[ Started: 2025-03-04 00:17:37 CET ]
[ OmnipathR v3.15.11 for BioC-3.21 from https://github.com/saezlab/OmnipathR@devel (7c69da1 2025-02-25 22:51:58) ]

* using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-03-04_0007/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 ‘3.15.11’
* 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 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-3.21/2025-03-04_0007/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
[2025-03-04 00:18:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-04 00:18:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-04 00:18:05] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-03-04 00:18:05] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-03-03 23:16:32 UTC; omnipath
[2025-03-04 00:18:05] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-03-04 00:18:05] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-03 23:17:39 UTC; unix
[2025-03-04 00:18:05] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.11
[2025-03-04 00:18:05] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-03-04 00:18:05] [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=2025-03-04; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-03-04 00:18:05] [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]
[2025-03-04 00:18:05] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.5.0.1(2024-12-03); 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); 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 1.1.0(2025-01-18); igraph 2.1.4(2025-01-23); jsonlite 1.9.0(2025-02-19); knitr 1.49(2024-11-08); 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(2025-03-03); pillar 1.10.1(2025-01-07); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); 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 1.4.4(2025-02-27); 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 0.4.0(2023-05-12); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.7(2025-02-28); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-03-04 00:18:05] [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
[2025-03-04 00:18:05] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-04 00:18:05] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-03-04 00:18:05] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-04 00:18:05] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-04 00:18:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-04 00:18:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-04 00:18:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-03-04 00:18:05] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-03-04 00:18:05] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-03-04_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-04 00:18:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-04 00:18:05] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-03-04_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-04 00:18:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-04 00:18:05] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-03-04_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-04 00:18:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-04 00:18:05] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-03-04_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-04 00:18:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-04 00:18:05] [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
[2025-03-04 00:18:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-04 00:18:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-04 00:18:15] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-03-04 00:18:15] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-03-03 23:16:32 UTC; omnipath
[2025-03-04 00:18:15] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-03-04 00:18:15] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-03 23:17:39 UTC; unix
[2025-03-04 00:18:15] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.11
[2025-03-04 00:18:15] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-03-04 00:18:15] [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=2025-03-04; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-03-04 00:18:15] [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]
[2025-03-04 00:18:15] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.5.0.1(2024-12-03); 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); 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 1.1.0(2025-01-18); igraph 2.1.4(2025-01-23); jsonlite 1.9.0(2025-02-19); knitr 1.49(2024-11-08); 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(2025-03-03); pillar 1.10.1(2025-01-07); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); 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 1.4.4(2025-02-27); 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 0.4.0(2023-05-12); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.7(2025-02-28); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-03-04 00:18:15] [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
[2025-03-04 00:18:15] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-04 00:18:15] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-03-04 00:18:15] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-04 00:18:15] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-04 00:18:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-04 00:18:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-04 00:18:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-03-04 00:18:15] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-03-04 00:18:15] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-03-04_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-04 00:18:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-04 00:18:15] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-03-04_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-04 00:18:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-04 00:18:15] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-03-04_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-04 00:18:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-04 00:18:15] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-03-04_0007/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-04 00:18:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-04 00:18:15] [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 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: ensembl_id_mapping_table
> ### Title: Identifier translation table from Ensembl
> ### Aliases: ensembl_id_mapping_table
> 
> ### ** Examples
> 
> ensp_up <- ensembl_id_mapping_table("ensp")
[2025-03-04 00:20:51] [TRACE]   [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `ensembl_peptide_id`, for organism hsapiens
[2025-03-04 00:20:51] [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>
[2025-03-04 00:20:51] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-03-04 00:20:51] [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`.
[2025-03-04 00:20:51] [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`
[2025-03-04 00:20:51] [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`.
[2025-03-04 00:20:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-04 00:20:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-04 00:20:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-04 00:20:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-04 00:20:51] [INFO]    [OmnipathR] Cache item `5146291739ab7fee3dd9b2830721d4357888383d` version 1: status changed from `unknown` to `started`.
[2025-03-04 00:20:51] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5146291739ab7fee3dd9b2830721d4357888383d-1.rds`.
[2025-03-04 00:20:51] [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`
[2025-03-04 00:20:51] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-03-04 00:20:51] [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`
[2025-03-04 00:20:51] [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`.
