| Back to Build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-02-27 02:34:32 -0000 (Mon, 27 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4259 |
| 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: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 485/2169 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| decoupleR 2.5.0 (landing page) Pau Badia-i-Mompel
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: decoupleR |
| Version: 2.5.0 |
| 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/library --timings decoupleR_2.5.0.tar.gz |
| StartedAt: 2023-02-24 09:54:45 -0000 (Fri, 24 Feb 2023) |
| EndedAt: 2023-02-24 10:03:05 -0000 (Fri, 24 Feb 2023) |
| EllapsedTime: 499.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: decoupleR.Rcheck |
| Warnings: NA |
##############################################################################
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###
### 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/library --timings decoupleR_2.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/decoupleR.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* 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 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.5.0’
* 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
[2023-02-24 09:55:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-24 09:55:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 09:55:18] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-02-24 09:55:18] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-02-24 09:55:18] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-02-24 09:55:18] [TRACE] [OmnipathR] Contains 3 files.
[2023-02-24 09:55:18] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-02-24 09:55:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-24 09:55:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 09:55:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-02-24 09:55:19] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-02-24 09:55:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-02-24 09:55:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 09:55:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-02-24 09:55:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 09:55:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-02-24 09:55:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 09:55:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-02-24 09:55:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 09:55:19] [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 ... ERROR
Running examples in ‘decoupleR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_dorothea
> ### Title: DoRothEA gene regulatory network.
> ### Aliases: get_dorothea
>
> ### ** Examples
>
> dorothea <- get_dorothea(organism='human', levels=c('A', 'B', 'C'))
[2023-02-24 09:55:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-24 09:55:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 09:55:54] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-02-24 09:55:54] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-02-24 09:55:54] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-02-24 09:55:54] [TRACE] [OmnipathR] Contains 1 files.
[2023-02-24 09:55:54] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-02-24 09:55:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-24 09:55:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 09:55:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-02-24 09:55:54] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-02-24 09:55:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-02-24 09:55:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 09:55:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-02-24 09:55:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 09:55:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-02-24 09:55:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 09:55:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-02-24 09:55:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 09:55:54] [TRACE] [OmnipathR] Cache locked: FALSE
[2023-02-24 09:55:54] [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`
[2023-02-24 09:55:54] [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`
[2023-02-24 09:55:54] [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`
[2023-02-24 09:55:55] [WARN] [OmnipathR] Failed to download `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` (attempt 1/3); error: HTTP error 500.
[2023-02-24 09:56:00] [TRACE] [OmnipathR] Attempt 2/3: `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`
[2023-02-24 09:56:01] [WARN] [OmnipathR] Failed to download `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` (attempt 2/3); error: HTTP error 500.
[2023-02-24 09:56:06] [TRACE] [OmnipathR] Attempt 3/3: `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`
[2023-02-24 09:56:07] [ERROR] [OmnipathR] Failed to download `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` (attempt 3/3); error: HTTP error 500.
Error in open.connection(5L, "rb") : HTTP error 500.
Calls: get_dorothea ... import_omnipath -> do.call -> <Anonymous> -> download_base
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:
[120] 0.112 | 0.112 [120]
[121] 0.991 - 1.000 [121]
[122] 0.991 - 1.000 [122]
[123] 0.123 - 0.126 [123]
[124] 0.123 - 0.126 [124]
[125] 0.156 | 0.156 [125]
[126] 0.156 | 0.156 [126]
[127] 0.592 | 0.592 [127]
`actual$p_value[132:139]`: 0.125 0.592 0.592 0.175 0.175 0.198 0.198 0.592
`expected$p_value[132:139]`: 0.125 0.592 0.592 0.184 0.184 0.198 0.198 0.592
[ FAIL 6 | WARN 324 | SKIP 0 | PASS 29 ]
Error: Test failures
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 ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘decoupleR.Rmd’ using rmarkdown
--- finished re-building ‘decoupleR.Rmd’
--- re-building ‘pw_bk.Rmd’ using rmarkdown
[2023-02-24 10:00:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-24 10:00:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 10:00:52] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-02-24 10:00:52] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-02-24 10:00:52] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-02-24 10:00:52] [TRACE] [OmnipathR] Contains 1 files.
