| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-03-27 11:41 -0400 (Thu, 27 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4783 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4552 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4581 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4533 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4463 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1470/2315 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.15.11 (landing page) Denes Turei
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the OmnipathR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: OmnipathR |
| Version: 3.15.11 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings OmnipathR_3.15.11.tar.gz |
| StartedAt: 2025-03-27 00:55:39 -0400 (Thu, 27 Mar 2025) |
| EndedAt: 2025-03-27 01:25:32 -0400 (Thu, 27 Mar 2025) |
| EllapsedTime: 1793.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: OmnipathR.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings OmnipathR_3.15.11.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* 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 24.04.2 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 ... 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 ... WARNING
Found the following significant warnings:
Note: possible error in 'download_to_cache(url_key = url_key, ': unused argument (http_param = http_param)
See ‘/home/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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2025-03-27 00:56:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-27 00:56:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-27 00:56:09] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-03-27 00:56:09] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-03-27 00:56:09] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-03-26
[2025-03-27 00:56:09] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-03-26 19:18:44 UTC; unix
[2025-03-27 00:56:09] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.11
[2025-03-27 00:56:09] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-03-27 00:56:09] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-03-13 r87965); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-03-27; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-03-27 00:56:10] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; 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=/home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-03-27 00:56:10] [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 6.2.2(2025-03-24); 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 1.6.5(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 1.1.2(2025-03-26); 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(2025-03-26); 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)
[2025-03-27 00:56:10] [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
[2025-03-27 00:56:10] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-03-27 00:56:10] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-03-27 00:56:10] [TRACE] [OmnipathR] Contains 1 files.
[2025-03-27 00:56:10] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-03-27 00:56:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-27 00:56:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-27 00:56:10] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-03-27 00:56:10] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-27 00:56:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-27 00:56:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-27 00:56:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-27 00:56:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-27 00:56:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-27 00:56:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-27 00:56:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-27 00:56:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-27 00:56:10] [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
[2025-03-27 00:56:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-27 00:56:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-27 00:56:26] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-03-27 00:56:26] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-03-27 00:56:26] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-03-26
[2025-03-27 00:56:26] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-03-26 19:18:44 UTC; unix
[2025-03-27 00:56:26] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.11
[2025-03-27 00:56:26] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-03-27 00:56:27] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-03-13 r87965); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-03-27; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-03-27 00:56:27] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; 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=/home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-03-27 00:56:27] [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 6.2.2(2025-03-24); 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 1.6.5(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 1.1.2(2025-03-26); 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(2025-03-26); 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)
[2025-03-27 00:56:27] [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
[2025-03-27 00:56:27] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-03-27 00:56:27] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-03-27 00:56:27] [TRACE] [OmnipathR] Contains 1 files.
[2025-03-27 00:56:27] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-03-27 00:56:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-27 00:56:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-27 00:56:27] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-03-27 00:56:27] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-27 00:56:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-27 00:56:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-27 00:56:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-27 00:56:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-27 00:56:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-27 00:56:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-27 00:56:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-27 00:56:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-27 00:56:27] [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()
[2025-03-27 01:04:59] [TRACE] [OmnipathR] Organism(s): 9606
[2025-03-27 01:04:59] [TRACE] [OmnipathR] Orthology targets:
[2025-03-27 01:04:59] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/queries/interactions?format=json&license=academic`
[2025-03-27 01:04:59] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/queries/interactions?format=json&license=academic`
[2025-03-27 01:04:59] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/queries/interactions?format=json&license=academic`
[2025-03-27 01:04:59] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/queries/interactions?format=json&license=academic`
[2025-03-27 01:04:59] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/queries/interactions?format=json&license=academic`
[2025-03-27 01:04:59] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/queries/interactions?format=json&license=academic`
[2025-03-27 01:04:59] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/queries/interactions?format=json&license=academic`
[2025-03-27 01:04:59] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-03-27 01:04:59] [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]
[2025-03-27 01:05:00] [TRACE] [OmnipathR] Downloaded 3.9 Kb in 0.282761s from omnipathdb.org (13.8 Kb/s); Redirect: 0s, DNS look up: 0.001715s, Connection: 0.003082s, Pretransfer: 0.191551s, First byte at: 0.282734s
[2025-03-27 01:05:00] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/queries/interactions?format=json&license=academic`
[2025-03-27 01:05:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-27 01:05:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-27 01:05:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-27 01:05:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-27 01:05:00] [INFO] [OmnipathR] Cache item `d4a3f6fd0083bc974e7269e2ff6b02df9633e303` version 1: status changed from `unknown` to `started`.
