| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-10 10:04:29 -0000 (Wed, 10 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6211 |
| 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 | ||||
|
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 501/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| decoupleR 2.7.0 (landing page) Pau Badia-i-Mompel
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: decoupleR |
| Version: 2.7.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings decoupleR_2.7.0.tar.gz |
| StartedAt: 2023-05-09 13:48:44 -0000 (Tue, 09 May 2023) |
| EndedAt: 2023-05-09 14:09:13 -0000 (Tue, 09 May 2023) |
| EllapsedTime: 1228.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: decoupleR.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings decoupleR_2.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/decoupleR.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.7.0’
* 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 ‘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 R 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 ... NOTE
[2023-05-09 13:49:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-09 13:49:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:49:17] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-05-09 13:49:17] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-05-09 13:49:17] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-05-09 13:49:17] [TRACE] [OmnipathR] Contains 6 files.
[2023-05-09 13:49:17] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-05-09 13:49:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-09 13:49:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:49:17] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-05-09 13:49:17] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-05-09 13:49:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-05-09 13:49:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:49:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-05-09 13:49:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:49:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-05-09 13:49:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:49:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-05-09 13:49:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:49:17] [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 ... 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
get_dorothea 30.101 0.436 39.560
run_fgsea 25.176 0.464 25.639
run_aucell 10.256 0.412 10.669
get_progeny 7.901 0.557 112.965
get_collectri 5.682 0.250 27.042
get_resource 0.839 0.055 5.017
* 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:
`actual$p_value[106:113]`: 0.20 0.21 0.21 0.87 0.87 0.19 0.19 0.18
`expected$p_value[106:113]`: 0.20 0.21 0.21 0.94 0.94 0.19 0.19 0.18
`actual$p_value[118:127]`: 0.13 0.11 0.11 0.99 0.99 0.12 0.12 0.16 0.16 0.59
`expected$p_value[118:127]`: 0.13 0.11 0.11 1.00 1.00 0.13 0.13 0.16 0.16 0.59
`actual$p_value[132:139]`: 0.12 0.59 0.59 0.17 0.17 0.20 0.20 0.59
`expected$p_value[132:139]`: 0.12 0.59 0.59 0.18 0.18 0.20 0.20 0.59
[ FAIL 1 | WARN 357 | SKIP 0 | PASS 34 ]
Error: Test failures
In addition: Warning message:
In for (i in seq_len(n_col)) { :
closing unused connection 4 (https://omnipathdb.org/annotations?resources=PROGENy&license=academic)
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘decoupleR.Rmd’ using ‘UTF-8’... OK
‘pw_bk.Rmd’ using ‘UTF-8’... OK
‘pw_sc.Rmd’ using ‘UTF-8’... OK
‘tf_bk.Rmd’ using ‘UTF-8’... OK
‘tf_sc.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/decoupleR.Rcheck/00check.log’
for details.
decoupleR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL decoupleR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/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) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
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")
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[2023-05-09 13:55:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-09 13:55:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:55:05] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-05-09 13:55:05] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-05-09 13:55:05] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-05-09 13:55:05] [TRACE] [OmnipathR] Contains 5 files.
[2023-05-09 13:55:05] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-05-09 13:55:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-09 13:55:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:55:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-05-09 13:55:05] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-05-09 13:55:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-05-09 13:55:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:55:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-05-09 13:55:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:55:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-05-09 13:55:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:55:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-05-09 13:55:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:55:05] [TRACE] [OmnipathR] Cache locked: FALSE
[2023-05-09 13:55:07] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-09 13:55:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:55:08] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-09 13:55:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:55:10] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-09 13:55:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:55:10] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2023-05-09 13:55:10] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2023-05-09 13:55:10] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2023-05-09 13:55:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-09 13:55:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:55:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-09 13:55:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:55:11] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`.
[2023-05-09 13:55:11] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2023-05-09 13:55:11] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2023-05-09 13:55:11] [INFO] [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1]
[2023-05-09 13:55:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-09 13:55:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:55:11] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`.
[2023-05-09 13:55:11] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2023-05-09 13:55:13] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-09 13:55:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:55:17] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-09 13:55:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:55:17] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-05-09 13:55:17] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-05-09 13:55:17] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-05-09 13:55:50] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` (attempt 1/3); error: OpenSSL SSL_read: Connection reset by peer, errno 104
[2023-05-09 13:55:55] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-05-09 13:57:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-09 13:57:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:57:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-09 13:57:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:57:23] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2023-05-09 13:57:23] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2023-05-09 13:57:26] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2023-05-09 13:57:26] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2023-05-09 13:57:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-09 13:57:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:57:26] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2023-05-09 13:57:26] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records.
