:37:44] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2024-11-27 22:37:44] [TRACE] [OmnipathR] Organism(s): 9606
[2024-11-27 22:37:44] [TRACE] [OmnipathR] Orthology targets:
[2024-11-27 22:37:44] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-27 22:37:44] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-27 22:37:44] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-27 22:37:44] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-27 22:37:44] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-27 22:37:44] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-27 22:37:44] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-27 22:37:46] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-27 22:37:46] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-27 22:37:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-27 22:37:46] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-27 22:37:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-27 22:37:46] [INFO] [OmnipathR] Cache item `41c8055b20002c0dbf8ddf485403332479b715a1` version 1: status changed from `unknown` to `started`.
[2024-11-27 22:37:46] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/41c8055b20002c0dbf8ddf485403332479b715a1-1.rds`.
[2024-11-27 22:37:46] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/41c8055b20002c0dbf8ddf485403332479b715a1-1.rds`.
[2024-11-27 22:37:46] [INFO] [OmnipathR] Download ready [key=41c8055b20002c0dbf8ddf485403332479b715a1, version=1]
[2024-11-27 22:37:46] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-27 22:37:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-27 22:37:46] [INFO] [OmnipathR] Cache item `41c8055b20002c0dbf8ddf485403332479b715a1` version 1: status changed from `started` to `ready`.
[2024-11-27 22:37:46] [SUCCESS] [OmnipathR] Downloaded 11118 interactions.
[2024-11-27 22:37:46] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=TransmiR,organisms=9606,query_type=interactions,datasets=tf_mirna]
[2024-11-27 22:37:46] [TRACE] [OmnipathR] Organism(s): 9606
[2024-11-27 22:37:46] [TRACE] [OmnipathR] Orthology targets:
[2024-11-27 22:37:47] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-27 22:37:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-27 22:37:47] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-27 22:37:47] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-27 22:37:47] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-27 22:37:47] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-27 22:37:47] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-27 22:37:47] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-27 22:37:47] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-27 22:37:48] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-27 22:37:48] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-27 22:37:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-27 22:37:48] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-27 22:37:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-27 22:37:48] [INFO] [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `unknown` to `started`.
[2024-11-27 22:37:48] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`.
[2024-11-27 22:37:48] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`.
[2024-11-27 22:37:48] [INFO] [OmnipathR] Download ready [key=2e2b496d72e1686af2bd8a26a0b6d2f96d90e687, version=1]
[2024-11-27 22:37:48] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-27 22:37:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-27 22:37:48] [INFO] [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `started` to `ready`.
[2024-11-27 22:37:48] [SUCCESS] [OmnipathR] Downloaded 3868 interactions.
[2024-11-27 22:37:48] [TRACE] [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions,datasets=tf_target]
[2024-11-27 22:37:48] [TRACE] [OmnipathR] Organism(s): 9606
[2024-11-27 22:37:48] [TRACE] [OmnipathR] Orthology targets:
[2024-11-27 22:37:48] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-27 22:37:48] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-27 22:37:48] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-27 22:37:48] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-27 22:37:48] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-27 22:37:48] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-27 22:37:48] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-27 22:37:50] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-27 22:37:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-27 22:37:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-27 22:37:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-27 22:37:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-27 22:37:50] [INFO] [OmnipathR] Cache item `6ed1bdfc7230bcb2925f9cb360e0b77190c82237` version 1: status changed from `unknown` to `started`.
[2024-11-27 22:37:50] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6ed1bdfc7230bcb2925f9cb360e0b77190c82237-1.rds`.
[2024-11-27 22:37:50] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6ed1bdfc7230bcb2925f9cb360e0b77190c82237-1.rds`.
[2024-11-27 22:37:50] [INFO] [OmnipathR] Download ready [key=6ed1bdfc7230bcb2925f9cb360e0b77190c82237, version=1]
[2024-11-27 22:37:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-27 22:37:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-27 22:37:50] [INFO] [OmnipathR] Cache item `6ed1bdfc7230bcb2925f9cb360e0b77190c82237` version 1: status changed from `started` to `ready`.
[2024-11-27 22:37:52] [SUCCESS] [OmnipathR] Downloaded 59469 interactions.
2162 genes were dropped because they have exons located on both strands of
the same reference sequence or on more than one reference sequence, so cannot
be represented by a single genomic range.
Use 'single.strand.genes.only=FALSE' to get all the genes in a GRangesList
object, or use suppressMessages() to suppress this message.
'select()' returned 1:many mapping between keys and columns
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
Generating interactions
2162 genes were dropped because they have exons located on both strands of
the same reference sequence or on more than one reference sequence, so cannot
be represented by a single genomic range.
Use 'single.strand.genes.only=FALSE' to get all the genes in a GRangesList
object, or use suppressMessages() to suppress this message.
'select()' returned 1:many mapping between keys and columns
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 204 ]
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 204 ]
>
> proc.time()
user system elapsed
123.549 10.630 77.342
gINTomics.Rcheck/gINTomics-Ex.timings
| name | user | system | elapsed | |
| create_multiassay | 0.518 | 0.020 | 0.540 | |
| dot_plotly | 0.441 | 0.020 | 0.464 | |
| extract_model_res | 8.683 | 0.456 | 9.171 | |
| mirna_hsa | 0.013 | 0.002 | 0.014 | |
| mmultiassay_ov | 0.078 | 0.002 | 0.080 | |
| plot_chr_distribution | 0.369 | 0.015 | 0.386 | |
| plot_heatmap | 0.384 | 0.014 | 0.399 | |
| plot_network | 0.376 | 0.017 | 0.395 | |
| plot_ridge | 6.035 | 0.336 | 6.391 | |
| plot_tf_distribution | 0.371 | 0.014 | 0.386 | |
| plot_venn | 0.387 | 0.016 | 0.404 | |
| plot_volcano | 9.789 | 0.642 | 23.232 | |
| run_cnv_integration | 0.721 | 0.024 | 0.753 | |
| run_genomic_enrich | 0.418 | 0.019 | 0.439 | |
| run_genomic_integration | 0.806 | 0.033 | 0.851 | |
| run_met_integration | 0.713 | 0.022 | 0.742 | |
| run_multiomics | 3.283 | 0.045 | 3.924 | |
| run_shiny | 0.435 | 0.016 | 0.458 | |
| run_tf_enrich | 0.490 | 0.019 | 0.516 | |
| run_tf_integration | 1.977 | 0.028 | 2.014 | |