[2025-03-27 01:05:00] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/d4a3f6fd0083bc974e7269e2ff6b02df9633e303-1.rds`.
[2025-03-27 01:05:00] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/d4a3f6fd0083bc974e7269e2ff6b02df9633e303-1.rds`.
[2025-03-27 01:05:00] [INFO] [OmnipathR] Download ready [key=d4a3f6fd0083bc974e7269e2ff6b02df9633e303, version=1]
[2025-03-27 01:05:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-27 01:05:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-27 01:05:00] [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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotation_categories 84.869 0.065 86.640
curated_ligrec_stats 37.302 3.316 112.168
filter_extra_attrs 31.400 6.082 43.011
giant_component 20.871 0.627 28.265
go_annot_download 20.456 0.916 32.325
extra_attrs_to_cols 11.574 1.359 12.972
has_extra_attrs 11.186 1.282 13.923
extra_attr_values 10.954 1.481 15.076
find_all_paths 8.948 0.217 14.420
filter_intercell 7.481 0.549 14.060
filter_by_resource 6.969 0.516 9.946
extra_attrs 6.142 1.138 7.300
curated_ligand_receptor_interactions 6.043 0.777 16.564
all_uniprots 1.706 0.238 22.725
ensembl_id_mapping_table 1.407 0.085 12.719
* 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
‘/home/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘OmnipathR’ ... ** this is package ‘OmnipathR’ version ‘3.15.11’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Note: possible error in 'download_to_cache(url_key = url_key, ': unused argument (http_param = http_param) ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2025-03-26 15:18:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-26 15:18:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-26 15:18:57] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-03-26 15:18:57] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-03-26 15:18:57] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-03-26 [2025-03-26 15:18:57] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-03-26 19:18:44 UTC; unix [2025-03-26 15:18:57] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.11 [2025-03-26 15:18:57] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-03-26 15:18:57] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-03-13 r87965); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-03-26; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto] [2025-03-26 15:18:57] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; 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=/home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-03-26 15:18:57] [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 6.2.2(2025-03-24); 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 1.6.5(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 1.1.2(2025-03-26); 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(2025-03-26); 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) [2025-03-26 15:18:57] [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 [2025-03-26 15:18:57] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-26 15:18:57] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-03-26 15:18:57] [TRACE] [OmnipathR] Contains 8 files. [2025-03-26 15:18:57] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-26 15:18:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-26 15:18:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-26 15:18:57] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-03-26 15:18:57] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-03-26 15:18:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-26 15:18:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-26 15:18:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-26 15:18:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-26 15:18:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-26 15:18:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-26 15:18:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-26 15:18:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-26 15:18:57] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-03-26 15:18:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-26 15:18:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-26 15:18:59] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-03-26 15:18:59] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-03-26 15:18:59] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-03-26 [2025-03-26 15:18:59] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-03-26 19:18:44 UTC; unix [2025-03-26 15:18:59] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.11 [2025-03-26 15:18:59] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-03-26 15:19:00] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-03-13 r87965); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-03-26; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto] [2025-03-26 15:19:00] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; 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=/home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-03-26 15:19:00] [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 6.2.2(2025-03-24); 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 1.6.5(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 1.1.2(2025-03-26); 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(2025-03-26); 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) [2025-03-26 15:19:00] [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 [2025-03-26 15:19:00] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-26 15:19:00] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-03-26 15:19:00] [TRACE] [OmnipathR] Contains 1 files. [2025-03-26 15:19:00] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-26 15:19:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-26 15:19:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-26 15:19:00] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-03-26 15:19:00] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-03-26 15:19:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-26 15:19:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-26 15:19:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-26 15:19:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-26 15:19:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-26 15:19:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-26 15:19:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-26 15:19:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-26 15:19:00] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
OmnipathR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #!/usr/bin/env Rscript
>
> #
> # This file is part of the `OmnipathR` R package
> #
> # Copyright
> # 2018-2024
> # Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> # File author(s): Alberto Valdeolivas
> # Dénes Türei (turei.denes@gmail.com)
> # Attila Gábor
> #
> # Distributed under the MIT (Expat) License.
