Christina Schmidt
| Snapshot Date: 2026-03-17 13:40 -0400 (Tue, 17 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/MetaProViz |
| git_branch: devel |
| git_last_commit: 33d7172 |
| git_last_commit_date: 2026-02-18 17:57:31 -0400 (Wed, 18 Feb 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-18 11:34 -0400 (Wed, 18 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4857 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences" | 4060 |
| 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 1261/2367 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MetaProViz 3.99.40 (landing page) Christina Schmidt
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | 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. |
| Package: MetaProViz |
| Version: 3.99.40 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:MetaProViz.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings MetaProViz_3.99.40.tar.gz |
| StartedAt: 2026-03-18 01:16:12 -0400 (Wed, 18 Mar 2026) |
| EndedAt: 2026-03-18 01:27:00 -0400 (Wed, 18 Mar 2026) |
| EllapsedTime: 647.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: MetaProViz.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:MetaProViz.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings MetaProViz_3.99.40.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/MetaProViz.Rcheck’
* using R Under development (unstable) (2026-03-05 r89546)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-18 05:16:13 UTC
* checking for file ‘MetaProViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MetaProViz’ version ‘3.99.40’
* 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
[2026-03-18 01:18:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-18 01:18:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:18:05] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-03-18 01:18:05] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-03-18 01:18:05] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-03-17
[2026-03-18 01:18:05] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-17 19:09:17 UTC; unix
[2026-03-18 01:18:05] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.7
[2026-03-18 01:18:05] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-03-18 01:18:06] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-05 r89546); os=Ubuntu 24.04.4 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-18; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2026-03-18 01:18:06] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-03-18 01:18:06] [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 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); colorspace 2.1-2(2025-09-22); ComplexUpset 1.3.3(2021-12-11); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); EnhancedVolcano 1.29.1(2026-03-17); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 1.6.7(2026-03-06); generics 0.1.4(2025-05-09); ggplot2 4.0.2(2026-02-03); ggrepel 0.9.8(2026-03-17); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); MetaProViz 3.99.40(2026-03-17); OmnipathR 3.19.7(2026-03-17); 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 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); scales 1.4.0(2025-04-24); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-18 01:18:06] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-03-18 01:18:06] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-03-18 01:18:06] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-03-18 01:18:06] [TRACE] [OmnipathR] Contains 1 files.
[2026-03-18 01:18:06] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-03-18 01:18:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-18 01:18:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:18:06] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-03-18 01:18:06] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2026-03-18 01:18:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-18 01:18:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:18:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-18 01:18:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:18:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-18 01:18:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:18:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-18 01:18:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:18:06] [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
[2026-03-18 01:19:22] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-18 01:19:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:19:22] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-03-18 01:19:22] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-03-18 01:19:22] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-03-17
[2026-03-18 01:19:22] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-17 19:09:17 UTC; unix
[2026-03-18 01:19:22] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.7
[2026-03-18 01:19:22] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-03-18 01:19:22] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-05 r89546); os=Ubuntu 24.04.4 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-18; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2026-03-18 01:19:23] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-03-18 01:19:23] [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 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); colorspace 2.1-2(2025-09-22); ComplexUpset 1.3.3(2021-12-11); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); EnhancedVolcano 1.29.1(2026-03-17); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 1.6.7(2026-03-06); generics 0.1.4(2025-05-09); ggplot2 4.0.2(2026-02-03); ggrepel 0.9.8(2026-03-17); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); MetaProViz 3.99.40(2026-03-17); OmnipathR 3.19.7(2026-03-17); 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 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); scales 1.4.0(2025-04-24); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-18 01:19:23] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-03-18 01:19:23] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-03-18 01:19:23] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-03-18 01:19:23] [TRACE] [OmnipathR] Contains 1 files.
