Christina Schmidt
| Snapshot Date: 2026-05-05 13:45 -0400 (Tue, 05 May 2026) |
| git_url: https://git.bioconductor.org/packages/MetaProViz |
| git_branch: devel |
| git_last_commit: 02799d0 |
| git_last_commit_date: 2026-04-28 09:06:33 -0400 (Tue, 28 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-06 11:34 -0400 (Wed, 06 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4878 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4663 |
| 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 1262/2366 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MetaProViz 4.1.0 (landing page) Christina Schmidt
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| taishan | 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: 4.1.0 |
| 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_4.1.0.tar.gz |
| StartedAt: 2026-05-05 11:45:52 -0000 (Tue, 05 May 2026) |
| EndedAt: 2026-05-05 12:02:25 -0000 (Tue, 05 May 2026) |
| EllapsedTime: 993.1 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_4.1.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/MetaProViz.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MetaProViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MetaProViz’ version ‘4.1.0’
* 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
[2026-05-05 11:48:14] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-05 11:48:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-05 11:48:14] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-05-05 11:48:14] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-05-05 11:48:14] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-05-04
[2026-05-05 11:48:14] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2026-05-04 23:32:07 UTC; unix
[2026-05-05 11:48:14] [INFO] [OmnipathR] Package `OmnipathR` version: 4.1.0
[2026-05-05 11:48:14] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.24
[2026-05-05 11:48:14] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2026-05-05; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2026-05-05 11:48:14] [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=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; 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=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0]
[2026-05-05 11:48:15] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.0(2026-04-21); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.6(2026-04-09); colorspace 2.1-2(2025-09-22); ComplexUpset 1.3.3(2021-12-11); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); dplyr 1.1.4(2023-11-17); EnhancedVolcano 1.31.0(2026-05-04); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 2.1.0(2026-04-18); generics 0.1.4(2025-05-09); ggplot2 4.0.0(2025-09-11); ggrepel 0.9.6(2024-09-07); glue 1.8.1(2026-04-17); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); MetaProViz 4.1.0(2026-05-04); OmnipathR 4.1.0(2026-05-04); otel 0.2.0(2025-08-29); patchwork 1.3.2(2025-08-25); pillar 1.11.1(2025-09-17); 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 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); 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 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); 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 0.54(2025-10-30); XML 3.99-0.19(2025-08-22); xml2 1.4.1(2025-10-27); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2026-05-05 11:48:15] [INFO] [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; 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
[2026-05-05 11:48:15] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-05-05 11:48:15] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-05-05 11:48:15] [TRACE] [OmnipathR] Contains 1 files.
[2026-05-05 11:48:15] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-05-05 11:48:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-05 11:48:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-05 11:48:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-05-05 11:48:15] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2026-05-05 11:48:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-05-05 11:48:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-05 11:48:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-05-05 11:48:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-05 11:48:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-05-05 11:48:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-05 11:48:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-05-05 11:48:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-05 11:48:15] [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
[2026-05-05 11:49:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-05 11:49:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-05 11:49:49] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-05-05 11:49:49] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-05-05 11:49:49] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-05-04
[2026-05-05 11:49:49] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2026-05-04 23:32:07 UTC; unix
[2026-05-05 11:49:49] [INFO] [OmnipathR] Package `OmnipathR` version: 4.1.0
[2026-05-05 11:49:49] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.24
[2026-05-05 11:49:50] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2026-05-05; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2026-05-05 11:49:50] [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=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; 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=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0]
[2026-05-05 11:49:50] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.0(2026-04-21); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.6(2026-04-09); colorspace 2.1-2(2025-09-22); ComplexUpset 1.3.3(2021-12-11); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); dplyr 1.1.4(2023-11-17); EnhancedVolcano 1.31.0(2026-05-04); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 2.1.0(2026-04-18); generics 0.1.4(2025-05-09); ggplot2 4.0.0(2025-09-11); ggrepel 0.9.6(2024-09-07); glue 1.8.1(2026-04-17); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); MetaProViz 4.1.0(2026-05-04); OmnipathR 4.1.0(2026-05-04); otel 0.2.0(2025-08-29); patchwork 1.3.2(2025-08-25); pillar 1.11.1(2025-09-17); 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 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); 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 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); 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 0.54(2025-10-30); XML 3.99-0.19(2025-08-22); xml2 1.4.1(2025-10-27); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2026-05-05 11:49:50] [INFO] [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; 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
[2026-05-05 11:49:50] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-05-05 11:49:50] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-05-05 11:49:50] [TRACE] [OmnipathR] Contains 1 files.
