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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.16.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 35 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘OmnipathR’ can be installed ... OK
* 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
[2025-05-27 07:51:51] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 07:51:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 07:51:51] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-05-27 07:51:51] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-05-27 07:51:51] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-05-26
[2025-05-27 07:51:51] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-26 19:58:37 UTC; unix
[2025-05-27 07:51:51] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-05-27 07:51:51] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-05-27 07:51:52] [INFO]    [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-05-27; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-05-27 07:51:52] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-05-27 07:51:53] [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 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.2.3(2025-05-24); 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 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); 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 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); 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 3.16.0(2025-05-26); pillar 1.10.2(2025-04-05); 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 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); 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 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.11(2025-05-04); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); 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 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-05-27 07:51:53] [INFO]    [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-05-27 07:51:53] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-27 07:51:53] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-05-27 07:51:53] [TRACE]   [OmnipathR] Contains 1 files.
[2025-05-27 07:51:53] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-27 07:51:53] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 07:51:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 07:51:53] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-05-27 07:51:53] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-05-27 07:51:53] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-27 07:51:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 07:51:53] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-27 07:51:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 07:51:53] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-27 07:51:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 07:51:53] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-27 07:51:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 07:51:53] [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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2025-05-27 07:52:37] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 07:52:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 07:52:37] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-05-27 07:52:37] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-05-27 07:52:37] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-05-26
[2025-05-27 07:52:37] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-26 19:58:37 UTC; unix
[2025-05-27 07:52:37] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-05-27 07:52:37] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-05-27 07:52:38] [INFO]    [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-05-27; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-05-27 07:52:39] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-05-27 07:52:39] [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 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.2.3(2025-05-24); 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 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); 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 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); 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 3.16.0(2025-05-26); pillar 1.10.2(2025-04-05); 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 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); 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 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.11(2025-05-04); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); 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 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-05-27 07:52:39] [INFO]    [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-05-27 07:52:39] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-27 07:52:39] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-05-27 07:52:39] [TRACE]   [OmnipathR] Contains 1 files.
[2025-05-27 07:52:39] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-27 07:52:39] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 07:52:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 07:52:39] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-05-27 07:52:39] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-05-27 07:52:39] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-27 07:52:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 07:52:39] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-27 07:52:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 07:52:39] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-27 07:52:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 07:52:39] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-27 07:52:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 07:52:39] [TRACE]   [OmnipathR] Cache locked: FALSE
* 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 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: ensembl_id_mapping_table
> ### Title: Identifier translation table from Ensembl
> ### Aliases: ensembl_id_mapping_table
> 
> ### ** Examples
> 
> ensp_up <- ensembl_id_mapping_table("ensp")
[2025-05-27 07:59:54] [TRACE]   [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `ensembl_peptide_id`, for organism hsapiens
[2025-05-27 07:59:54] [TRACE]   [OmnipathR] BioMart query: <?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query  virtualSchemaName="default" formatter="TSV" header="0" uniqueRows="0" count="" datasetConfigVersion="0.6" completionStamp="1" >
    <Dataset name="hsapiens_gene_ensembl" interface="default" >
        <Attribute name="uniprotswissprot"/>
        <Attribute name="ensembl_peptide_id"/>
    </Dataset>
</Query>
[2025-05-27 07:59:54] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-05-27 07:59:54] [TRACE]   [OmnipathR] Looking up in cache: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2025-05-27 07:59:54] [INFO]    [OmnipathR] Cache record does not exist: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2025-05-27 07:59:54] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2025-05-27 07:59:54] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 07:59:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 07:59:54] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 07:59:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 07:59:54] [INFO]    [OmnipathR] Cache item `5146291739ab7fee3dd9b2830721d4357888383d` version 1: status changed from `unknown` to `started`.
[2025-05-27 07:59:54] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/5146291739ab7fee3dd9b2830721d4357888383d-1.rds`.