[2023-02-24 10:00:52] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-02-24 10:00:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-24 10:00:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 10:00:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-02-24 10:00:52] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-02-24 10:00:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-02-24 10:00:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 10:00:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-02-24 10:00:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 10:00:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-02-24 10:00:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 10:00:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-02-24 10:00:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 10:00:52] [TRACE] [OmnipathR] Cache locked: FALSE
[2023-02-24 10:00:54] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-02-24 10:00:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 10:00:56] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-02-24 10:00:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 10:00:56] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-02-24 10:00:56] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-02-24 10:00:56] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-02-24 10:00:57] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` (attempt 1/3); error: HTTP error 500.
[2023-02-24 10:01:02] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-02-24 10:01:03] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` (attempt 2/3); error: HTTP error 500.
[2023-02-24 10:01:08] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-02-24 10:01:09] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` (attempt 3/3); error: HTTP error 500.
Quitting from lines 101-103 (pw_bk.Rmd)
Error: processing vignette 'pw_bk.Rmd' failed with diagnostics:
HTTP error 500.
--- failed re-building ‘pw_bk.Rmd’
--- re-building ‘pw_sc.Rmd’ using rmarkdown
[2023-02-24 10:01:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-24 10:01:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 10:01:41] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-02-24 10:01:41] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-02-24 10:01:41] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-02-24 10:01:41] [TRACE] [OmnipathR] Contains 1 files.
[2023-02-24 10:01:41] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-02-24 10:01:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-24 10:01:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 10:01:41] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-02-24 10:01:41] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-02-24 10:01:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-02-24 10:01:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 10:01:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-02-24 10:01:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 10:01:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-02-24 10:01:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 10:01:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-02-24 10:01:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 10:01:41] [TRACE] [OmnipathR] Cache locked: FALSE
[2023-02-24 10:01:43] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-02-24 10:01:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 10:01:45] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-02-24 10:01:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 10:01:56] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-02-24 10:01:56] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-02-24 10:01:56] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-02-24 10:01:57] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` (attempt 1/3); error: HTTP error 500.
[2023-02-24 10:02:02] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-02-24 10:02:03] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` (attempt 2/3); error: HTTP error 500.
[2023-02-24 10:02:08] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-02-24 10:02:09] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` (attempt 3/3); error: HTTP error 500.
Quitting from lines 78-80 (pw_sc.Rmd)
Error: processing vignette 'pw_sc.Rmd' failed with diagnostics:
HTTP error 500.
--- failed re-building ‘pw_sc.Rmd’
--- re-building ‘tf_bk.Rmd’ using rmarkdown
[2023-02-24 10:02:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-24 10:02:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 10:02:13] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-02-24 10:02:13] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-02-24 10:02:13] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-02-24 10:02:13] [TRACE] [OmnipathR] Contains 1 files.
[2023-02-24 10:02:13] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-02-24 10:02:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-24 10:02:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 10:02:13] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-02-24 10:02:13] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-02-24 10:02:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-02-24 10:02:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 10:02:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-02-24 10:02:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 10:02:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-02-24 10:02:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 10:02:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-02-24 10:02:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 10:02:13] [TRACE] [OmnipathR] Cache locked: FALSE
[2023-02-24 10:02:13] [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`
[2023-02-24 10:02:13] [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`
[2023-02-24 10:02:13] [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`
[2023-02-24 10:02:15] [WARN] [OmnipathR] Failed to download `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` (attempt 1/3); error: HTTP error 500.
[2023-02-24 10:02:20] [TRACE] [OmnipathR] Attempt 2/3: `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`
[2023-02-24 10:02:20] [WARN] [OmnipathR] Failed to download `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` (attempt 2/3); error: HTTP error 500.
[2023-02-24 10:02:25] [TRACE] [OmnipathR] Attempt 3/3: `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`
[2023-02-24 10:02:26] [ERROR] [OmnipathR] Failed to download `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` (attempt 3/3); error: HTTP error 500.