[2026-05-05 11:49:50] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-05-05 11:49:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-05 11:49:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-05 11:49:50] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-05-05 11:49:50] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2026-05-05 11:49:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-05-05 11:49:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-05 11:49:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-05-05 11:49:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-05 11:49:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-05-05 11:49:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-05 11:49:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-05-05 11:49:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-05 11:49:50] [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 97.592 15.524 369.860
traverse_ids 43.695 1.115 44.759
dma 33.023 2.924 36.058
mca_2cond 13.643 1.036 14.718
processing 13.345 1.325 14.709
equivalent_id 11.947 0.488 12.471
pool_estimation 10.539 0.655 11.209
metadata_analysis 6.543 0.445 6.991
viz_superplot 4.674 0.387 5.095
metsigdb_metalinks 3.900 0.377 15.967
* 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-3.24-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-4.5.0/site-library’ * installing *source* package ‘MetaProViz’ ... ** this is package ‘MetaProViz’ version ‘4.1.0’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading [2026-05-04 23:56:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-04 23:56:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-04 23:56:36] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2026-05-04 23:56:36] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-05-04 23:56:36] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-05-04 [2026-05-04 23:56:36] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2026-05-04 23:32:07 UTC; unix [2026-05-04 23:56:36] [INFO] [OmnipathR] Package `OmnipathR` version: 4.1.0 [2026-05-04 23:56:36] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.24 [2026-05-04 23:56:36] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2026-05-04; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto] [2026-05-04 23:56:37] [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=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; 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=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0] [2026-05-04 23:56:37] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.0(2026-04-21); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.6(2026-04-09); colorspace 2.1-2(2025-09-22); ComplexUpset 1.3.3(2021-12-11); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); dplyr 1.1.4(2023-11-17); EnhancedVolcano 1.31.0(2026-05-04); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 2.1.0(2026-04-18); generics 0.1.4(2025-05-09); ggplot2 4.0.0(2025-09-11); ggrepel 0.9.6(2024-09-07); glue 1.8.1(2026-04-17); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); MetaProViz 4.1.0(2026-05-04); OmnipathR 4.1.0(2026-05-04); otel 0.2.0(2025-08-29); patchwork 1.3.2(2025-08-25); pillar 1.11.1(2025-09-17); 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 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); 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 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); 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 0.54(2025-10-30); XML 3.99-0.19(2025-08-22); xml2 1.4.1(2025-10-27); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2026-05-04 23:56:37] [INFO] [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; 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 [2026-05-04 23:56:37] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-05-04 23:56:37] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2026-05-04 23:56:37] [TRACE] [OmnipathR] Contains 1 files. [2026-05-04 23:56:37] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-05-04 23:56:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-04 23:56:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-04 23:56:37] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2026-05-04 23:56:37] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2026-05-04 23:56:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-05-04 23:56:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-04 23:56:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-05-04 23:56:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-04 23:56:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-05-04 23:56:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-04 23:56:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-05-04 23:56:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-04 23:56:37] [TRACE] [OmnipathR] Cache locked: FALSE ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2026-05-04 23:57:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-04 23:57:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-04 23:57:10] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2026-05-04 23:57:10] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-05-04 23:57:10] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-05-04 [2026-05-04 23:57:10] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2026-05-04 23:32:07 UTC; unix [2026-05-04 23:57:10] [INFO] [OmnipathR] Package `OmnipathR` version: 4.1.0 [2026-05-04 23:57:10] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.24 [2026-05-04 23:57:11] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2026-05-04; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto] [2026-05-04 23:57:11] [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=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; 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=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0] [2026-05-04 23:57:11] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.0(2026-04-21); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.6(2026-04-09); colorspace 2.1-2(2025-09-22); ComplexUpset 1.3.3(2021-12-11); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); dplyr 1.1.4(2023-11-17); EnhancedVolcano 1.31.0(2026-05-04); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 2.1.0(2026-04-18); generics 0.1.4(2025-05-09); ggplot2 4.0.0(2025-09-11); ggrepel 0.9.6(2024-09-07); glue 1.8.1(2026-04-17); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); MetaProViz 4.1.0(2026-05-04); OmnipathR 4.1.0(2026-05-04); otel 0.2.0(2025-08-29); patchwork 1.3.2(2025-08-25); pillar 1.11.1(2025-09-17); 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 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); 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 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); 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 0.54(2025-10-30); XML 3.99-0.19(2025-08-22); xml2 1.4.1(2025-10-27); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2026-05-04 23:57:11] [INFO] [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; 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 [2026-05-04 23:57:11] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-05-04 23:57:11] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2026-05-04 23:57:11] [TRACE] [OmnipathR] Contains 1 files. [2026-05-04 23:57:11] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-05-04 23:57:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-04 23:57:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-04 