| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:36:22 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 523/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| decoupleR 2.9.6 (landing page) Pau Badia-i-Mompel
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the decoupleR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/decoupleR.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: decoupleR |
| Version: 2.9.6 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings decoupleR_2.9.6.tar.gz |
| StartedAt: 2024-03-27 21:44:21 -0400 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 22:11:41 -0400 (Wed, 27 Mar 2024) |
| EllapsedTime: 1639.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: decoupleR.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings decoupleR_2.9.6.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/decoupleR.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.9.6’
* 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 ‘decoupleR’ 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 ... NOTE
[2024-03-27 21:44:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 21:44:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:44:54] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-03-27 21:44:54] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-03-27 21:44:54] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-03-27 21:44:55] [TRACE] [OmnipathR] Contains 8 files.
[2024-03-27 21:44:55] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-03-27 21:44:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 21:44:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:44:55] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-03-27 21:44:55] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-03-27 21:44:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-27 21:44:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:44:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-27 21:44:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:44:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-27 21:44:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:44:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-27 21:44:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:44:55] [TRACE] [OmnipathR] Cache locked: FALSE
* 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 ... WARNING
Missing link or links in Rd file 'run_gsva.Rd':
‘GSVA::gsva’ ‘GeneSetCollection’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 ... ERROR
Running examples in ‘decoupleR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: run_gsva
> ### Title: Gene Set Variation Analysis (GSVA)
> ### Aliases: run_gsva
>
> ### ** Examples
>
> inputs_dir <- system.file("testdata", "inputs", package = "decoupleR")
>
> mat <- readRDS(file.path(inputs_dir, "mat.rds"))
> net <- readRDS(file.path(inputs_dir, "net.rds"))
>
> run_gsva(mat, net, minsize=1, verbose = FALSE)
Error in GSVA::gsva(expr = exec(param, exprData = mat, geneSets = regulons, :
Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva').
Calls: run_gsva ... as.data.frame -> <Anonymous> -> <Anonymous> -> .Defunct
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
Backtrace:
▆
1. ├─decoupleR::run_gsva(mat, net, minsize = 1L, verbose = FALSE) at test-statistic-gsva.R:22:5
2. │ ├─... %>% ...
3. │ ├─GSVA::gsva(...)
4. │ └─GSVA::gsva(...)
5. │ └─base::.Defunct(new = "gsva()", package = "GSVA", msg = "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva').")
6. ├─dplyr::mutate(...)
7. ├─tidyr::pivot_longer(...)
8. ├─tibble::rownames_to_column(., var = "source")
9. └─base::as.data.frame(.)
[ FAIL 2 | WARN 1 | SKIP 0 | PASS 33 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.19-bioc/meat/decoupleR.Rcheck/00check.log’
for details.
decoupleR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL decoupleR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘decoupleR’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (decoupleR)
decoupleR.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.
> library(testthat)
> library(decoupleR)
>
> test_check("decoupleR")
[2024-03-27 21:53:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 21:53:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:53:27] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-03-27 21:53:27] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-03-27 21:53:27] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-03-27 21:53:27] [TRACE] [OmnipathR] Contains 8 files.
[2024-03-27 21:53:27] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-03-27 21:53:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 21:53:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:53:27] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-03-27 21:53:27] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-03-27 21:53:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-27 21:53:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:53:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-27 21:53:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:53:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-27 21:53:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:53:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-27 21:53:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:53:27] [TRACE] [OmnipathR] Cache locked: FALSE
[2024-03-27 21:53:28] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-03-27 21:53:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:53:29] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-03-27 21:53:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:53:29] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-03-27 21:53:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 21:53:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:53:29] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-03-27 21:53:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 21:53:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:53:29] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-03-27 21:53:29] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-03-27 21:53:29] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-03-27 21:53:29] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-03-27 21:53:30] [TRACE] [OmnipathR] HTTP 200
[2024-03-27 21:53:30] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2024-03-27 21:53:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 21:53:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:53:30] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2024-03-27 21:53:30] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-03-27 21:53:30] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2024-03-27 21:53:30] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2024-03-27 21:53:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 21:53:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:53:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 21:53:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:53:30] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2024-03-27 21:53:30] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-03-27 21:53:30] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2024-03-27 21:53:30] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2024-03-27 21:53:32] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-03-27 21:53:32] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2024-03-27 21:53:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 21:53:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:53:32] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2024-03-27 21:53:32] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2024-03-27 21:53:33] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-03-27 21:53:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:53:33] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-03-27 21:53:33] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-03-27 21:53:33] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-03-27 21:53:33] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-03-27 21:53:33] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-03-27 21:53:33] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-03-27 21:53:33] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-03-27 21:53:34] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2024-03-27 21:53:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 21:53:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:53:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 21:53:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:53:34] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`.
