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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OmnipathR.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings OmnipathR_3.15.11.tar.gz
###
##############################################################################
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck'
* using R Under development (unstable) (2025-03-01 r87860 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'OmnipathR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'OmnipathR' version '3.15.11'
* 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 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 'E:/biocbuild/bbs-3.21-bioc/meat/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 ... OK
* 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 whether startup messages can be suppressed ... NOTE
[2025-03-22 04:13:46] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-22 04:13:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-22 04:13:46] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-03-22 04:13:46] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-03-22 04:13:46] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-03-21
[2025-03-22 04:13:46] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-21 19:28:28 UTC; windows
[2025-03-22 04:13:46] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.11
[2025-03-22 04:13:46] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-03-22 04:13:47] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-03-01 r87860 ucrt); os=Windows Server 2022 x64 (build 20348); system=x86_64, mingw32; ui=RTerm; language=(EN); collate=C; ctype=English_United States.utf8; tz=America/New_York; date=2025-03-22; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA]
[2025-03-22 04:13:47] [INFO]    [OmnipathR] External libraries: [cairo=1.18.2; cairoFT=; pango=; png=1.6.45; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.13; curl=8.11.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=76.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.0]
[2025-03-22 04:13:47] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.0(2025-03-21); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.1(2025-02-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.5(2024-10-30); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.1(2025-03-08); igraph 2.1.4(2025-01-23); jsonlite 1.9.1(2025-03-03); knitr 1.50(2025-03-16); later 1.4.1(2024-11-27); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.15.11(2025-03-21); pillar 1.10.1(2025-01-07); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.2(2024-11-28); ps 1.9.0(2025-02-18); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.5(2025-01-17); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.4(2024-05-06); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.2(2024-07-22); withr 3.0.2(2024-10-28); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-03-22 04:13:47] [INFO]    [OmnipathR] CURL: version: 8.10.1; headers: 8.10.1; ssl_version: (OpenSSL/3.4.0) Schannel; libz_version: 1.3; libssh_version: libssh2/1.11.0; libidn_version: NA; host: x86_64-w64-mingw32; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-03-22 04:13:47] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-22 04:13:47] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-03-22 04:13:47] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-22 04:13:47] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-22 04:13:47] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-22 04:13:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-22 04:13:47] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-03-22 04:13:47] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-22 04:13:47] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-22 04:13:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-22 04:13:47] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-22 04:13:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-22 04:13:47] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-22 04:13:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-22 04:13:47] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-22 04:13:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-22 04:13:47] [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
[2025-03-22 04:14:10] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-22 04:14:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-22 04:14:10] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-03-22 04:14:10] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-03-22 04:14:10] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-03-21
[2025-03-22 04:14:10] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-21 19:28:28 UTC; windows
[2025-03-22 04:14:10] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.11
[2025-03-22 04:14:10] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-03-22 04:14:11] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-03-01 r87860 ucrt); os=Windows Server 2022 x64 (build 20348); system=x86_64, mingw32; ui=RTerm; language=(EN); collate=C; ctype=English_United States.utf8; tz=America/New_York; date=2025-03-22; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA]
[2025-03-22 04:14:11] [INFO]    [OmnipathR] External libraries: [cairo=1.18.2; cairoFT=; pango=; png=1.6.45; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.13; curl=8.11.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=76.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.0]