[2025-03-04 00:20:51] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-03-04 00:20:51] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-04 00:20:51] [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=1,ssl_verifyhost=2]
[2025-03-04 00:20:51] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-03-04 00:20:51] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-03-04 00:20:52] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-03-04 00:20:52] [TRACE]   [OmnipathR] Downloaded 1015 bytes in 0.133872s from www.ensembl.org (7.4 Kb/s); Redirect: 0s, DNS look up: 6e-05s, Connection: 0.020298s, Pretransfer: 0.020348s, First byte at: 0.133738s
[2025-03-04 00:20:52] [TRACE]   [OmnipathR] Response headers: [X-GitHub-Request-Id=B209:D7FA0:1CBF555:1CFA437:67C4BDE9,Server=GitHub.com,X-Cache-Hits=0,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=e7925914492f0e8eb676aa72dea9fec0a5ea9722,Content-Encoding=gzip,Date=Mon, 03 Mar 2025 23:20:52 GMT,Expires=0,X-Served-By=cache-lcy-eglc8600074-LCY,Pragma=no-cache,X-Timer=S1741044052.023988,VS0,VE89,Access-Control-Allow-Origin=*,Accept-Ranges=bytes,ETag=W/"67177dde-8aa",Via=1.1 varnish,Connection=keep-alive,Age=0,Content-Length=1015]
[2025-03-04 00:20:52] [TRACE]   [OmnipathR] Calling reader callback on response.
[2025-03-04 00:20:52] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5146291739ab7fee3dd9b2830721d4357888383d-1.rds`.
[2025-03-04 00:20:52] [INFO]    [OmnipathR] Download ready [key=5146291739ab7fee3dd9b2830721d4357888383d, version=1]
[2025-03-04 00:20:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-04 00:20:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-04 00:20:52] [INFO]    [OmnipathR] Cache item `5146291739ab7fee3dd9b2830721d4357888383d` version 1: status changed from `started` to `ready`.
[2025-03-04 00:20:52] [WARN]    [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message!
[2025-03-04 00:20:52] [WARN]    [OmnipathR] <html>
[2025-03-04 00:20:52] [WARN]    [OmnipathR] <head>
[2025-03-04 00:20:52] [WARN]    [OmnipathR] <title>Service unavailable</title>
[2025-03-04 00:20:52] [WARN]    [OmnipathR] <meta name="robots" content="noindex">
[2025-03-04 00:20:52] [WARN]    [OmnipathR] <base href="//status.ensembl.org">
[2025-03-04 00:20:52] [WARN]    [OmnipathR] <style>
[2025-03-04 00:20:52] [WARN]    [OmnipathR] html,
[2025-03-04 00:20:52] [WARN]    [OmnipathR] body {
[2025-03-04 00:20:52] [WARN]    [OmnipathR] padding: 0;
[2025-03-04 00:20:52] [WARN]    [OmnipathR] margin: 0;
[2025-03-04 00:20:52] [WARN]    [OmnipathR] height: 100%;
[2025-03-04 00:20:52] [WARN]    [OmnipathR] }
[2025-03-04 00:20:52] [WARN]    [OmnipathR] body {
[2025-03-04 00:20:52] [WARN]    [OmnipathR] display: grid;
[2025-03-04 00:20:52] [WARN]    [OmnipathR] grid-template-rows: [header] auto [main] 1fr [footer] auto;
[2025-03-04 00:20:52] [WARN]    [OmnipathR] font-family: Luxi Sans, Helvetica, Arial, Geneva, sans-serif;
[2025-03-04 00:20:52] [WARN]    [OmnipathR] font-size: 90%;
[2025-03-04 00:20:52] [WARN]    [OmnipathR] }
[2025-03-04 00:20:52] [WARN]    [OmnipathR] h1 {
[2025-03-04 00:20:52] [WARN]    [OmnipathR] font-size: 1.5rem;
[2025-03-04 00:20:52] [WARN]    [OmnipathR] }
[2025-03-04 00:20:52] [WARN]    [OmnipathR] h2 {
[2025-03-04 00:20:52] [WARN]    [OmnipathR] font-size: 1.2rem;
[2025-03-04 00:20:52] [WARN]    [OmnipathR] }
[2025-03-04 00:20:52] [WARN]    [OmnipathR] h3 {
[2025-03-04 00:20:52] [WARN]    [OmnipathR] font-size: 1.1rem;
[2025-03-04 00:20:52] [WARN]    [OmnipathR] }
[2025-03-04 00:20:52] [WARN]    [OmnipathR] header {
[2025-03-04 00:20:52] [WARN]    [OmnipathR] grid-row: header;
[2025-03-04 00:20:52] [WARN]    [OmnipathR] padding: 5px;
[2025-03-04 00:20:52] [WARN]    [OmnipathR] height: 60px;
[2025-03-04 00:20:52] [WARN]    [OmnipathR] background-color: #333366;