[2025-05-27 07:59:55] [INFO]    [OmnipathR] Retrieving URL: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2025-05-27 07:59:55] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-05-27 07:59:55] [TRACE]   [OmnipathR] Attempt 1/3: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2025-05-27 07:59:55] [TRACE]   [OmnipathR] Preparing httr2 request to URL `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2025-05-27 07:59:55] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-27 07:59:55] [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]
[2025-05-27 07:59:55] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-27 07:59:55] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-27 07:59:55] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-05-27 07:59:55] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-05-27 07:59:55] [TRACE]   [OmnipathR] Downloaded 1014 bytes in 0.185869s from www.ensembl.org (5.3 Kb/s); Redirect: 0s, DNS look up: 0.005784s, Connection: 0.094388s, Pretransfer: 0.094527s, First byte at: 0.185728s
[2025-05-27 07:59:55] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; X-GitHub-Request-Id: A8A3:39575D:C18216:C240AC:68344FD7; Server: GitHub.com; X-Cache-Hits: 15; Vary: Accept-Encoding; Cache-Control: no-cache, no-store, must-revalidate; x-proxy-cache: MISS; X-Cache: HIT; Content-Type: text/html; charset=utf-8; X-Fastly-Request-ID: b2f386aacfbf47eb2bfe8e51e8bc360495b21b0a; Content-Encoding: gzip; Date: Tue, 27 May 2025 11:59:55 GMT; Expires: 0; X-Served-By: cache-lcy-eglc8600038-LCY; Pragma: no-cache; X-Timer: S1748347195.283783,VS0,VE1; Access-Control-Allow-Origin: *; Accept-Ranges: bytes; ETag: W/"681dc811-8aa"; Via: 1.1 varnish; Connection: keep-alive; Age: 341; Content-Length: 1014
[2025-05-27 07:59:55] [TRACE]   [OmnipathR] Response headers: [X-GitHub-Request-Id=A8A3:39575D:C18216:C240AC:68344FD7,Server=GitHub.com,X-Cache-Hits=15,Vary=Accept-Encoding,Cache-Control=no-cache, no-store, must-revalidate,x-proxy-cache=MISS,X-Cache=HIT,Content-Type=text/html; charset=utf-8,X-Fastly-Request-ID=b2f386aacfbf47eb2bfe8e51e8bc360495b21b0a,Content-Encoding=gzip,Date=Tue, 27 May 2025 11:59:55 GMT,Expires=0,X-Served-By=cache-lcy-eglc8600038-LCY,Pragma=no-cache,X-Timer=S1748347195.283783,VS0,VE1,Access-Control-Allow-Origin=*,Accept-Ranges=bytes,ETag=W/"681dc811-8aa",Via=1.1 varnish,Connection=keep-alive,Age=341,Content-Length=1014]
[2025-05-27 07:59:55] [TRACE]   [OmnipathR] Calling reader callback on response.
[2025-05-27 07:59:55] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/5146291739ab7fee3dd9b2830721d4357888383d-1.rds`.
[2025-05-27 07:59:55] [INFO]    [OmnipathR] Download ready [key=5146291739ab7fee3dd9b2830721d4357888383d, version=1]
[2025-05-27 07:59:55] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-27 07:59:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-27 07:59:55] [INFO]    [OmnipathR] Cache item `5146291739ab7fee3dd9b2830721d4357888383d` version 1: status changed from `started` to `ready`.
[2025-05-27 07:59:55] [WARN]    [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message!