Quitting from lines 107-109 (tf_bk.Rmd)
Error: processing vignette 'tf_bk.Rmd' failed with diagnostics:
HTTP error 500.
--- failed re-building ‘tf_bk.Rmd’
--- re-building ‘tf_sc.Rmd’ using rmarkdown
[2023-02-24 10:02:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-24 10:02:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 10:02:46] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-02-24 10:02:46] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-02-24 10:02:46] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-02-24 10:02:46] [TRACE] [OmnipathR] Contains 1 files.
[2023-02-24 10:02:46] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-02-24 10:02:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-24 10:02:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 10:02:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-02-24 10:02:46] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-02-24 10:02:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-02-24 10:02:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 10:02:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-02-24 10:02:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 10:02:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-02-24 10:02:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 10:02:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-02-24 10:02:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 10:02:46] [TRACE] [OmnipathR] Cache locked: FALSE
[2023-02-24 10:02:47] [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`
[2023-02-24 10:02:47] [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`
[2023-02-24 10:02:47] [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`
[2023-02-24 10:02:48] [WARN] [OmnipathR] Failed to download `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` (attempt 1/3); error: HTTP error 500.
[2023-02-24 10:02:53] [TRACE] [OmnipathR] Attempt 2/3: `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`
[2023-02-24 10:02:53] [WARN] [OmnipathR] Failed to download `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` (attempt 2/3); error: HTTP error 500.
[2023-02-24 10:02:58] [TRACE] [OmnipathR] Attempt 3/3: `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`
[2023-02-24 10:03:00] [ERROR] [OmnipathR] Failed to download `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` (attempt 3/3); error: HTTP error 500.
Quitting from lines 84-86 (tf_sc.Rmd)
Error: processing vignette 'tf_sc.Rmd' failed with diagnostics:
HTTP error 500.
--- failed re-building ‘tf_sc.Rmd’
SUMMARY: processing the following files failed:
‘pw_bk.Rmd’ ‘pw_sc.Rmd’ ‘tf_bk.Rmd’ ‘tf_sc.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 3 ERRORs, 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/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) (2023-01-14 r83615) -- "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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[2023-02-24 09:57:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-24 09:57:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 09:57:58] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-02-24 09:57:58] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-02-24 09:57:58] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-02-24 09:57:58] [TRACE] [OmnipathR] Contains 1 files.
[2023-02-24 09:57:58] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-02-24 09:57:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-24 09:57:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 09:57:58] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-02-24 09:57:58] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-02-24 09:57:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-02-24 09:57:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 09:57:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-02-24 09:57:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 09:57:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-02-24 09:57:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 09:57:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-02-24 09:57:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 09:57:58] [TRACE] [OmnipathR] Cache locked: FALSE
[2023-02-24 09:58:00] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-02-24 09:58:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 09:58:02] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-02-24 09:58:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 09:58:03] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-02-24 09:58:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 09:58:04] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2023-02-24 09:58:04] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2023-02-24 09:58:04] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2023-02-24 09:58:04] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` (attempt 1/3); error: HTTP error 500.
[2023-02-24 09:58:09] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2023-02-24 09:58:13] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` (attempt 2/3); error: HTTP error 500.
[2023-02-24 09:58:18] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2023-02-24 09:58:18] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` (attempt 3/3); error: HTTP error 500.
[2023-02-24 09:58:22] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-02-24 09:58:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 09:58:23] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-02-24 09:58:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 09:58:23] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-02-24 09:58:23] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-02-24 09:58:23] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-02-24 09:58:24] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` (attempt 1/3); error: HTTP error 500.
[2023-02-24 09:58:29] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-02-24 09:58:30] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` (attempt 2/3); error: HTTP error 500.
[2023-02-24 09:58:35] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-02-24 09:58:36] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` (attempt 3/3); error: HTTP error 500.
[2023-02-24 09:58:38] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-02-24 09:58:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 09:58:41] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2023-02-24 09:58:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-24 09:58:41] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-02-24 09:58:41] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-02-24 09:58:41] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-02-24 09:58:45] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` (attempt 1/3); error: GnuTLS recv error (-110): The TLS connection was non-properly terminated.
