[ Started: 2025-02-16 00:18:49 CET ]
[ OmnipathR v3.15.9 for BioC-3.21 from https://github.com/saezlab/OmnipathR@devel (0a92537 2025-02-13 19:46:14) ]

* using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-16_0008/OmnipathR/OmnipathR.Rcheck’
* using R Under development (unstable) (2025-02-12 r87715)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.15.9’
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OmnipathR’ can be installed ... WARNING
Found the following significant warnings:
  Note: possible error in 'download_to_cache(url_key = url_key, ': unused argument (http_param = http_param) 
See ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-16_0008/OmnipathR/OmnipathR.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* checking installed package size ... INFO
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
* checking package 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 whether startup messages can be suppressed ... NOTE
[2025-02-16 00:19:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-16 00:19:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-16 00:19:16] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-16 00:19:16] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-15 23:17:45 UTC; omnipath
[2025-02-16 00:19:16] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-16 00:19:16] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-15 23:18:52 UTC; unix
[2025-02-16 00:19:16] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-16 00:19:16] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-16 00:19:16] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-02-16; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-16 00:19:16] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-02-16 00:19:16] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-02-16 00:19:16] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-16 00:19:16] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-16 00:19:16] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-16 00:19:16] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-16 00:19:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-16 00:19:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-16 00:19:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-16 00:19:16] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-16 00:19:16] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-16_0008/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-16 00:19:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-16 00:19:16] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-16_0008/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-16 00:19:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-16 00:19:16] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-16_0008/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-16 00:19:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-16 00:19:17] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-16_0008/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-16 00:19:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-16 00:19:17] [TRACE]   [OmnipathR] Cache locked: FALSE

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
ungroup:
  function(x, ...)
ungroup.tbl_attrs:
  function(.data, ...)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2025-02-16 00:19:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-16 00:19:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-16 00:19:26] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-16 00:19:26] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-15 23:17:45 UTC; omnipath
[2025-02-16 00:19:26] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-16 00:19:26] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-15 23:18:52 UTC; unix
[2025-02-16 00:19:26] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-16 00:19:26] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-16 00:19:26] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-12 r87715); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-02-16; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-16 00:19:26] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-02-16 00:19:26] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-02-16 00:19:26] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-16 00:19:26] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-16 00:19:26] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-16 00:19:26] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-16 00:19:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-16 00:19:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-16 00:19:26] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-16 00:19:26] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-16 00:19:26] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-16_0008/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-16 00:19:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-16 00:19:26] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-16_0008/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-16 00:19:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-16 00:19:26] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-16_0008/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-16 00:19:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-16 00:19:26] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-16_0008/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-16 00:19:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-16 00:19:26] [TRACE]   [OmnipathR] Cache locked: FALSE
ambiguity_summarize: no visible binding for global variable ‘data’
download_base : fun: no visible binding for global variable
  ‘resp_status_desc’
download_base : fun: no visible global function definition for
  ‘headers’
download_base : fun: no visible binding for global variable ‘response’
log_welcome: no visible binding for global variable ‘pkgname’
translate_ids : <anonymous>: no visible binding for global variable
  ‘From’
xls_downloader: possible error in download_to_cache(url_key = url_key,
  url_key_param = url_key_param, url_param = url_param, ext = ext,
  http_param = http_param, post = post): unused argument (http_param =
  http_param)
Undefined global functions or variables:
  From data headers pkgname resp_status_desc response
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
* 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 ... WARNING
Undocumented arguments in Rd file 'ambiguity.Rd'
  ‘from_col’ ‘to_col’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
'::' or ':::' import not declared from: ‘httr’
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:

> ### Name: interaction_datasets
> ### Title: Datasets in the OmniPath Interactions database
> ### Aliases: interaction_datasets
> 
> ### ** Examples
> 
> interaction_datasets()
[2025-02-16 00:27:00] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-02-16 00:27:00] [TRACE]   [OmnipathR] Orthology targets: 
[2025-02-16 00:27:00] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/queries/interactions?format=json&license=academic`
[2025-02-16 00:27:00] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/queries/interactions?format=json&license=academic`
[2025-02-16 00:27:00] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/queries/interactions?format=json&license=academic`
[2025-02-16 00:27:00] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/queries/interactions?format=json&license=academic`
[2025-02-16 00:27:00] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/queries/interactions?format=json&license=academic`
[2025-02-16 00:27:00] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/queries/interactions?format=json&license=academic`
[2025-02-16 00:27:00] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/queries/interactions?format=json&license=academic`
[2025-02-16 00:27:00] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-16 00:27:00] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-16 00:27:00] [TRACE]   [OmnipathR] Downloaded 3.9 Kb in 0.076147s from omnipathdb.org (51.2 Kb/s); Redirect: 0s, DNS look up: 0.00102s, Connection: 0.020589s, Pretransfer: 0.054017s, First byte at: 0.076129s
[2025-02-16 00:27:00] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/queries/interactions?format=json&license=academic`
[2025-02-16 00:27:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-16 00:27:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-16 00:27:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-16 00:27:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-16 00:27:00] [INFO]    [OmnipathR] Cache item `d4a3f6fd0083bc974e7269e2ff6b02df9633e303` version 1: status changed from `unknown` to `started`.
[2025-02-16 00:27:00] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d4a3f6fd0083bc974e7269e2ff6b02df9633e303-1.rds`.
[2025-02-16 00:27:00] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d4a3f6fd0083bc974e7269e2ff6b02df9633e303-1.rds`.
[2025-02-16 00:27:00] [INFO]    [OmnipathR] Download ready [key=d4a3f6fd0083bc974e7269e2ff6b02df9633e303, version=1]
[2025-02-16 00:27:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-16 00:27:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-16 00:27:00] [INFO]    [OmnipathR] Cache item `d4a3f6fd0083bc974e7269e2ff6b02df9633e303` version 1: status changed from `started` to `ready`.
Error in `map()`:
ℹ In index: 2.
ℹ With name: format.
Caused by error in `x[[key]]`:
! subscript out of bounds
Backtrace:
     ▆
  1. ├─OmnipathR::interaction_datasets()
  2. │ └─OmnipathR::query_info("interactions")
  3. │   └─query_type %>% sprintf("queries/%s", .) %>% ...
  4. ├─OmnipathR::omnipath_query(., format = "json")
  5. │ └─do.call(omnipath_download, download_args) %>% ...
  6. ├─OmnipathR:::omnipath_post_download(...)
  7. │ └─result %<>% deserialize_extra_attrs(!!!param$json_param)
  8. ├─OmnipathR:::deserialize_extra_attrs(., !!!param$json_param)
  9. │ └─data %>% deserialize_json_col("extra_attrs", ...)
 10. ├─OmnipathR:::deserialize_json_col(., "extra_attrs", ...)
 11. │ └─... %>% ...
 12. ├─purrr::map(., ~exec(json_in_list, .x, key = col, !!!fromjson_args))
 13. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
 14. │   ├─purrr:::with_indexed_errors(...)
 15. │   │ └─base::withCallingHandlers(...)
 16. │   ├─purrr:::call_with_cleanup(...)
 17. │   └─OmnipathR (local) .f(.x[[i]], ...)
 18. │     ├─rlang::exec(json_in_list, .x, key = col, !!!fromjson_args)
 19. │     └─OmnipathR (local) `<fn>`(`<chr>`, key = "extra_attrs", simplifyVector = FALSE)
 20. └─purrr (local) `<fn>`(`<sbscOOBE>`)
 21.   └─cli::cli_abort(...)
 22.     └─rlang::abort(...)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 4 WARNINGs, 2 NOTEs
See
  ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-02-16_0008/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.

[ Finished: 2025-02-16 00:36:01 CET ]