[2025-05-27 07:59:55] [WARN]    [OmnipathR] <html>
[2025-05-27 07:59:55] [WARN]    [OmnipathR] <head>
[2025-05-27 07:59:55] [WARN]    [OmnipathR] <title>Service unavailable</title>
[2025-05-27 07:59:55] [WARN]    [OmnipathR] <meta name="robots" content="noindex">
[2025-05-27 07:59:55] [WARN]    [OmnipathR] <base href="//status.ensembl.org">
[2025-05-27 07:59:55] [WARN]    [OmnipathR] <style>
[2025-05-27 07:59:55] [WARN]    [OmnipathR] html,
[2025-05-27 07:59:55] [WARN]    [OmnipathR] body {
[2025-05-27 07:59:55] [WARN]    [OmnipathR] padding: 0;
[2025-05-27 07:59:55] [WARN]    [OmnipathR] margin: 0;
[2025-05-27 07:59:55] [WARN]    [OmnipathR] height: 100%;
[2025-05-27 07:59:55] [WARN]    [OmnipathR] }
[2025-05-27 07:59:55] [WARN]    [OmnipathR] body {
[2025-05-27 07:59:55] [WARN]    [OmnipathR] display: grid;
[2025-05-27 07:59:55] [WARN]    [OmnipathR] grid-template-rows: [header] auto [main] 1fr [footer] auto;
[2025-05-27 07:59:55] [WARN]    [OmnipathR] font-family: Luxi Sans, Helvetica, Arial, Geneva, sans-serif;
[2025-05-27 07:59:55] [WARN]    [OmnipathR] font-size: 90%;
[2025-05-27 07:59:55] [WARN]    [OmnipathR] }
[2025-05-27 07:59:55] [WARN]    [OmnipathR] h1 {
[2025-05-27 07:59:55] [WARN]    [OmnipathR] font-size: 1.5rem;
[2025-05-27 07:59:55] [WARN]    [OmnipathR] }
[2025-05-27 07:59:55] [WARN]    [OmnipathR] h2 {
[2025-05-27 07:59:55] [WARN]    [OmnipathR] font-size: 1.2rem;
[2025-05-27 07:59:55] [WARN]    [OmnipathR] }
[2025-05-27 07:59:55] [WARN]    [OmnipathR] h3 {
[2025-05-27 07:59:55] [WARN]    [OmnipathR] font-size: 1.1rem;
[2025-05-27 07:59:55] [WARN]    [OmnipathR] }
[2025-05-27 07:59:55] [WARN]    [OmnipathR] header {
[2025-05-27 07:59:55] [WARN]    [OmnipathR] grid-row: header;
[2025-05-27 07:59:55] [WARN]    [OmnipathR] padding: 5px;
[2025-05-27 07:59:55] [WARN]    [OmnipathR] height: 60px;
[2025-05-27 07:59:55] [WARN]    [OmnipathR] background-color: #333366;
[2025-05-27 07:59:55] [WARN]    [OmnipathR] }
[2025-05-27 07:59:55] [WARN]    [OmnipathR] header img {
[2025-05-27 07:59:55] [WARN]    [OmnipathR] width: 185px;
[2025-05-27 07:59:55] [WARN]    [OmnipathR] height: 45px
[2025-05-27 07:59:55] [WARN]    [OmnipathR] }
[2025-05-27 07:59:55] [WARN]    [OmnipathR] main {
[2025-05-27 07:59:55] [WARN]    [OmnipathR] grid-row: main;
[2025-05-27 07:59:55] [WARN]    [OmnipathR] padding: 20px;
[2025-05-27 07:59:55] [WARN]    [OmnipathR] }
[2025-05-27 07:59:55] [WARN]    [OmnipathR] .mirrors {
[2025-05-27 07:59:55] [WARN]    [OmnipathR] border: solid 1px #ccc;
[2025-05-27 07:59:55] [WARN]    [OmnipathR] margin-top: 20px;
[2025-05-27 07:59:55] [WARN]    [OmnipathR] padding: 10px;
[2025-05-27 07:59:55] [WARN]    [OmnipathR] }
[2025-05-27 07:59:55] [WARN]    [OmnipathR] footer {
[2025-05-27 07:59:55] [WARN]    [OmnipathR] grid-row: footer;
[2025-05-27 07:59:55] [WARN]    [OmnipathR] padding: 0 20px;
[2025-05-27 07:59:55] [WARN]    [OmnipathR] }
[2025-05-27 07:59:55] [WARN]    [OmnipathR] </style>
[2025-05-27 07:59:55] [WARN]    [OmnipathR] </head>
[2025-05-27 07:59:55] [WARN]    [OmnipathR] <body>
[2025-05-27 07:59:55] [WARN]    [OmnipathR] <header>
[2025-05-27 07:59:55] [WARN]    [OmnipathR] <img src="/e-ensembl.png" alt="ensembl-logo" />
[2025-05-27 07:59:55] [WARN]    [OmnipathR] </header>
[2025-05-27 07:59:55] [WARN]    [OmnipathR] <main>
[2025-05-27 07:59:55] [WARN]    [OmnipathR] <h1>Server Status</h1>
[2025-05-27 07:59:55] [WARN]    [OmnipathR] <p>
[2025-05-27 07:59:55] [WARN]    [OmnipathR] <img src="/exclamation_alert.png" alt="[!]" style="float:left;padding:0 10px;width:100px;height:89px" />
[2025-05-27 07:59:55] [WARN]    [OmnipathR] The Ensembl web service you requested is temporarily unavailable.