[2026-03-18 01:19:23] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-03-18 01:19:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-18 01:19:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:19:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-03-18 01:19:23] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2026-03-18 01:19:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-18 01:19:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:19:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-18 01:19:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:19:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-18 01:19:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:19:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-18 01:19:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:19:23] [TRACE] [OmnipathR] Cache locked: FALSE
* 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
equivalent_id 55.058 8.122 69.061
dma 20.447 2.267 22.428
processing 9.930 1.280 11.065
mca_2cond 9.900 1.012 10.761
cluster_ora 9.542 1.221 30.702
pool_estimation 7.780 0.626 8.308
metadata_analysis 4.996 0.476 5.410
standard_ora 3.962 0.730 5.760
metsigdb_metalinks 2.462 1.070 12.340
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘quick-start.Rmd’ using rmarkdown
[2026-03-18 01:25:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-18 01:25:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:25:28] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-03-18 01:25:28] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-03-18 01:25:28] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-03-17
[2026-03-18 01:25:28] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-17 19:09:17 UTC; unix
[2026-03-18 01:25:28] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.7
[2026-03-18 01:25:28] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-03-18 01:25:28] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-05 r89546); os=Ubuntu 24.04.4 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-18; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2026-03-18 01:25:28] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-03-18 01:25:29] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.39.0(2026-03-17); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); colorspace 2.1-2(2025-09-22); ComplexUpset 1.3.3(2021-12-11); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); EnhancedVolcano 1.29.1(2026-03-17); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 1.6.7(2026-03-06); generics 0.1.4(2025-05-09); ggplot2 4.0.2(2026-02-03); ggrepel 0.9.8(2026-03-17); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); MetaProViz 3.99.40(2026-03-17); OmnipathR 3.19.7(2026-03-17); 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 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-18 01:25:29] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-03-18 01:25:29] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-03-18 01:25:29] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-03-18 01:25:29] [TRACE] [OmnipathR] Contains 1 files.
[2026-03-18 01:25:29] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-03-18 01:25:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-18 01:25:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:25:29] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-03-18 01:25:29] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2026-03-18 01:25:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-18 01:25:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:25:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-18 01:25:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:25:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-18 01:25:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:25:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-18 01:25:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:25:29] [TRACE] [OmnipathR] Cache locked: FALSE
[2026-03-18 01:25:41] [INFO] [MetaProViz] feature_filtering: Here we apply the modified 80%-filtering rule that takes the class information (Column `Conditions`) into account, which additionally reduces the effect of missing values (REF: Yang et. al., (2015), doi: 10.3389/fmolb.2015.00004). Filtering value selected: 0.8
[2026-03-18 01:25:41] [INFO] [MetaProViz] 3 metabolites where removed: AICAR, FAICAR, SAICAR
[2026-03-18 01:25:42] [INFO] [MetaProViz] Missing Value Imputation: Missing value imputation is performed, as a complementary approach to address the missing value problem, where the missing values are imputing using the `half minimum value`. REF: Wei et. al., (2018), Reports, 8, 663, doi:https://doi.org/10.1038/s41598-017-19120-0
[2026-03-18 01:25:43] [INFO] [MetaProViz] total Ion Count (tic) normalization: total Ion Count (tic) normalization is used to reduce the variation from non-biological sources, while maintaining the biological variation. REF: Wulff et. al., (2018), Advances in Bioscience and Biotechnology, 9, 339-351, doi:https://doi.org/10.4236/abb.2018.98022
[2026-03-18 01:25:49] [INFO] [MetaProViz] Outlier detection: Identification of outlier samples is performed using Hotellin's T2 test to define sample outliers in a mathematical way (Confidence = 0.99 ~ p.val < 0.01) (REF: Hotelling, H. (1931), Annals of Mathematical Statistics. 2 (3), 360-378, doi:https://doi.org/10.1214/aoms/1177732979). hotellins_confidence value selected: 0.99
[2026-03-18 01:25:49] [INFO] [MetaProViz] viz_pca: PCA plot visualization
[2026-03-18 01:25:49] [INFO] [MetaProViz] character(0)
[2026-03-18 01:25:49] [INFO] [MetaProViz] viz_pca colour: #88CCEE, #DDCC77, #661100, #332288, #AA4499, #999933, #44AA99, #882215, #6699CC, #117733, #888888, #CC6677, black, gold1, darkorchid4, red, orange, blue
[2026-03-18 01:25:49] [INFO] [MetaProViz] viz_pca shape: 15, 17, 16, 18, 6, 7, 8, 11, 12
[2026-03-18 01:25:49] [INFO] [MetaProViz] viz_pca scale_color: discrete
[2026-03-18 01:25:49] [TRACE] [MetaProViz] The plot has legend, adjusting layout to accommodate it.
