Christina Schmidt
| Snapshot Date: 2026-04-17 13:40 -0400 (Fri, 17 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/MetaProViz |
| git_branch: devel |
| git_last_commit: 47b2175 |
| git_last_commit_date: 2026-03-27 04:09:49 -0400 (Fri, 27 Mar 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-18 11:37 -0400 (Sat, 18 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4957 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4686 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4627 |
| 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 1278/2404 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MetaProViz 3.99.50 (landing page) Christina Schmidt
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
| See other builds for MetaProViz in R Universe. | ||||||||||||||
|
To the developers/maintainers of the MetaProViz package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MetaProViz.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: MetaProViz |
| Version: 3.99.50 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:MetaProViz.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MetaProViz_3.99.50.tar.gz |
| StartedAt: 2026-04-17 04:44:10 -0000 (Fri, 17 Apr 2026) |
| EndedAt: 2026-04-17 05:01:37 -0000 (Fri, 17 Apr 2026) |
| EllapsedTime: 1046.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MetaProViz.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:MetaProViz.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MetaProViz_3.99.50.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/MetaProViz.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MetaProViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MetaProViz’ version ‘3.99.50’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 39 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 ‘MetaProViz’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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
[2026-04-17 04:46:38] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 04:46:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 04:46:38] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-04-17 04:46:38] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-04-17 04:46:38] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-04-16
[2026-04-17 04:46:38] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2026-04-16 20:22:07 UTC; unix
[2026-04-17 04:46:38] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.12
[2026-04-17 04:46:38] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-04-17 04:46:38] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2026-04-17; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2026-04-17 04:46:38] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0]
[2026-04-17 04:46:39] [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 0.5.0(2025-03-21); cli 3.6.4(2025-02-13); colorspace 2.1-1(2024-07-26); ComplexUpset 1.3.3(2021-12-11); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); EnhancedVolcano 1.29.1(2026-04-16); evaluate 1.0.3(2025-01-10); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); ggplot2 4.0.0(2025-09-11); ggrepel 0.9.6(2024-09-07); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); 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); MetaProViz 3.99.50(2026-04-16); OmnipathR 3.19.12(2026-04-16); patchwork 1.3.0(2024-09-16); 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 1.27.0(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); RColorBrewer 1.1-3(2022-04-03); 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 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); S7 0.2.0(2024-11-07); scales 1.4.0(2025-04-24); 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 2.3.2(2025-02-01)
[2026-04-17 04:46:39] [INFO] [OmnipathR] CURL: version: 8.12.1; headers: 8.4.0; ssl_version: OpenSSL/3.4.1; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2026-04-17 04:46:39] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-04-17 04:46:39] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-04-17 04:46:39] [TRACE] [OmnipathR] Contains 1 files.
[2026-04-17 04:46:39] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-04-17 04:46:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 04:46:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 04:46:39] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-04-17 04:46:39] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2026-04-17 04:46:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-04-17 04:46:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 04:46:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-04-17 04:46:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 04:46:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-04-17 04:46:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 04:46:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-04-17 04:46:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 04:46:39] [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
[2026-04-17 04:48:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 04:48:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 04:48:19] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-04-17 04:48:19] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-04-17 04:48:19] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-04-16
[2026-04-17 04:48:19] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2026-04-16 20:22:07 UTC; unix
[2026-04-17 04:48:19] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.12
[2026-04-17 04:48:19] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-04-17 04:48:19] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2026-04-17; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2026-04-17 04:48:19] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0]
[2026-04-17 04:48:19] [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); colorspace 2.1-1(2024-07-26); ComplexUpset 1.3.3(2021-12-11); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); EnhancedVolcano 1.29.1(2026-04-16); evaluate 1.0.3(2025-01-10); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); ggplot2 4.0.0(2025-09-11); ggrepel 0.9.6(2024-09-07); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); 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); MetaProViz 3.99.50(2026-04-16); OmnipathR 3.19.12(2026-04-16); patchwork 1.3.0(2024-09-16); 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 1.27.0(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); RColorBrewer 1.1-3(2022-04-03); 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 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); S7 0.2.0(2024-11-07); scales 1.4.0(2025-04-24); 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 2.3.2(2025-02-01)
[2026-04-17 04:48:19] [INFO] [OmnipathR] CURL: version: 8.12.1; headers: 8.4.0; ssl_version: OpenSSL/3.4.1; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2026-04-17 04:48:19] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-04-17 04:48:19] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-04-17 04:48:19] [TRACE] [OmnipathR] Contains 1 files.