[2023-05-09 13:57:32] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-09 13:57:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:57:35] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-05-09 13:57:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:57:38] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2023-05-09 13:57:38] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-05-09 13:57:38] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.
[2023-05-09 13:57:41] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-05-09 13:57:41] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-05-09 13:57:41] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-05-09 13:58:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-09 13:58:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:58:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-09 13:58:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:58:34] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `unknown` to `started`.
[2023-05-09 13:58:34] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2023-05-09 13:58:36] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2023-05-09 13:58:36] [INFO] [OmnipathR] Download ready [key=46d37339bbc3f9a05bb89ccb79278cf1233f5cdf, version=1]
[2023-05-09 13:58:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-09 13:58:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:58:36] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `started` to `ready`.
[2023-05-09 13:58:49] [SUCCESS] [OmnipathR] Downloaded 278830 interactions.
[2023-05-09 13:59:02] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-05-09 13:59:02] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-05-09 13:59:02] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2023-05-09 13:59:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-09 13:59:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:59:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-09 13:59:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:59:12] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `unknown` to `started`.
[2023-05-09 13:59:12] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2023-05-09 13:59:13] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2023-05-09 13:59:13] [INFO] [OmnipathR] Download ready [key=ff347dedf78ef5e38c9c6d8eed291fa901aa3791, version=1]
[2023-05-09 13:59:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-09 13:59:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:59:13] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `started` to `ready`.
[2023-05-09 13:59:23] [SUCCESS] [OmnipathR] Downloaded 234298 interactions.
[2023-05-09 13:59:35] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&license=academic`
[2023-05-09 13:59:35] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&license=academic`
[2023-05-09 13:59:35] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&license=academic`
[2023-05-09 13:59:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-09 13:59:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:59:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-09 13:59:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:59:40] [INFO] [OmnipathR] Cache item `485498a0b8637e8a936f7efbf1fcc7b742d7867a` version 1: status changed from `unknown` to `started`.
[2023-05-09 13:59:40] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/485498a0b8637e8a936f7efbf1fcc7b742d7867a-1.rds`.
[2023-05-09 13:59:40] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/485498a0b8637e8a936f7efbf1fcc7b742d7867a-1.rds`.
[2023-05-09 13:59:40] [INFO] [OmnipathR] Download ready [key=485498a0b8637e8a936f7efbf1fcc7b742d7867a, version=1]
[2023-05-09 13:59:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-09 13:59:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-05-09 13:59:41] [INFO] [OmnipathR] Cache item `485498a0b8637e8a936f7efbf1fcc7b742d7867a` version 1: status changed from `started` to `ready`.
[2023-05-09 13:59:44] [SUCCESS] [OmnipathR] Downloaded 68297 interactions.
[2023-05-09 13:59:44] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/485498a0b8637e8a936f7efbf1fcc7b742d7867a-1.rds`.
[2023-05-09 13:59:44] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&license=academic`
[2023-05-09 13:59:48] [SUCCESS] [OmnipathR] Loaded 68297 interactions from cache.
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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 1 | WARN 357 | SKIP 0 | PASS 34 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-statistic-fgsea.R:26:3'): test run_fgsea ─────────────────────
`res_1` (`actual`) not equal to `exp_1` (`expected`).
actual vs expected
p_value
actual[1, ] 0.075479709
actual[2, ] 0.075479709
- actual[3, ] 0.511687342
+ expected[3, ] 0.548454870
- actual[4, ] 0.511687342
+ expected[4, ] 0.548454870
actual[5, ] 0.010000000
actual[6, ] 0.010000000
actual[7, ] 0.076411558
actual vs expected
p_value
actual[12, ] 0.010000000
actual[13, ] 0.114238030
actual[14, ] 0.114238030
- actual[15, ] 0.510665738
+ expected[15, ] 0.522337972
- actual[16, ] 0.510665738
+ expected[16, ] 0.522337972
actual[17, ] 0.010000000
actual[18, ] 0.010000000
actual[19, ] 0.004682543
actual[20, ] 0.004682543
- actual[21, ] 0.219233595
+ expected[21, ] 0.294730294
and 10 more ...