> # See accompanying file `LICENSE` or find a copy at
> # https://directory.fsf.org/wiki/License:Expat
> #
> # Website: https://r.omnipathdb.org/
> # Git repo: https://github.com/saezlab/OmnipathR
> #
>
>
> library(testthat)
> library(OmnipathR)
[2025-03-27 01:05:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-27 01:05:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-27 01:05:03] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-03-27 01:05:03] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-03-27 01:05:03] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-03-26
[2025-03-27 01:05:03] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-03-26 19:18:44 UTC; unix
[2025-03-27 01:05:03] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.11
[2025-03-27 01:05:03] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-03-27 01:05:04] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-03-13 r87965); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-03-27; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-03-27 01:05:04] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; 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=/home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-03-27 01:05:04] [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); brio 1.1.5(2024-04-24); 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 6.2.2(2025-03-24); 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 1.6.5(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 1.1.2(2025-03-26); 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(2025-03-26); 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 1.4.5(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); testthat 3.2.3(2025-01-13); 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); 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)
[2025-03-27 01:05:04] [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
[2025-03-27 01:05:04] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-03-27 01:05:04] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-03-27 01:05:04] [TRACE] [OmnipathR] Contains 46 files.
[2025-03-27 01:05:04] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-03-27 01:05:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-27 01:05:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-27 01:05:04] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-03-27 01:05:04] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-27 01:05:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-27 01:05:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-27 01:05:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-27 01:05:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-27 01:05:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-27 01:05:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-27 01:05:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-27 01:05:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-27 01:05:04] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 38 ]
>
> proc.time()
user system elapsed
23.438 1.773 58.729
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0 | 0 | 0 | |
| all_uniprot_acs | 0.014 | 0.003 | 0.018 | |
| all_uniprots | 1.706 | 0.238 | 22.725 | |
| ancestors | 0.009 | 0.000 | 0.009 | |
| annotated_network | 1.341 | 0.142 | 4.527 | |