[2026-04-17 04:48:19] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-04-17 04:48:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 04:48:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 04:48:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-04-17 04:48:19] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2026-04-17 04:48:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-04-17 04:48:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 04:48:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-04-17 04:48:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 04:48:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-04-17 04:48:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 04:48:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-04-17 04:48:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 04:48:20] [TRACE] [OmnipathR] Cache locked: FALSE
build_seed_neighbors: no visible binding for global variable ‘type1’
build_seed_neighbors: no visible binding for global variable ‘id1’
build_seed_neighbors: no visible binding for global variable ‘type2’
build_seed_neighbors: no visible binding for global variable ‘id2’
Undefined global functions or variables:
id1 id2 type1 type2
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'reexports.Rd':
‘[magrittr:pipe]{%>%}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
cluster_ora 106.460 17.750 388.848
traverse_ids 48.526 1.013 49.616
dma 30.492 2.153 32.981
mca_2cond 14.595 1.084 15.877
processing 14.203 1.092 15.505
equivalent_id 13.622 0.363 14.050
pool_estimation 10.937 0.633 11.702
metadata_analysis 6.844 0.399 7.323
viz_superplot 4.978 0.278 5.326
metsigdb_metalinks 4.415 0.392 15.640
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.23-bioc/meat/MetaProViz.Rcheck/00check.log’
for details.
MetaProViz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL MetaProViz ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘MetaProViz’ ... ** this is package ‘MetaProViz’ version ‘3.99.50’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading [2026-04-16 20:48:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-16 20:48:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-16 20:48:08] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2026-04-16 20:48:08] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-04-16 20:48:08] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-04-16 [2026-04-16 20:48:08] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2026-04-16 20:22:07 UTC; unix [2026-04-16 20:48:08] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.12 [2026-04-16 20:48:08] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2026-04-16 20:48:08] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2026-04-16; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto] [2026-04-16 20:48:08] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0] [2026-04-16 20:48:08] [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); colorspace 2.1-1(2024-07-26); ComplexUpset 1.3.3(2021-12-11); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); EnhancedVolcano 1.29.1(2026-04-16); evaluate 1.0.3(2025-01-10); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); ggplot2 4.0.0(2025-09-11); ggrepel 0.9.6(2024-09-07); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); 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); MetaProViz 3.99.50(2026-04-16); OmnipathR 3.19.12(2026-04-16); patchwork 1.3.0(2024-09-16); 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 1.27.0(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); RColorBrewer 1.1-3(2022-04-03); 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 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); S7 0.2.0(2024-11-07); scales 1.4.0(2025-04-24); 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 2.3.2(2025-02-01) [2026-04-16 20:48:08] [INFO] [OmnipathR] CURL: version: 8.12.1; headers: 8.4.0; ssl_version: OpenSSL/3.4.1; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2026-04-16 20:48:08] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-16 20:48:08] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2026-04-16 20:48:08] [TRACE] [OmnipathR] Contains 1 files. [2026-04-16 20:48:08] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-16 20:48:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-16 20:48:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-16 20:48:08] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2026-04-16 20:48:08] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2026-04-16 20:48:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-16 20:48:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-16 20:48:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-16 20:48:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-16 20:48:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-16 20:48:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-16 20:48:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-16 20:48:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-16 20:48:09] [TRACE] [OmnipathR] Cache locked: FALSE ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2026-04-16 20:48:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-16 20:48:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-16 20:48:47] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2026-04-16 20:48:47] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-04-16 20:48:47] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-04-16 [2026-04-16 20:48:47] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2026-04-16 20:22:07 UTC; unix [2026-04-16 20:48:47] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.12 [2026-04-16 20:48:47] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2026-04-16 20:48:47] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2026-04-16; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto] [2026-04-16 20:48:47] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0] [2026-04-16 20:48:48] [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); colorspace 2.1-1(2024-07-26); ComplexUpset 1.3.3(2021-12-11); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); EnhancedVolcano 1.29.1(2026-04-16); evaluate 1.0.3(2025-01-10); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); ggplot2 4.0.0(2025-09-11); ggrepel 0.9.6(2024-09-07); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); 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); MetaProViz 3.99.50(2026-04-16); OmnipathR 3.19.12(2026-04-16); patchwork 1.3.0(2024-09-16); 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 1.27.0(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); RColorBrewer 1.1-3(2022-04-03); 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 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); S7 0.2.0(2024-11-07); scales 1.4.0(2025-04-24); 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 2.3.2(2025-02-01) [2026-04-16 20:48:48] [INFO] [OmnipathR] CURL: version: 8.12.1; headers: 8.4.0; ssl_version: OpenSSL/3.4.1; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2026-04-16 20:48:48] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-16 20:48:48] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2026-04-16 20:48:48] [TRACE] [OmnipathR] Contains 1 files. [2026-04-16 20:48:48] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-16 20:48:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-16 20:48:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-16 20:48:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2026-04-16 20:48:48] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2026-04-16 20:48:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-16 20:48:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-16 