actual vs expected
p_value
actual[34, ] 1.000000000
actual[35, ] 0.010000000
actual[36, ] 0.010000000
- actual[37, ] 0.091542106
+ expected[37, ] 0.103646587
- actual[38, ] 0.091542106
+ expected[38, ] 0.103646587
actual[39, ] 0.592371428
actual[40, ] 0.592371428
actual[41, ] 0.010000000
actual vs expected
p_value
actual[52, ] 0.976649086
actual[53, ] 0.010000000
actual[54, ] 0.010000000
- actual[55, ] 0.066624941
+ expected[55, ] 0.076411558
- actual[56, ] 0.066624941
+ expected[56, ] 0.076411558
actual[57, ] 0.592371428
actual[58, ] 0.592371428
actual[59, ] 0.010000000
actual[60, ] 0.010000000
- actual[61, ] 0.111211902
+ expected[61, ] 0.108185775
and 4 more ...
actual vs expected
p_value
actual[70, ] 1.000000000
actual[71, ] 0.010000000
actual[72, ] 0.010000000
- actual[73, ] 0.256981914
+ expected[73, ] 0.469812943
- actual[74, ] 0.256981914
+ expected[74, ] 0.469812943
- actual[75, ] 0.133907888
+ expected[75, ] 0.132394821
- actual[76, ] 0.133907888
+ expected[76, ] 0.132394821
actual[77, ] 0.123204721
actual[78, ] 0.123204721
- actual[79, ] 0.146641013
+ expected[79, ] 0.207618744
and 4 more ...
actual vs expected
p_value
actual[88, ] 0.177906190
actual[89, ] 0.154281338
actual[90, ] 0.154281338
- actual[91, ] 0.434796297
+ expected[91, ] 0.487321278
- actual[92, ] 0.434796297
+ expected[92, ] 0.487321278
actual[93, ] 0.009411332
actual[94, ] 0.009411332
actual[95, ] 0.005020222
actual[96, ] 0.005020222
- actual[97, ] 0.294730294
+ expected[97, ] 0.493157392
and 4 more ...
actual vs expected
p_value
actual[106, ] 0.199193619
actual[107, ] 0.213918294
actual[108, ] 0.213918294
- actual[109, ] 0.873886766
+ expected[109, ] 0.944265891
- actual[110, ] 0.873886766
+ expected[110, ] 0.944265891
actual[111, ] 0.187029368
actual[112, ] 0.187029368
actual[113, ] 0.180210408
actual vs expected
p_value
actual[118, ] 0.126342554
actual[119, ] 0.111593916
actual[120, ] 0.111593916
- actual[121, ] 0.991185346
+ expected[121, ] 1.000000000
- actual[122, ] 0.991185346
+ expected[122, ] 1.000000000
- actual[123, ] 0.123316421
+ expected[123, ] 0.126342554
- actual[124, ] 0.123316421
+ expected[124, ] 0.126342554
actual[125, ] 0.155922629
actual[126, ] 0.155922629
actual[127, ] 0.592371428
actual vs expected
p_value
actual[132, ] 0.124515409
actual[133, ] 0.592371428
actual[134, ] 0.592371428
- actual[135, ] 0.174865133
+ expected[135, ] 0.183988307
- actual[136, ] 0.174865133
+ expected[136, ] 0.183988307
actual[137, ] 0.198360798
actual[138, ] 0.198360798
actual[139, ] 0.592371428
`actual$p_value[1:7]`: 0.08 0.08 0.51 0.51 0.01 0.01 0.08
`expected$p_value[1:7]`: 0.08 0.08 0.55 0.55 0.01 0.01 0.08
actual$p_value | expected$p_value
[12] 0.01 | 0.01 [12]
[13] 0.11 | 0.11 [13]
[14] 0.11 | 0.11 [14]
[15] 0.51 - 0.52 [15]
[16] 0.51 - 0.52 [16]
[17] 0.01 | 0.01 [17]
[18] 0.01 | 0.01 [18]
[19] 0.00 | 0.00 [19]
[20] 0.00 | 0.00 [20]
[21] 0.22 - 0.29 [21]
... ... ... and 10 more ...