[2023-02-24 09:58:50] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-02-24 09:58:51] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` (attempt 2/3); error: HTTP error 500.
[2023-02-24 09:58:56] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2023-02-24 09:58:57] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` (attempt 3/3); error: HTTP error 500.
[2023-02-24 09:58:57] [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`
[2023-02-24 09:58:57] [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`
[2023-02-24 09:58:57] [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`
[2023-02-24 09:58:57] [WARN] [OmnipathR] Failed to download `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` (attempt 1/3); error: HTTP error 500.
[2023-02-24 09:59:02] [TRACE] [OmnipathR] Attempt 2/3: `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`
[2023-02-24 09:59:03] [WARN] [OmnipathR] Failed to download `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` (attempt 2/3); error: HTTP error 500.
[2023-02-24 09:59:08] [TRACE] [OmnipathR] Attempt 3/3: `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`
[2023-02-24 09:59:09] [ERROR] [OmnipathR] Failed to download `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` (attempt 3/3); error: HTTP error 500.
[2023-02-24 09:59:09] [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`
[2023-02-24 09:59:09] [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`
[2023-02-24 09:59:09] [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`
[2023-02-24 09:59:10] [WARN] [OmnipathR] Failed to download `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` (attempt 1/3); error: HTTP error 500.
[2023-02-24 09:59:15] [TRACE] [OmnipathR] Attempt 2/3: `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`
[2023-02-24 09:59:16] [WARN] [OmnipathR] Failed to download `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` (attempt 2/3); error: HTTP error 500.
[2023-02-24 09:59:21] [TRACE] [OmnipathR] Attempt 3/3: `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`
[2023-02-24 09:59:22] [ERROR] [OmnipathR] Failed to download `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` (attempt 3/3); error: HTTP error 500.
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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 6 | WARN 324 | SKIP 0 | PASS 29 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-omnipath.R:9'): test get_resource ──────────────────────────────
Error in `open.connection(structure(6L, class = c("curl", "connection"), conn_id = <pointer: 0x88c>),
"rb")`: HTTP error 500.
Backtrace:
▆
1. ├─decoupleR::get_resource("TFcensus") at test-omnipath.R:9:2
2. │ ├─... %>% OmnipathR::pivot_annotations(.)
3. │ └─OmnipathR::import_omnipath_annotations(resources = name)
4. │ └─OmnipathR:::import_omnipath(...)
5. │ ├─base::do.call(omnipath_download, download_args)
6. │ └─OmnipathR (local) `<fn>`(...)
7. │ └─OmnipathR:::download_base(url, fun, ...)
8. ├─OmnipathR::pivot_annotations(.)
9. │ └─annotations %>% pull(source) %>% unique %>% length %>% ...
10. ├─base::unique(.)
11. └─dplyr::pull(., source)
── Error ('test-omnipath.R:14'): test get_progeny human ────────────────────────
Error in `open.connection(structure(9L, class = c("curl", "connection"), conn_id = <pointer: 0x8b6>),
"rb")`: HTTP error 500.
Backtrace:
▆
1. ├─decoupleR::get_progeny(organism = "human") at test-omnipath.R:14:2
2. │ ├─... %>% ...
3. │ └─decoupleR::get_resource("PROGENy")
4. │ ├─... %>% OmnipathR::pivot_annotations(.)
5. │ └─OmnipathR::import_omnipath_annotations(resources = name)
6. │ └─OmnipathR:::import_omnipath(...)
7. │ ├─base::do.call(omnipath_download, download_args)
8. │ └─OmnipathR (local) `<fn>`(...)
9. │ └─OmnipathR:::download_base(url, fun, ...)
10. ├─dplyr::select(...)
11. ├─dplyr::bind_rows(.)
12. │ └─rlang::list2(...)
13. ├─purrr::map(...)
14. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
15. │ └─purrr:::vctrs_vec_compat(.x, .purrr_user_env)
16. ├─dplyr::group_split(.)
17. ├─dplyr::group_by(., .data$pathway)
18. ├─dplyr::select(...)