23:57:11] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2026-05-04 23:57:11] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2026-05-04 23:57:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-05-04 23:57:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-04 23:57:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-05-04 23:57:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-04 23:57:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-05-04 23:57:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-04 23:57:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-05-04 23:57:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-04 23:57:11] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2026-05-04 23:57:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-04 23:57:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-04 23:57:29] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2026-05-04 23:57:29] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-05-04 23:57:29] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-05-04 [2026-05-04 23:57:29] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2026-05-04 23:32:07 UTC; unix [2026-05-04 23:57:29] [INFO] [OmnipathR] Package `OmnipathR` version: 4.1.0 [2026-05-04 23:57:29] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.24 [2026-05-04 23:57:29] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2026-05-04; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto] [2026-05-04 23:57:29] [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=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; 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=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0] [2026-05-04 23:57:29] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.0(2026-04-21); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.6(2026-04-09); colorspace 2.1-2(2025-09-22); ComplexUpset 1.3.3(2021-12-11); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); dplyr 1.1.4(2023-11-17); EnhancedVolcano 1.31.0(2026-05-04); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 2.1.0(2026-04-18); generics 0.1.4(2025-05-09); ggplot2 4.0.0(2025-09-11); ggrepel 0.9.6(2024-09-07); glue 1.8.1(2026-04-17); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); MetaProViz 4.1.0(2026-05-04); OmnipathR 4.1.0(2026-05-04); otel 0.2.0(2025-08-29); patchwork 1.3.2(2025-08-25); pillar 1.11.1(2025-09-17); 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 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); 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 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); 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 0.54(2025-10-30); XML 3.99-0.19(2025-08-22); xml2 1.4.1(2025-10-27); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2026-05-04 23:57:29] [INFO] [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; 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 [2026-05-04 23:57:29] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-05-04 23:57:29] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2026-05-04 23:57:30] [TRACE] [OmnipathR] Contains 1 files. [2026-05-04 23:57:30] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-05-04 23:57:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-04 23:57:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-04 23:57:30] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2026-05-04 23:57:30] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2026-05-04 23:57:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-05-04 23:57:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-04 23:57:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-05-04 23:57:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-04 23:57:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-05-04 23:57:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-04 23:57:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-05-04 23:57:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-04 23:57:30] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (MetaProViz)
MetaProViz.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.
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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)
[2026-05-05 12:02:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-05 12:02:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-05 12:02:04] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-05-05 12:02:04] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-05-05 12:02:04] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-05-04
[2026-05-05 12:02:04] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2026-05-04 23:32:07 UTC; unix
[2026-05-05 12:02:04] [INFO] [OmnipathR] Package `OmnipathR` version: 4.1.0
[2026-05-05 12:02:04] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.24
[2026-05-05 12:02:05] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=UTC; date=2026-05-05; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2026-05-05 12:02:05] [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=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; 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=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0]
[2026-05-05 12:02:05] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.0(2026-04-21); 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 2.3.3(2025-08-18); cli 3.6.6(2026-04-09); colorspace 2.1-2(2025-09-22); ComplexUpset 1.3.3(2021-12-11); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.1.4(2023-11-17); EnhancedVolcano 1.31.0(2026-05-04); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 2.1.0(2026-04-18); generics 0.1.4(2025-05-09); ggplot2 4.0.0(2025-09-11); ggrepel 0.9.6(2024-09-07); glue 1.8.1(2026-04-17); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); MetaProViz 4.1.0(2026-05-04); OmnipathR 4.1.0(2026-05-04); otel 0.2.0(2025-08-29); patchwork 1.3.2(2025-08-25); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); 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 1.5.2(2025-09-08); testthat 3.2.3(2025-01-13); tibble 3.3.0(2025-06-08); 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 0.54(2025-10-30); XML 3.99-0.19(2025-08-22); xml2 1.4.1(2025-10-27); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2026-05-05 12:02:05] [INFO] [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; 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
[2026-05-05 12:02:05] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-05-05 12:02:05] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-05-05 12:02:05] [TRACE] [OmnipathR] Contains 23 files.
[2026-05-05 12:02:05] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-05-05 12:02:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-05 12:02:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-05 12:02:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-05-05 12:02:05] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2026-05-05 12:02:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-05-05 12:02:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-05 12:02:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-05-05 12:02:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-05 12:02:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-05-05 12:02:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-05 12:02:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-05-05 12:02:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-05-05 12:02:05] [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%.