[2024-03-27 21:53:34] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2024-03-27 21:53:34] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2024-03-27 21:53:34] [INFO] [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1]
[2024-03-27 21:53:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 21:53:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:53:34] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`.
[2024-03-27 21:53:34] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2024-03-27 21:53:34] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-03-27 21:53:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:53:35] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-03-27 21:53:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:53:35] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-03-27 21:53:35] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-03-27 21:53:35] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-03-27 21:53:35] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-03-27 21:53:35] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-03-27 21:53:35] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-03-27 21:53:35] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-03-27 21:53:46] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-03-27 21:53:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 21:53:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:53:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 21:53:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:53:46] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2024-03-27 21:53:46] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2024-03-27 21:53:48] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2024-03-27 21:53:48] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2024-03-27 21:53:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 21:53:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:53:48] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2024-03-27 21:53:48] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records.
[2024-03-27 21:53:51] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-03-27 21:53:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:53:52] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-03-27 21:53:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:53:52] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-03-27 21:53:55] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2024-03-27 21:53:55] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2024-03-27 21:53:55] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.
[2024-03-27 21:53:57] [INFO] [OmnipathR] Loading database `Orthologous Matrix (OMA) gene pairs`.
[2024-03-27 21:53:57] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/cgi-bin/gateway.pl?f=PairwiseOrthologs&p1=HUMAN&p2=MOUSE&p3=UniProt`.
[2024-03-27 21:53:57] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/cgi-bin/gateway.pl?f=PairwiseOrthologs&p1=HUMAN&p2=MOUSE&p3=UniProt`
[2024-03-27 21:53:57] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/cgi-bin/gateway.pl?f=PairwiseOrthologs&p1=HUMAN&p2=MOUSE&p3=UniProt`.
[2024-03-27 21:53:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 21:53:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:53:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 21:53:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:53:57] [INFO] [OmnipathR] Cache item `793353c9f6658b9d85f18fc09a6b36ba7f0d71db` version 1: status changed from `unknown` to `started`.
[2024-03-27 21:53:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/793353c9f6658b9d85f18fc09a6b36ba7f0d71db-1.rds`.
[2024-03-27 21:53:57] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/cgi-bin/gateway.pl?f=PairwiseOrthologs&p1=HUMAN&p2=MOUSE&p3=UniProt`
[2024-03-27 21:53:57] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/cgi-bin/gateway.pl?f=PairwiseOrthologs&p1=HUMAN&p2=MOUSE&p3=UniProt`
[2024-03-27 21:53:59] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/793353c9f6658b9d85f18fc09a6b36ba7f0d71db-1.rds`.
[2024-03-27 21:53:59] [INFO] [OmnipathR] Download ready [key=793353c9f6658b9d85f18fc09a6b36ba7f0d71db, version=1]
[2024-03-27 21:53:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 21:53:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:53:59] [INFO] [OmnipathR] Cache item `793353c9f6658b9d85f18fc09a6b36ba7f0d71db` version 1: status changed from `started` to `ready`.
[2024-03-27 21:53:59] [INFO] [OmnipathR] Loaded database `Orthologous Matrix (OMA) gene pairs`.
[2024-03-27 21:53:59] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2024-03-27 21:53:59] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 10090 (only reviewed: TRUE)
[2024-03-27 21:53:59] [TRACE] [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: accession,gene_primary
[2024-03-27 21:53:59] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`.
[2024-03-27 21:53:59] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2024-03-27 21:53:59] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`.
[2024-03-27 21:53:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 21:53:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:53:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 21:53:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:53:59] [INFO] [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `unknown` to `started`.
[2024-03-27 21:53:59] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`.
[2024-03-27 21:53:59] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2024-03-27 21:53:59] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2024-03-27 21:54:18] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`.
[2024-03-27 21:54:18] [INFO] [OmnipathR] Download ready [key=3ec84ba713c02573704adb50f1a94dab684df34b, version=1]
[2024-03-27 21:54:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 21:54:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:54:18] [INFO] [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `started` to `ready`.
[2024-03-27 21:54:18] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17207 records
[2024-03-27 21:54:20] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-27 21:54:20] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-27 21:54:20] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-27 21:54:20] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-27 21:54:20] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-27 21:54:20] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-27 21:54:20] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-27 21:54:29] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-27 21:54:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 21:54:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:54:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 21:54:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:54:29] [INFO] [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `unknown` to `started`.
[2024-03-27 21:54:29] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`.
[2024-03-27 21:54:32] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/2acacccd183a8fe4538b649c1e593e2140fcddf6-1.rds`.
[2024-03-27 21:54:32] [INFO] [OmnipathR] Download ready [key=2acacccd183a8fe4538b649c1e593e2140fcddf6, version=1]
[2024-03-27 21:54:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 21:54:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:54:32] [INFO] [OmnipathR] Cache item `2acacccd183a8fe4538b649c1e593e2140fcddf6` version 1: status changed from `started` to `ready`.