20:48:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-16 20:48:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-16 20:48:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-16 20:48:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-16 20:48:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-16 20:48:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-16 20:48:48] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2026-04-16 20:49:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-16 20:49:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-16 20:49:06] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2026-04-16 20:49:06] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-04-16 20:49:06] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-04-16 [2026-04-16 20:49:06] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2026-04-16 20:22:07 UTC; unix [2026-04-16 20:49:06] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.12 [2026-04-16 20:49:06] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2026-04-16 20:49:06] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2026-04-16; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto] [2026-04-16 20:49:06] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0] [2026-04-16 20:49:07] [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); colorspace 2.1-1(2024-07-26); ComplexUpset 1.3.3(2021-12-11); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); EnhancedVolcano 1.29.1(2026-04-16); evaluate 1.0.3(2025-01-10); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); ggplot2 4.0.0(2025-09-11); ggrepel 0.9.6(2024-09-07); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); 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); MetaProViz 3.99.50(2026-04-16); OmnipathR 3.19.12(2026-04-16); patchwork 1.3.0(2024-09-16); 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 1.27.0(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); RColorBrewer 1.1-3(2022-04-03); 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 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); S7 0.2.0(2024-11-07); scales 1.4.0(2025-04-24); 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 2.3.2(2025-02-01) [2026-04-16 20:49:07] [INFO] [OmnipathR] CURL: version: 8.12.1; headers: 8.4.0; ssl_version: OpenSSL/3.4.1; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2026-04-16 20:49:07] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-16 20:49:07] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2026-04-16 20:49:07] [TRACE] [OmnipathR] Contains 1 files. [2026-04-16 20:49:07] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-16 20:49:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-16 20:49:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-16 20:49:07] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2026-04-16 20:49:07] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2026-04-16 20:49:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-16 20:49:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-16 20:49:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-16 20:49:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-16 20:49:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-16 20:49:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-16 20:49:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-16 20:49:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-16 20:49:07] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (MetaProViz)
MetaProViz.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
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Type 'license()' or 'licence()' for distribution details.
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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(MetaProViz)
[2026-04-17 05:01:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 05:01:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 05:01:15] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-04-17 05:01:15] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-04-17 05:01:15] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-04-16
[2026-04-17 05:01:15] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2026-04-16 20:22:07 UTC; unix
[2026-04-17 05:01:15] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.12
[2026-04-17 05:01:15] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-04-17 05:01:15] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=UTC; date=2026-04-17; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2026-04-17 05:01:15] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0]
[2026-04-17 05:01:15] [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); colorspace 2.1-1(2024-07-26); ComplexUpset 1.3.3(2021-12-11); 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); EnhancedVolcano 1.29.1(2026-04-16); evaluate 1.0.3(2025-01-10); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); ggplot2 4.0.0(2025-09-11); ggrepel 0.9.6(2024-09-07); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); 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); MetaProViz 3.99.50(2026-04-16); OmnipathR 3.19.12(2026-04-16); patchwork 1.3.0(2024-09-16); pillar 1.10.2(2025-04-05); 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); RColorBrewer 1.1-3(2022-04-03); 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 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); S7 0.2.0(2024-11-07); scales 1.4.0(2025-04-24); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); 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 0.52(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 2.3.2(2025-02-01)
[2026-04-17 05:01:15] [INFO] [OmnipathR] CURL: version: 8.12.1; headers: 8.4.0; ssl_version: OpenSSL/3.4.1; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2026-04-17 05:01:15] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-04-17 05:01:15] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-04-17 05:01:15] [TRACE] [OmnipathR] Contains 23 files.
[2026-04-17 05:01:15] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-04-17 05:01:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-17 05:01:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 05:01:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-04-17 05:01:16] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2026-04-17 05:01:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-04-17 05:01:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 05:01:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-04-17 05:01:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 05:01:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-04-17 05:01:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 05:01:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-04-17 05:01:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-17 05:01:16] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check("MetaProViz")
Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
data has multiple IDs per measurement = FALSE. input_pk has multiple IDs per entry = FALSE.
data has 3 unique entries with 3 unique HMDB IDs. Of those IDs, 3 match, which is 100%.
input_pk has 3 unique entries with 3 unique HMDB IDs. Of those IDs, 3 are detected in the data, which is 100%.
data has multiple IDs per measurement = FALSE. input_pk has multiple IDs per entry = FALSE.
data has 4 unique entries with 4 unique HMDB IDs. Of those IDs, 2 match, which is 50%.
input_pk has 3 unique entries with 3 unique HMDB IDs. Of those IDs, 2 are detected in the data, which is 66.6666666666667%.
[2026-04-17 05:01:31] [TRACE] [MetaProViz] Error The HMDB column selected as InpuID in metadata_info was not found in data. Please check your input.