`actual$p_value[34:41]`: 1.00 0.01 0.01 0.09 0.09 0.59 0.59 0.01
`expected$p_value[34:41]`: 1.00 0.01 0.01 0.10 0.10 0.59 0.59 0.01
`actual$p_value[52:59]`: 0.98 0.01 0.01 0.07 0.07 0.59 0.59 0.01
`expected$p_value[52:59]`: 0.98 0.01 0.01 0.08 0.08 0.59 0.59 0.01
actual$p_value | expected$p_value
[70] 1.00 | 1.00 [70]
[71] 0.01 | 0.01 [71]
[72] 0.01 | 0.01 [72]
[73] 0.26 - 0.47 [73]
[74] 0.26 - 0.47 [74]
[75] 0.13 | 0.13 [75]
[76] 0.13 | 0.13 [76]
[77] 0.12 | 0.12 [77]
[78] 0.12 | 0.12 [78]
[79] 0.15 - 0.21 [79]
... ... ... and 4 more ...
actual$p_value | expected$p_value
[88] 0.18 | 0.18 [88]
[89] 0.15 | 0.15 [89]
[90] 0.15 | 0.15 [90]
[91] 0.43 - 0.49 [91]
[92] 0.43 - 0.49 [92]
[93] 0.01 | 0.01 [93]
[94] 0.01 | 0.01 [94]
[95] 0.01 | 0.01 [95]
[96] 0.01 | 0.01 [96]
[97] 0.29 - 0.49 [97]
... ... ... and 4 more ...
`actual$p_value[106:113]`: 0.20 0.21 0.21 0.87 0.87 0.19 0.19 0.18
`expected$p_value[106:113]`: 0.20 0.21 0.21 0.94 0.94 0.19 0.19 0.18
`actual$p_value[118:127]`: 0.13 0.11 0.11 0.99 0.99 0.12 0.12 0.16 0.16 0.59
`expected$p_value[118:127]`: 0.13 0.11 0.11 1.00 1.00 0.13 0.13 0.16 0.16 0.59
`actual$p_value[132:139]`: 0.12 0.59 0.59 0.17 0.17 0.20 0.20 0.59
`expected$p_value[132:139]`: 0.12 0.59 0.59 0.18 0.18 0.20 0.20 0.59
[ FAIL 1 | WARN 357 | SKIP 0 | PASS 34 ]
Error: Test failures
In addition: Warning message:
In for (i in seq_len(n_col)) { :
closing unused connection 4 (https://omnipathdb.org/annotations?resources=PROGENy&license=academic)
Execution halted
decoupleR.Rcheck/decoupleR-Ex.timings
| name | user | system | elapsed | |
| check_corr | 0.116 | 0.020 | 0.137 | |
| convert_f_defaults | 0.100 | 0.004 | 0.104 | |
| decouple | 0.001 | 0.001 | 0.001 | |
| dot-fit_preprocessing | 0.031 | 0.000 | 0.032 | |
| extract_sets | 0.031 | 0.004 | 0.034 | |
| filt_minsize | 0.059 | 0.000 | 0.059 | |
| get_collectri | 5.682 | 0.250 | 27.042 | |
| get_dorothea | 30.101 | 0.436 | 39.560 | |
| get_profile_of | 0.001 | 0.000 | 0.000 | |
| get_progeny | 7.901 | 0.557 | 112.965 | |
| get_resource | 0.839 | 0.055 | 5.017 | |
| get_toy_data | 0.004 | 0.000 | 0.004 | |
| intersect_regulons | 0.034 | 0.000 | 0.034 | |
| pipe | 0.000 | 0.000 | 0.001 | |
| pivot_wider_profile | 0 | 0 | 0 | |
| randomize_matrix | 0 | 0 | 0 | |
| rename_net | 0.046 | 0.004 | 0.050 | |
| run_aucell | 10.256 | 0.412 | 10.669 | |
| run_consensus | 3.237 | 0.180 | 3.417 | |
| run_fgsea | 25.176 | 0.464 | 25.639 | |
| run_gsva | 1.272 | 0.096 | 1.367 | |
| run_mdt | 0.405 | 0.012 | 0.412 | |
| run_mlm | 0.131 | 0.004 | 0.136 | |
| run_ora | 0.695 | 0.004 | 0.699 | |
| run_udt | 0.506 | 0.000 | 0.506 | |
| run_ulm | 0.269 | 0.000 | 0.269 | |
| run_viper | 0.872 | 0.040 | 0.911 | |
| run_wmean | 1.273 | 0.020 | 1.292 | |
| run_wsum | 1.348 | 0.168 | 1.516 | |
| show_methods | 0.064 | 0.008 | 0.071 | |
| show_resources | 0.273 | 0.032 | 1.756 | |
| tidyeval | 0.000 | 0.000 | 0.001 | |