[2024-03-27 21:54:32] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2024-03-27 21:54:51] [TRACE] [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any
[2024-03-27 21:55:10] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: dorothea; and resources: any
[2024-03-27 21:59:36] [SUCCESS] [OmnipathR] Downloaded 278830 interactions.
[2024-03-27 21:59:44] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-27 21:59:44] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-27 21:59:44] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-27 21:59:44] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-27 21:59:44] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-27 21:59:44] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-27 21:59:44] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-27 21:59:50] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-27 21:59:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 21:59:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:59:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 21:59:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:59:50] [INFO] [OmnipathR] Cache item `73101f94a89eabbc8c12583d15dce08671d9e187` version 1: status changed from `unknown` to `started`.
[2024-03-27 21:59:50] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/73101f94a89eabbc8c12583d15dce08671d9e187-1.rds`.
[2024-03-27 21:59:52] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/73101f94a89eabbc8c12583d15dce08671d9e187-1.rds`.
[2024-03-27 21:59:52] [INFO] [OmnipathR] Download ready [key=73101f94a89eabbc8c12583d15dce08671d9e187, version=1]
[2024-03-27 21:59:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 21:59:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 21:59:52] [INFO] [OmnipathR] Cache item `73101f94a89eabbc8c12583d15dce08671d9e187` version 1: status changed from `started` to `ready`.
[2024-03-27 21:59:52] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2024-03-27 22:00:00] [TRACE] [OmnipathR] Restricting interaction records to datasets: dorothea; and resources: any
[2024-03-27 22:00:13] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: dorothea; and resources: any
[2024-03-27 22:03:11] [SUCCESS] [OmnipathR] Downloaded 234298 interactions.
[2024-03-27 22:03:18] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-03-27 22:03:18] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-03-27 22:03:18] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-03-27 22:03:18] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-03-27 22:03:18] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-03-27 22:03:18] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-03-27 22:03:18] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-03-27 22:03:22] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-03-27 22:03:22] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 22:03:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 22:03:22] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 22:03:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 22:03:22] [INFO] [OmnipathR] Cache item `82abc02990e13a4b0186ba97e7e04cb7c5c780b2` version 1: status changed from `unknown` to `started`.
[2024-03-27 22:03:22] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`.
[2024-03-27 22:03:23] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`.
[2024-03-27 22:03:23] [INFO] [OmnipathR] Download ready [key=82abc02990e13a4b0186ba97e7e04cb7c5c780b2, version=1]
[2024-03-27 22:03:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 22:03:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 22:03:23] [INFO] [OmnipathR] Cache item `82abc02990e13a4b0186ba97e7e04cb7c5c780b2` version 1: status changed from `started` to `ready`.
[2024-03-27 22:03:23] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2024-03-27 22:03:28] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any
[2024-03-27 22:03:32] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: collectri; and resources: any
[2024-03-27 22:04:41] [SUCCESS] [OmnipathR] Downloaded 64958 interactions.
[2024-03-27 22:04:42] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-03-27 22:04:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 22:04:42] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-03-27 22:04:42] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-03-27 22:04:42] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-03-27 22:04:42] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-03-27 22:04:42] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-03-27 22:04:42] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-03-27 22:04:42] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-03-27 22:04:42] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-03-27 22:04:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 22:04:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 22:04:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 22:04:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 22:04:42] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`.
[2024-03-27 22:04:42] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2024-03-27 22:04:42] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2024-03-27 22:04:42] [INFO] [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1]
[2024-03-27 22:04:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-27 22:04:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 22:04:43] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`.
[2024-03-27 22:04:43] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2024-03-27 22:04:43] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2024-03-27 22:04:43] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI
[2024-03-27 22:04:43] [SUCCESS] [OmnipathR] Downloaded 232 interactions.
[2024-03-27 22:04:43] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-03-27 22:04:43] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/82abc02990e13a4b0186ba97e7e04cb7c5c780b2-1.rds`.
[2024-03-27 22:04:43] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&loops=yes&license=academic`
[2024-03-27 22:04:43] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2024-03-27 22:04:47] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any
[2024-03-27 22:04:51] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: collectri; and resources: any
[2024-03-27 22:05:59] [SUCCESS] [OmnipathR] Downloaded 64958 interactions.
[2024-03-27 22:06:00] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-03-27 22:06:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-27 22:06:00] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-03-27 22:06:00] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2024-03-27 22:06:00] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2024-03-27 22:06:00] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2024-03-27 22:06:00] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2024-03-27 22:06:00] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI
[2024-03-27 22:06:01] [SUCCESS] [OmnipathR] Downloaded 232 interactions.