| annotation_categories | 84.869 | 0.065 | 86.640 | |
| annotation_resources | 0.119 | 0.014 | 0.933 | |
| annotations | 0.544 | 0.048 | 1.581 | |
| biomart_query | 0.992 | 0.064 | 2.056 | |
| bioplex1 | 0.008 | 0.001 | 0.009 | |
| bioplex2 | 0.008 | 0.000 | 0.009 | |
| bioplex3 | 0.008 | 0.001 | 0.009 | |
| bioplex_all | 0.007 | 0.002 | 0.009 | |
| bioplex_hct116_1 | 0.008 | 0.000 | 0.009 | |
| bma_motif_es | 0.722 | 0.073 | 1.587 | |
| bma_motif_vs | 0.275 | 0.013 | 0.995 | |
| chalmers_gem | 0.009 | 0.001 | 0.010 | |
| chalmers_gem_id_mapping_table | 0.008 | 0.000 | 0.008 | |
| chalmers_gem_id_type | 0.002 | 0.000 | 0.002 | |
| chalmers_gem_metabolites | 0.008 | 0.000 | 0.009 | |
| chalmers_gem_network | 0.007 | 0.002 | 0.009 | |
| chalmers_gem_raw | 0.006 | 0.002 | 0.008 | |
| chalmers_gem_reactions | 0.008 | 0.000 | 0.008 | |
| common_name | 0.031 | 0.002 | 0.034 | |
| complex_genes | 0.805 | 0.036 | 2.773 | |
| complex_resources | 0.085 | 0.004 | 0.805 | |
| complexes | 0.216 | 0.005 | 0.994 | |
| consensuspathdb_download | 0.000 | 0.001 | 0.001 | |
| consensuspathdb_raw_table | 0.005 | 0.002 | 0.008 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 6.043 | 0.777 | 16.564 | |
| curated_ligrec_stats | 37.302 | 3.316 | 112.168 | |
| database_summary | 1.438 | 0.072 | 2.885 | |
| descendants | 0.009 | 0.000 | 0.009 | |
| ensembl_dataset | 0.010 | 0.001 | 0.012 | |
| ensembl_id_mapping_table | 1.407 | 0.085 | 12.719 | |
| ensembl_id_type | 0.002 | 0.001 | 0.002 | |
| ensembl_name | 0.057 | 0.005 | 0.062 | |
| ensembl_organisms | 0.116 | 0.008 | 0.125 | |
| ensembl_organisms_raw | 0.093 | 0.007 | 0.100 | |
| ensembl_orthology | 0.000 | 0.000 | 0.001 | |
| enzsub_graph | 1.893 | 0.126 | 4.287 | |
| enzsub_resources | 0.080 | 0.005 | 0.917 | |
| enzyme_substrate | 0.933 | 0.028 | 1.753 | |
| evex_download | 0.005 | 0.003 | 0.008 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 10.954 | 1.481 | 15.076 | |
| extra_attrs | 6.142 | 1.138 | 7.300 | |
| extra_attrs_to_cols | 11.574 | 1.359 | 12.972 | |
| filter_by_resource | 6.969 | 0.516 | 9.946 | |
| filter_extra_attrs | 31.400 | 6.082 | 43.011 | |
| filter_intercell | 7.481 | 0.549 | 14.060 | |
| filter_intercell_network | 0.025 | 0.003 | 0.028 | |
| find_all_paths | 8.948 | 0.217 | 14.420 | |
| from_evidences | 0.000 | 0.001 | 0.000 | |
| get_db | 0.000 | 0.001 | 0.001 | |
| get_ontology_db | 0.016 | 0.002 | 0.017 | |
| giant_component | 20.871 | 0.627 | 28.265 | |
| go_annot_download | 20.456 | 0.916 | 32.325 | |
| go_annot_slim | 0 | 0 | 0 | |
| go_ontology_download | 0.030 | 0.005 | 0.035 | |
| guide2pharma_download | 0.027 | 0.001 | 0.028 | |
| harmonizome_download | 0.028 | 0.001 | 0.029 | |
| has_extra_attrs | 11.186 | 1.282 | 13.923 | |
| hmdb_id_mapping_table | 0.01 | 0.00 | 0.01 | |
| hmdb_id_type | 0.002 | 0.001 | 0.003 | |
| hmdb_metabolite_fields | 0 | 0 | 0 | |
| hmdb_protein_fields | 0.001 | 0.000 | 0.000 | |
| hmdb_table | 0.008 | 0.001 | 0.009 | |
| homologene_download | 0.008 | 0.000 | 0.008 | |
| homologene_raw | 0.018 | 0.002 | 0.020 | |
| homologene_uniprot_orthology | 0.009 | 0.001 | 0.010 | |
| hpo_download | 2.409 | 0.219 | 3.241 | |
| htridb_download | 0.009 | 0.000 | 0.009 | |
| id_translation_resources | 0 | 0 | 0 | |
| id_types | 0.043 | 0.005 | 0.048 | |
| inbiomap_download | 0 | 0 | 0 | |
| inbiomap_raw | 0 | 0 | 0 | |