[2026-03-18 01:25:49] [TRACE] [MetaProViz] Sections: color, shape
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Legend nchar: 2.50cm, Legend width: 2.60cm
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Parsing unit from `2.60cm`
[2026-03-18 01:25:50] [TRACE] [MetaProViz] The plot has title, adjusting layout to accommodate it.
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Parsing unit from `0.5cm`
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Parsing unit from `12`
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Parsing unit from `11`
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Parsing unit from `8cm`
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Setting widths[7] to 8cm [name=axis-b, offset=0, empty=FALSE, original=1null]
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Setting widths[1] to 0cm [name=ylab-l, offset=-4, empty=FALSE, original=5.5points]
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Setting widths[6] to 1cm [name=axis-l, offset=0, empty=FALSE, original=sum(0cm, 1null, 0.70406615677321cm, 0null, max(0points, -0.0966514459665145cm), 0.0966514459665145cm)]
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Setting widths[5] to 1cm [name=ylab-l, offset=0, empty=FALSE, original=1grobwidth]
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Setting widths[3] to 0cm [name=guide-box-left, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Setting widths[8] to 0cm [name=axis-r, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Setting widths[9] to 0cm [name=ylab-r, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Setting widths[4] to 1cm [name=ylab-l, offset=-1, empty=TRUE, original=0points]
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Setting widths[11] to 1cm [name=guide-box-right, offset=0, empty=FALSE, original=sum(0.5null, 0points, 2.55729867579909cm, 0points, 0.5null)]
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Parsing unit from `8cm`
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Setting heights[9] to 8cm [name=axis-l, offset=0, empty=FALSE, original=1null]
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Setting heights[10] to 1cm [name=axis-b, offset=0, empty=FALSE, original=sum(0.0966514459665145cm, max(0points, -0.0966514459665145cm), 0null, 0.375136156773213cm, 1null, 0cm)]
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Parsing unit from `.5cm`
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Setting heights[11] to 0.5cm [name=xlab-b, offset=0, empty=FALSE, original=1grobheight]
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Setting heights[12] to 1cm [name=xlab-b, offset=1, empty=TRUE, original=0points]
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Setting heights[1] to 0cm [name=title, offset=-2, empty=FALSE, original=5.5points]
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Setting heights[2] to 0cm [name=title, offset=-1, empty=TRUE, original=0points]
[2026-03-18 01:25:50] [TRACE] [MetaProViz] Parsing unit from `0.25cm`
[2026-03-18 01:25:51] [TRACE] [MetaProViz] Setting heights[3] to 0.25cm [name=title, offset=0, empty=FALSE, original=1grobheight]
[2026-03-18 01:25:51] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:51] [TRACE] [MetaProViz] Setting heights[4] to 0cm [name=subtitle, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:25:51] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:51] [TRACE] [MetaProViz] Setting heights[5] to 0cm [name=guide-box-top, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:25:51] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:51] [TRACE] [MetaProViz] Setting heights[6] to 0cm [name=xlab-t, offset=-1, empty=TRUE, original=0points]
[2026-03-18 01:25:51] [TRACE] [MetaProViz] Setting heights[3] to 0.5cm [name=title, main, offset=0, empty=FALSE, original=0.25cm]
[2026-03-18 01:25:51] [TRACE] [MetaProViz] Parsing unit from `0.5cm`
[2026-03-18 01:25:51] [TRACE] [MetaProViz] Setting heights[4] to 0.5cm [name=subtitle, main, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:25:51] [TRACE] [MetaProViz] Parsing unit from `-2.45cm`
[2026-03-18 01:25:51] [TRACE] [MetaProViz] Setting widths[11] to max(-2.45cm, 1cm) [name=guide-box-right, legend, offset=0, empty=FALSE, original=1cm]
[2026-03-18 01:25:51] [TRACE] [MetaProViz] Adding sum(max(2.6cm, -2.45cm, 1cm), -1*max(-2.45cm, 1cm)) to the total width of the gtable, growing it from 12cm to sum(12cm, max(2.6cm, -2.45cm, 1cm), -1*max(-2.45cm, 1cm)).