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Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
[ FAIL 2 | WARN 1 | SKIP 0 | PASS 33 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-decoupleR-decouple.R:66:5'): decouple same results as independent functions ──
<purrr_error_indexed/rlang_error/error/condition>
Error in `map2(.x, .y, .f, ...)`: i In index: 8.
Caused by error in `GSVA::gsva()`:
! Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva').
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-decoupleR-decouple.R:66:5
2. │ └─base::withCallingHandlers(...)
3. ├─... %>% ...
4. ├─dplyr::arrange(., .data$statistic, .data$source, .data$condition)
5. ├─dplyr::filter(., statistic != "consensus")
6. ├─dplyr::select(., -.data$run_id, -statistic_time)
7. ├─decoupleR (local) partial_decouple(show_toy_call = FALSE, include_time = TRUE)
8. │ └─decoupleR::decouple(...)
9. │ ├─... %>% mutate(run_id = as.numeric(run_id))
10. │ └─purrr::map2_dfr(...)
11. │ └─purrr::map2(.x, .y, .f, ...)
12. │ └─purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress)
13. │ ├─purrr:::with_indexed_errors(...)
14. │ │ └─base::withCallingHandlers(...)
15. │ ├─purrr:::call_with_cleanup(...)
16. │ └─decoupleR (local) .f(.x[[i]], .y[[i]], ...)
17. │ ├─eval(.call) %>% ...
18. │ ├─base::eval(.call)
19. │ │ └─base::eval(.call)
20. │ └─decoupleR::run_gsva(...)
21. │ ├─... %>% ...
22. │ ├─GSVA::gsva(...)
23. │ └─GSVA::gsva(...)
24. │ └─base::.Defunct(new = "gsva()", package = "GSVA", msg = "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva').")
25. │ └─base::stop(...)
26. ├─dplyr::mutate(., run_id = as.numeric(run_id))
27. ├─dplyr::select(...)
28. ├─tibble::add_column(...)
29. │ └─base::is.data.frame(.data)
30. ├─dplyr::mutate(...)
31. ├─tidyr::pivot_longer(...)
32. ├─tibble::rownames_to_column(., var = "source")
33. ├─base::as.data.frame(.)
34. └─purrr (local) `<fn>`(`<dfnctErr>`)
35. └─cli::cli_abort(...)
36. └─rlang::abort(...)
── Error ('test-statistic-gsva.R:22:5'): test run_gsva ─────────────────────────
<defunctError/error/condition>
Error in `GSVA::gsva(expr = exec(param, exprData = mat, geneSets = regulons,
minSize = minsize, maxSize = maxsize, !!!list(...)), verbose = verbose)`: Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva').
Backtrace:
▆
1. ├─decoupleR::run_gsva(mat, net, minsize = 1L, verbose = FALSE) at test-statistic-gsva.R:22:5
2. │ ├─... %>% ...
3. │ ├─GSVA::gsva(...)
4. │ └─GSVA::gsva(...)
5. │ └─base::.Defunct(new = "gsva()", package = "GSVA", msg = "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva').")
6. ├─dplyr::mutate(...)
7. ├─tidyr::pivot_longer(...)
8. ├─tibble::rownames_to_column(., var = "source")
9. └─base::as.data.frame(.)
[ FAIL 2 | WARN 1 | SKIP 0 | PASS 33 ]
Error: Test failures
Execution halted
decoupleR.Rcheck/decoupleR-Ex.timings
| name | user | system | elapsed | |
| check_corr | 0.094 | 0.004 | 0.099 | |
| convert_f_defaults | 0.026 | 0.004 | 0.030 | |
| decouple | 0.000 | 0.000 | 0.001 | |
| dot-fit_preprocessing | 0.021 | 0.007 | 0.028 | |
| extract_sets | 0.025 | 0.000 | 0.026 | |
| filt_minsize | 0.045 | 0.000 | 0.045 | |
| get_collectri | 80.848 | 1.762 | 89.377 | |
| get_dorothea | 318.703 | 3.302 | 324.444 | |
| get_profile_of | 0 | 0 | 0 | |
| get_progeny | 5.629 | 0.278 | 13.461 | |
| get_resource | 0.545 | 0.020 | 2.595 | |
| get_toy_data | 0.002 | 0.000 | 0.002 | |
| intersect_regulons | 0.022 | 0.000 | 0.022 | |
| pipe | 0 | 0 | 0 | |
| pivot_wider_profile | 0 | 0 | 0 | |
| randomize_matrix | 0 | 0 | 0 | |
| rename_net | 0.032 | 0.000 | 0.032 | |
| run_aucell | 8.421 | 0.212 | 8.633 | |
| run_consensus | 1.778 | 0.000 | 1.778 | |
| run_fgsea | 21.918 | 0.160 | 22.079 | |