19. ├─dplyr::mutate(., weight = as.double(.data$weight), p_value = as.double(.data$p_value))
20. ├─dplyr::distinct(., .data$pathway, .data$genesymbol, .keep_all = TRUE)
21. ├─OmnipathR::pivot_annotations(.)
22. │ └─annotations %>% pull(source) %>% unique %>% length %>% ...
23. ├─base::unique(.)
24. └─dplyr::pull(., source)
── Error ('test-omnipath.R:19'): test get_progeny mouse ────────────────────────
Error in `open.connection(structure(12L, class = c("curl", "connection"
), conn_id = <pointer: 0x8e0>), "rb")`: HTTP error 500.
Backtrace:
▆
1. ├─decoupleR::get_progeny(organism = "mouse") at test-omnipath.R:19:2
2. │ ├─... %>% ...
3. │ └─decoupleR::get_resource("PROGENy")
4. │ ├─... %>% OmnipathR::pivot_annotations(.)
5. │ └─OmnipathR::import_omnipath_annotations(resources = name)
6. │ └─OmnipathR:::import_omnipath(...)
7. │ ├─base::do.call(omnipath_download, download_args)
8. │ └─OmnipathR (local) `<fn>`(...)
9. │ └─OmnipathR:::download_base(url, fun, ...)
10. ├─dplyr::select(...)
11. ├─dplyr::bind_rows(.)
12. │ └─rlang::list2(...)
13. ├─purrr::map(...)
14. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
15. │ └─purrr:::vctrs_vec_compat(.x, .purrr_user_env)
16. ├─dplyr::group_split(.)
17. ├─dplyr::group_by(., .data$pathway)
18. ├─dplyr::select(...)
19. ├─dplyr::mutate(., weight = as.double(.data$weight), p_value = as.double(.data$p_value))
20. ├─dplyr::distinct(., .data$pathway, .data$genesymbol, .keep_all = TRUE)
21. ├─OmnipathR::pivot_annotations(.)
22. │ └─annotations %>% pull(source) %>% unique %>% length %>% ...
23. ├─base::unique(.)
24. └─dplyr::pull(., source)
── Error ('test-omnipath.R:24'): test get_dorothea human ───────────────────────
Error in `open.connection(structure(15L, class = c("curl", "connection"
), conn_id = <pointer: 0x8fb>), "rb")`: HTTP error 500.
Backtrace:
▆
1. ├─decoupleR::get_dorothea(organism = "human") at test-omnipath.R:24:2
2. │ ├─... %>% ...
3. │ └─OmnipathR::import_dorothea_interactions(...)
4. │ └─OmnipathR:::import_omnipath(...)
5. │ ├─base::do.call(omnipath_download, download_args)
6. │ └─OmnipathR (local) `<fn>`(...)
7. │ └─OmnipathR:::download_base(url, fun, ...)
8. ├─dplyr::select(...)
9. ├─dplyr::mutate(...)
10. ├─dplyr::mutate(...)
11. ├─dplyr::mutate(...)
12. ├─dplyr::distinct(...)
13. └─dplyr::select(...)
── Error ('test-omnipath.R:29'): test get_dorothea mouse ───────────────────────
Error in `open.connection(structure(18L, class = c("curl", "connection"
), conn_id = <pointer: 0x916>), "rb")`: HTTP error 500.
Backtrace:
▆
1. ├─decoupleR::get_dorothea(organism = "mouse") at test-omnipath.R:29:2
2. │ ├─... %>% ...
3. │ └─OmnipathR::import_dorothea_interactions(...)
4. │ └─OmnipathR:::import_omnipath(...)
5. │ ├─base::do.call(omnipath_download, download_args)
6. │ └─OmnipathR (local) `<fn>`(...)
7. │ └─OmnipathR:::download_base(url, fun, ...)
8. ├─dplyr::select(...)
9. ├─dplyr::mutate(...)
10. ├─dplyr::mutate(...)
11. ├─dplyr::mutate(...)
12. ├─dplyr::distinct(...)
13. └─dplyr::select(...)