[2026-05-05 12:02:19] [TRACE] [MetaProViz] Error The HMDB column selected as InpuID in metadata_info was not found in data. Please check your input.
[2026-05-05 12:02:19] [TRACE] [MetaProViz] Error The HMDB column selected as InpuID in metadata_info was not found in data. Please check your input.
[2026-05-05 12:02:19] [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
16.279 2.681 18.995
MetaProViz.Rcheck/MetaProViz-Ex.timings
| name | user | system | elapsed | |
| alanine_pathways | 0.058 | 0.009 | 0.066 | |
| biocrates_features | 0.081 | 0.024 | 0.106 | |
| cellular_meta | 0.038 | 0.000 | 0.037 | |
| checkmatch_pk_to_data | 0.001 | 0.000 | 0.000 | |
| cluster_ora | 97.592 | 15.524 | 369.860 | |
| cluster_pk | 0.293 | 0.068 | 0.363 | |
| compare_pk | 0.000 | 0.000 | 0.001 | |
| count_id | 2.359 | 0.433 | 2.789 | |
| dma | 33.023 | 2.924 | 36.058 | |
| equivalent_features | 0.039 | 0.004 | 0.044 | |
| equivalent_id | 11.947 | 0.488 | 12.471 | |
| gaude_pathways | 0.031 | 0.004 | 0.036 | |
| get_exclusion_metabolites | 0 | 0 | 0 | |
| hallmarks | 0.037 | 0.000 | 0.037 | |
| intracell_dma | 0.067 | 0.004 | 0.071 | |
| intracell_raw | 0.126 | 0.012 | 0.138 | |
| intracell_raw_se | 0.043 | 0.008 | 0.051 | |
| make_gene_metab_set | 1.823 | 0.473 | 2.372 | |
| mapping_ambiguity | 0 | 0 | 0 | |
| mca_2cond | 13.643 | 1.036 | 14.718 | |
| mca_core | 0.212 | 0.012 | 0.223 | |
| mca_core_rules | 0.037 | 0.012 | 0.049 | |
| mca_twocond_rules | 0.026 | 0.008 | 0.035 | |
| medium_raw | 0.086 | 0.024 | 0.109 | |
| meta_pk | 0.138 | 0.004 | 0.142 | |
| metadata_analysis | 6.543 | 0.445 | 6.991 | |
| metaproviz_config_path | 0.000 | 0.000 | 0.001 | |
| metaproviz_load_config | 0.004 | 0.000 | 0.004 | |
| metaproviz_log | 0.001 | 0.000 | 0.000 | |
| metaproviz_logfile | 0.002 | 0.000 | 0.002 | |
| metaproviz_reset_config | 0.011 | 0.000 | 0.011 | |
| metaproviz_save_config | 0.005 | 0.004 | 0.009 | |
| metaproviz_set_loglevel | 0.002 | 0.000 | 0.003 | |
| metsigdb_chemicalclass | 1.903 | 0.229 | 2.061 | |
| metsigdb_kegg | 2.118 | 0.156 | 2.278 | |
| metsigdb_metalinks | 3.900 | 0.377 | 15.967 | |
| metsigdb_reactome | 0 | 0 | 0 | |
| pool_estimation | 10.539 | 0.655 | 11.209 | |
| processing | 13.345 | 1.325 | 14.709 | |
| replicate_sum | 0.750 | 0.076 | 0.828 | |
| standard_ora | 1.966 | 0.134 | 2.106 | |
| tissue_dma | 0.080 | 0.004 | 0.084 | |
| tissue_dma_old | 0.071 | 0.012 | 0.084 | |
| tissue_dma_young | 0.074 | 0.012 | 0.086 | |
| tissue_meta | 0.057 | 0.008 | 0.065 | |
| tissue_norm | 0.185 | 0.020 | 0.206 | |
| tissue_norm_se | 0.048 | 0.004 | 0.051 | |
| tissue_tvn_proteomics | 0.067 | 0.012 | 0.079 | |
| tissue_tvn_rnaseq | 0.122 | 0.004 | 0.126 | |
| translate_id | 0 | 0 | 0 | |
| traverse_ids | 43.695 | 1.115 | 44.759 | |
| viz_graph | 0.724 | 0.039 | 0.769 | |
| viz_heatmap | 1.066 | 0.071 | 1.141 | |
| viz_pca | 4.785 | 0.169 | 4.961 | |
| viz_superplot | 4.674 | 0.387 | 5.095 | |
| viz_volcano | 0.977 | 0.079 | 1.065 | |