[2025-03-04 00:20:52] [WARN]    [OmnipathR] }
[2025-03-04 00:20:52] [WARN]    [OmnipathR] header img {
[2025-03-04 00:20:52] [WARN]    [OmnipathR] width: 185px;
[2025-03-04 00:20:52] [WARN]    [OmnipathR] height: 45px
[2025-03-04 00:20:52] [WARN]    [OmnipathR] }
[2025-03-04 00:20:52] [WARN]    [OmnipathR] main {
[2025-03-04 00:20:52] [WARN]    [OmnipathR] grid-row: main;
[2025-03-04 00:20:52] [WARN]    [OmnipathR] padding: 20px;
[2025-03-04 00:20:52] [WARN]    [OmnipathR] }
[2025-03-04 00:20:52] [WARN]    [OmnipathR] .mirrors {
[2025-03-04 00:20:52] [WARN]    [OmnipathR] border: solid 1px #ccc;
[2025-03-04 00:20:52] [WARN]    [OmnipathR] margin-top: 20px;
[2025-03-04 00:20:52] [WARN]    [OmnipathR] padding: 10px;
[2025-03-04 00:20:52] [WARN]    [OmnipathR] }
[2025-03-04 00:20:52] [WARN]    [OmnipathR] footer {
[2025-03-04 00:20:52] [WARN]    [OmnipathR] grid-row: footer;
[2025-03-04 00:20:52] [WARN]    [OmnipathR] padding: 0 20px;
[2025-03-04 00:20:52] [WARN]    [OmnipathR] }
[2025-03-04 00:20:52] [WARN]    [OmnipathR] </style>
[2025-03-04 00:20:52] [WARN]    [OmnipathR] </head>
[2025-03-04 00:20:52] [WARN]    [OmnipathR] <body>
[2025-03-04 00:20:52] [WARN]    [OmnipathR] <header>
[2025-03-04 00:20:52] [WARN]    [OmnipathR] <img src="/e-ensembl.png" alt="ensembl-logo" />
[2025-03-04 00:20:52] [WARN]    [OmnipathR] </header>
[2025-03-04 00:20:52] [WARN]    [OmnipathR] <main>
[2025-03-04 00:20:52] [WARN]    [OmnipathR] <h1>Server Status</h1>
[2025-03-04 00:20:52] [WARN]    [OmnipathR] <p>
[2025-03-04 00:20:52] [WARN]    [OmnipathR] <img src="/exclamation_alert.png" alt="[!]" style="float:left;padding:0 10px;width:100px;height:89px" />
[2025-03-04 00:20:52] [WARN]    [OmnipathR] The Ensembl web service you requested is temporarily unavailable.
[2025-03-04 00:20:52] [WARN]    [OmnipathR] We are working to restore the service as soon as possible, and apologise for any inconvenience caused.
[2025-03-04 00:20:52] [WARN]    [OmnipathR] </p>
[2025-03-04 00:20:52] [WARN]    [OmnipathR] <p>For all enquiries, please <a href="https://www.ensembl.info/contact-us/">contact our HelpDesk</a>.</p>
[2025-03-04 00:20:52] [WARN]    [OmnipathR] <div class="mirrors">
[2025-03-04 00:20:52] [WARN]    [OmnipathR] <h3>Ensembl mirrors</h3>
[2025-03-04 00:20:52] [WARN]    [OmnipathR] We now also manage two mirrors of the Ensembl website, hosted in different regions of the Amazon cloud:
[2025-03-04 00:20:52] [WARN]    [OmnipathR] <ul>
[2025-03-04 00:20:52] [WARN]    [OmnipathR] <li><a href="https://useast.ensembl.org/index.html?redirect=no">useast.ensembl.org</a></li>
[2025-03-04 00:20:52] [WARN]    [OmnipathR] <li><a href="https://asia.ensembl.org/index.html?redirect=no">asia.ensembl.org</a></li>
[2025-03-04 00:20:52] [WARN]    [OmnipathR] </ul>
[2025-03-04 00:20:52] [WARN]    [OmnipathR] These will be available while the main service is unavailable, although please note that some of the
[2025-03-04 00:20:52] [WARN]    [OmnipathR] facilities on these mirror may not be fully functional as they rely on resources hosted at our main
[2025-03-04 00:20:52] [WARN]    [OmnipathR] data centre.
[2025-03-04 00:20:52] [WARN]    [OmnipathR] </div>
[2025-03-04 00:20:52] [WARN]    [OmnipathR] </main>
[2025-03-04 00:20:52] [WARN]    [OmnipathR] <footer>
[2025-03-04 00:20:52] [WARN]    [OmnipathR] <p>&copy; 2024 EMBL-EBI</p>
[2025-03-04 00:20:52] [WARN]    [OmnipathR] </footer>
[2025-03-04 00:20:52] [WARN]    [OmnipathR] </body>
[2025-03-04 00:20:52] [WARN]    [OmnipathR] </html>
[2025-03-04 00:20:52] [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
* 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-3.21/2025-03-04_0007/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.

[ Finished: 2025-03-04 00:29:59 CET ]