[2025-03-22 04:14:12] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.0(2025-03-21); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.1(2025-02-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.5(2024-10-30); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.1(2025-03-08); igraph 2.1.4(2025-01-23); jsonlite 1.9.1(2025-03-03); knitr 1.50(2025-03-16); later 1.4.1(2024-11-27); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.15.11(2025-03-21); pillar 1.10.1(2025-01-07); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.2(2024-11-28); ps 1.9.0(2025-02-18); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.5(2025-01-17); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.4(2024-05-06); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.2(2024-07-22); withr 3.0.2(2024-10-28); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-03-22 04:14:12] [INFO]    [OmnipathR] CURL: version: 8.10.1; headers: 8.10.1; ssl_version: (OpenSSL/3.4.0) Schannel; libz_version: 1.3; libssh_version: libssh2/1.11.0; libidn_version: NA; host: x86_64-w64-mingw32; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-03-22 04:14:12] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-22 04:14:12] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-03-22 04:14:12] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-22 04:14:12] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-22 04:14:12] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-22 04:14:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-22 04:14:12] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-03-22 04:14:12] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-22 04:14:12] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-22 04:14:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-22 04:14:12] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-22 04:14:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-22 04:14:12] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-22 04:14:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-22 04:14:12] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-22 04:14:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-22 04:14:12] [TRACE]   [OmnipathR] Cache locked: FALSE
ambiguity_summarize: no visible binding for global variable 'data'
download_base : fun: no visible global function definition for
  'headers'
download_base : fun: no visible binding for global variable 'response'
inbiomap_cookie: no visible binding for global variable 'init_post'
inbiomap_cookie: no visible binding for global variable 'post'
inbiomap_cookie: no visible binding for global variable 'init_payload'
inbiomap_cookie: no visible binding for global variable 'payload'
inbiomap_cookie: no visible binding for global variable 'curl_verbose'
log_packages: no visible binding for global variable 'package'
log_packages: no visible binding for global variable 'loadedversion'
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 curl_verbose data headers init_payload init_post loadedversion
  package payload pkgname post 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 files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'OmnipathR-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: interaction_datasets
> ### Title: Datasets in the OmniPath Interactions database
> ### Aliases: interaction_datasets
> 
> ### ** Examples
> 
> interaction_datasets()
[2025-03-22 04:23:54] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-22 04:23:54] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-22 04:23:54] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/queries/interactions?format=json&license=academic`
[2025-03-22 04:23:54] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/queries/interactions?format=json&license=academic`
[2025-03-22 04:23:54] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/queries/interactions?format=json&license=academic`
[2025-03-22 04:23:54] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/queries/interactions?format=json&license=academic`
[2025-03-22 04:23:54] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/queries/interactions?format=json&license=academic`
[2025-03-22 04:23:54] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/queries/interactions?format=json&license=academic`
[2025-03-22 04:23:54] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/queries/interactions?format=json&license=academic`
[2025-03-22 04:23:54] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-22 04:23:54] [TRACE]   [OmnipathR] Downloaded 3.9 Kb in 0.264656s from omnipathdb.org (14.7 Kb/s); Redirect: 0s, DNS look up: 0.001736s, Connection: 0.085522s, Pretransfer: 0.179845s, First byte at: 0.264613s
[2025-03-22 04:23:55] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/queries/interactions?format=json&license=academic`
[2025-03-22 04:23:55] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-22 04:23:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-22 04:23:55] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-22 04:23:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-22 04:23:55] [INFO]    [OmnipathR] Cache item `d4a3f6fd0083bc974e7269e2ff6b02df9633e303` version 1: status changed from `unknown` to `started`.
[2025-03-22 04:23:55] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/d4a3f6fd0083bc974e7269e2ff6b02df9633e303-1.rds`.
[2025-03-22 04:23:55] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/d4a3f6fd0083bc974e7269e2ff6b02df9633e303-1.rds`.
[2025-03-22 04:23:55] [INFO]    [OmnipathR] Download ready [key=d4a3f6fd0083bc974e7269e2ff6b02df9633e303, version=1]
[2025-03-22 04:23:55] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-22 04:23:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-22 04:23:55] [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
Examples with CPU (user + system) or elapsed time > 5s
                                      user system elapsed
annotation_categories                75.63   0.03   76.37
curated_ligrec_stats                 36.29   1.67  102.86
filter_extra_attrs                   23.49   0.64   38.59
go_annot_download                    15.36   1.33   15.04
extra_attrs_to_cols                  15.73   0.29   19.59
extra_attr_values                    12.08   0.31   13.13
giant_component                      11.23   0.23   12.22
filter_by_resource                   10.39   0.44   13.63
extra_attrs                           8.05   0.18   17.07
has_extra_attrs                       7.50   0.13    7.77
filter_intercell                      6.53   0.52    7.06
curated_ligand_receptor_interactions  5.81   0.38   12.21
find_all_paths                        5.83   0.28    6.13
ensembl_id_mapping_table              1.86   0.09   71.40
all_uniprots                          1.48   0.06   22.51
biomart_query                         1.31   0.02   65.55
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 4 WARNINGs, 2 NOTEs
See
  'E:/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck/00check.log'
for details.