[2026-04-17 05:01:31] [TRACE] [MetaProViz] Error The HMDB column selected as InpuID in metadata_info was not found in data. Please check your input.
[2026-04-17 05:01:31] [TRACE] [MetaProViz] Error The HMDB column selected as InpuID in metadata_info was not found in input_pk. Please check your input.
data has multiple IDs per measurement = FALSE. input_pk has multiple IDs per entry = FALSE.
data has 3 unique entries with 3 unique HMDB IDs. Of those IDs, 1 match, which is 33.3333333333333%.
input_pk has 3 unique entries with 3 unique hmdb IDs. Of those IDs, 1 are detected in the data, which is 33.3333333333333%.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 9 ]
>
> proc.time()
user system elapsed
17.323 2.930 20.789
MetaProViz.Rcheck/MetaProViz-Ex.timings
| name | user | system | elapsed | |
| alanine_pathways | 0.060 | 0.000 | 0.061 | |
| biocrates_features | 0.095 | 0.008 | 0.102 | |
| cellular_meta | 0.037 | 0.000 | 0.037 | |
| checkmatch_pk_to_data | 0 | 0 | 0 | |
| cluster_ora | 106.460 | 17.750 | 388.848 | |
| cluster_pk | 0.297 | 0.028 | 0.325 | |
| compare_pk | 0 | 0 | 0 | |
| count_id | 2.036 | 0.245 | 2.275 | |
| dma | 30.492 | 2.153 | 32.981 | |
| equivalent_features | 0.040 | 0.004 | 0.045 | |
| equivalent_id | 13.622 | 0.363 | 14.050 | |
| gaude_pathways | 0.033 | 0.000 | 0.033 | |
| get_exclusion_metabolites | 0 | 0 | 0 | |
| hallmarks | 0.033 | 0.008 | 0.041 | |
| intracell_dma | 0.064 | 0.012 | 0.077 | |
| intracell_raw | 0.113 | 0.028 | 0.144 | |
| intracell_raw_se | 0.052 | 0.000 | 0.053 | |
| make_gene_metab_set | 2.046 | 0.509 | 2.649 | |
| mapping_ambiguity | 0 | 0 | 0 | |
| mca_2cond | 14.595 | 1.084 | 15.877 | |
| mca_core | 0.230 | 0.012 | 0.245 | |
| mca_core_rules | 0.048 | 0.000 | 0.049 | |
| mca_twocond_rules | 0.032 | 0.004 | 0.036 | |
| medium_raw | 0.103 | 0.008 | 0.110 | |
| meta_pk | 0.141 | 0.012 | 0.155 | |
| metadata_analysis | 6.844 | 0.399 | 7.323 | |
| metaproviz_config_path | 0.001 | 0.000 | 0.001 | |
| metaproviz_load_config | 0.003 | 0.001 | 0.003 | |
| metaproviz_log | 0 | 0 | 0 | |
| metaproviz_logfile | 0.002 | 0.000 | 0.002 | |
| metaproviz_reset_config | 0.010 | 0.000 | 0.011 | |
| metaproviz_save_config | 0.011 | 0.000 | 0.011 | |
| metaproviz_set_loglevel | 0.004 | 0.000 | 0.003 | |
| metsigdb_chemicalclass | 2.102 | 0.220 | 2.267 | |
| metsigdb_kegg | 2.387 | 0.088 | 2.497 | |
| metsigdb_metalinks | 4.415 | 0.392 | 15.640 | |
| metsigdb_reactome | 0 | 0 | 0 | |
| pool_estimation | 10.937 | 0.633 | 11.702 | |
| processing | 14.203 | 1.092 | 15.505 | |
| replicate_sum | 0.795 | 0.065 | 0.864 | |
| standard_ora | 2.226 | 0.129 | 2.381 | |
| tissue_dma | 0.076 | 0.008 | 0.084 | |
| tissue_dma_old | 0.073 | 0.011 | 0.086 | |
| tissue_dma_young | 0.074 | 0.012 | 0.088 | |
| tissue_meta | 0.042 | 0.024 | 0.067 | |
| tissue_norm | 0.162 | 0.031 | 0.197 | |
| tissue_norm_se | 0.051 | 0.000 | 0.053 | |
| tissue_tvn_proteomics | 0.070 | 0.012 | 0.084 | |
| tissue_tvn_rnaseq | 0.124 | 0.005 | 0.130 | |
| translate_id | 0 | 0 | 0 | |
| traverse_ids | 48.526 | 1.013 | 49.616 | |
| viz_graph | 0.692 | 0.051 | 0.748 | |
| viz_heatmap | 1.094 | 0.029 | 1.124 | |
| viz_pca | 4.822 | 0.137 | 4.991 | |
| viz_superplot | 4.978 | 0.278 | 5.326 | |
| viz_volcano | 0.982 | 0.040 | 1.034 | |