[2025-05-27 07:59:55] [WARN]    [OmnipathR] We are working to restore the service as soon as possible, and apologise for any inconvenience caused.
[2025-05-27 07:59:55] [WARN]    [OmnipathR] </p>
[2025-05-27 07:59:55] [WARN]    [OmnipathR] <p>For all enquiries, please <a href="https://www.ensembl.info/contact-us/">contact our HelpDesk</a>.</p>
[2025-05-27 07:59:55] [WARN]    [OmnipathR] <div class="mirrors">
[2025-05-27 07:59:55] [WARN]    [OmnipathR] <h3>Ensembl mirrors</h3>
[2025-05-27 07:59:55] [WARN]    [OmnipathR] We now also manage two mirrors of the Ensembl website, hosted in different regions of the Amazon cloud:
[2025-05-27 07:59:55] [WARN]    [OmnipathR] <ul>
[2025-05-27 07:59:55] [WARN]    [OmnipathR] <li><a href="https://useast.ensembl.org/index.html?redirect=no">useast.ensembl.org</a></li>
[2025-05-27 07:59:55] [WARN]    [OmnipathR] <li><a href="https://asia.ensembl.org/index.html?redirect=no">asia.ensembl.org</a></li>
[2025-05-27 07:59:55] [WARN]    [OmnipathR] </ul>
[2025-05-27 07:59:55] [WARN]    [OmnipathR] These will be available while the main service is unavailable, although please note that some of the
[2025-05-27 07:59:55] [WARN]    [OmnipathR] facilities on these mirror may not be fully functional as they rely on resources hosted at our main
[2025-05-27 07:59:55] [WARN]    [OmnipathR] data centre.
[2025-05-27 07:59:55] [WARN]    [OmnipathR] </div>
[2025-05-27 07:59:55] [WARN]    [OmnipathR] </main>
[2025-05-27 07:59:55] [WARN]    [OmnipathR] <footer>
[2025-05-27 07:59:55] [WARN]    [OmnipathR] <p>&copy; 2025 EMBL-EBI</p>
[2025-05-27 07:59:55] [WARN]    [OmnipathR] </footer>
[2025-05-27 07:59:55] [WARN]    [OmnipathR] </body>
[2025-05-27 07:59:55] [WARN]    [OmnipathR] </html>
[2025-05-27 07:59:55] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 81 records
Error in `set_names()`:
! The size of `nm` (2) must be compatible with the size of `x` (1).
Backtrace:
    ▆
 1. ├─OmnipathR::ensembl_id_mapping_table("ensp")
 2. │ └─... %>% trim_and_distinct
 3. ├─OmnipathR:::trim_and_distinct(.)
 4. │ └─d %>% mutate(across(everything(), str_trim)) %>% distinct
 5. ├─dplyr::distinct(.)
 6. ├─dplyr::mutate(., across(everything(), str_trim))
 7. ├─rlang::set_names(., c("From", "To"))
 8. └─rlang::abort(message = message)
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                                       user system elapsed
annotation_categories                91.693  0.403  94.873
curated_ligrec_stats                 66.772  6.798 129.099
curated_ligand_receptor_interactions 11.642  1.772  21.273
all_uniprots                          2.476  0.386  62.286
annotated_network                     1.949  0.214   7.111
* 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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.