── Failure ('test-statistic-fgsea.R:26'): 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$p_value[1:7]`: 0.075 0.075 0.512 0.512 0.010 0.010 0.076
`expected$p_value[1:7]`: 0.075 0.075 0.548 0.548 0.010 0.010 0.076
actual$p_value | expected$p_value
[12] 0.010 | 0.010 [12]
[13] 0.114 | 0.114 [13]
[14] 0.114 | 0.114 [14]
[15] 0.511 - 0.522 [15]
[16] 0.511 - 0.522 [16]
[17] 0.010 | 0.010 [17]
[18] 0.010 | 0.010 [18]
[19] 0.005 | 0.005 [19]
[20] 0.005 | 0.005 [20]
[21] 0.219 - 0.295 [21]
... ... ... and 10 more ...
`actual$p_value[34:41]`: 1.000 0.010 0.010 0.092 0.092 0.592 0.592 0.010
`expected$p_value[34:41]`: 1.000 0.010 0.010 0.104 0.104 0.592 0.592 0.010
actual$p_value | expected$p_value
[52] 0.977 | 0.977 [52]
[53] 0.010 | 0.010 [53]
[54] 0.010 | 0.010 [54]
[55] 0.067 - 0.076 [55]
[56] 0.067 - 0.076 [56]
[57] 0.592 | 0.592 [57]
[58] 0.592 | 0.592 [58]
[59] 0.010 | 0.010 [59]
[60] 0.010 | 0.010 [60]
[61] 0.111 - 0.108 [61]
... ... ... and 4 more ...
actual$p_value | expected$p_value
[70] 1.000 | 1.000 [70]
[71] 0.010 | 0.010 [71]
[72] 0.010 | 0.010 [72]
[73] 0.257 - 0.470 [73]
[74] 0.257 - 0.470 [74]
[75] 0.134 - 0.132 [75]
[76] 0.134 - 0.132 [76]
[77] 0.123 | 0.123 [77]
[78] 0.123 | 0.123 [78]
[79] 0.147 - 0.208 [79]
... ... ... and 4 more ...
actual$p_value | expected$p_value
[88] 0.178 | 0.178 [88]
[89] 0.154 | 0.154 [89]
[90] 0.154 | 0.154 [90]
[91] 0.435 - 0.487 [91]
[92] 0.435 - 0.487 [92]
[93] 0.009 | 0.009 [93]
[94] 0.009 | 0.009 [94]
[95] 0.005 | 0.005 [95]
[96] 0.005 | 0.005 [96]
[97] 0.295 - 0.493 [97]
... ... ... and 4 more ...
`actual$p_value[106:113]`: 0.199 0.214 0.214 0.874 0.874 0.187 0.187 0.180
`expected$p_value[106:113]`: 0.199 0.214 0.214 0.944 0.944 0.187 0.187 0.180
actual$p_value | expected$p_value
[118] 0.126 | 0.126 [118]
[119] 0.112 | 0.112 [119]
[120] 0.112 | 0.112 [120]
[121] 0.991 - 1.000 [121]
[122] 0.991 - 1.000 [122]
[123] 0.123 - 0.126 [123]
[124] 0.123 - 0.126 [124]
[125] 0.156 | 0.156 [125]
[126] 0.156 | 0.156 [126]
[127] 0.592 | 0.592 [127]
`actual$p_value[132:139]`: 0.125 0.592 0.592 0.175 0.175 0.198 0.198 0.592
`expected$p_value[132:139]`: 0.125 0.592 0.592 0.184 0.184 0.198 0.198 0.592
[ FAIL 6 | WARN 324 | SKIP 0 | PASS 29 ]
Error: Test failures
Execution halted
decoupleR.Rcheck/decoupleR-Ex.timings
| name | user | system | elapsed | |
| check_corr | 0.185 | 0.008 | 0.193 | |
| convert_f_defaults | 0.066 | 0.008 | 0.073 | |
| decouple | 0.001 | 0.000 | 0.001 | |
| dot-fit_preprocessing | 0.037 | 0.004 | 0.042 | |
| extract_sets | 0.044 | 0.000 | 0.045 | |
| filt_minsize | 0.096 | 0.000 | 0.096 | |