[2026-03-18 01:25:51] [TRACE] [MetaProViz] Setting widths[11] to max(2.6cm, -2.45cm, 1cm) [name=guide-box-right, offset=0, empty=FALSE, original=max(-2.45cm, 1cm)]
[2026-03-18 01:25:51] [TRACE] [MetaProViz] Sum of heights: 12.00, sum of widths: 13.60
[2026-03-18 01:25:51] [INFO] [MetaProViz] viz_pca: PCA plot visualization
[2026-03-18 01:25:51] [INFO] [MetaProViz] character(0)
[2026-03-18 01:25:51] [INFO] [MetaProViz] viz_pca colour: #88CCEE, #DDCC77, #661100, #332288, #AA4499, #999933, #44AA99, #882215, #6699CC, #117733, #888888, #CC6677, black, gold1, darkorchid4, red, orange, blue
[2026-03-18 01:25:51] [INFO] [MetaProViz] viz_pca shape: 15, 17, 16, 18, 6, 7, 8, 11, 12
[2026-03-18 01:25:51] [INFO] [MetaProViz] viz_pca scale_color: discrete
[2026-03-18 01:25:51] [TRACE] [MetaProViz] The plot has legend, adjusting layout to accommodate it.
[2026-03-18 01:25:51] [TRACE] [MetaProViz] Sections: color, shape
[2026-03-18 01:25:51] [TRACE] [MetaProViz] Legend nchar: 2.50cm, Legend width: 2.60cm
[2026-03-18 01:25:51] [TRACE] [MetaProViz] Parsing unit from `2.60cm`
[2026-03-18 01:25:51] [TRACE] [MetaProViz] The plot has title, adjusting layout to accommodate it.
[2026-03-18 01:25:51] [TRACE] [MetaProViz] Parsing unit from `0.5cm`
[2026-03-18 01:25:52] [TRACE] [MetaProViz] Parsing unit from `12`
[2026-03-18 01:25:52] [TRACE] [MetaProViz] Parsing unit from `11`
[2026-03-18 01:25:52] [TRACE] [MetaProViz] Parsing unit from `8cm`
[2026-03-18 01:25:52] [TRACE] [MetaProViz] Setting widths[7] to 8cm [name=axis-b, offset=0, empty=FALSE, original=1null]
[2026-03-18 01:25:52] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:52] [TRACE] [MetaProViz] Setting widths[1] to 0cm [name=ylab-l, offset=-4, empty=FALSE, original=5.5points]
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Setting widths[6] to 1cm [name=axis-l, offset=0, empty=FALSE, original=sum(0cm, 1null, 0.70406615677321cm, 0null, max(0points, -0.0966514459665145cm), 0.0966514459665145cm)]
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Setting widths[5] to 1cm [name=ylab-l, offset=0, empty=FALSE, original=1grobwidth]
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Setting widths[3] to 0cm [name=guide-box-left, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Setting widths[8] to 0cm [name=axis-r, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Setting widths[9] to 0cm [name=ylab-r, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Setting widths[4] to 1cm [name=ylab-l, offset=-1, empty=TRUE, original=0points]
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Setting widths[11] to 1cm [name=guide-box-right, offset=0, empty=FALSE, original=sum(0.5null, 0points, 2.55729867579909cm, 0points, 0.5null)]
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Parsing unit from `8cm`
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Setting heights[9] to 8cm [name=axis-l, offset=0, empty=FALSE, original=1null]
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Setting heights[10] to 1cm [name=axis-b, offset=0, empty=FALSE, original=sum(0.0966514459665145cm, max(0points, -0.0966514459665145cm), 0null, 0.375136156773213cm, 1null, 0cm)]
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Parsing unit from `.5cm`
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Setting heights[11] to 0.5cm [name=xlab-b, offset=0, empty=FALSE, original=1grobheight]
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Setting heights[12] to 1cm [name=xlab-b, offset=1, empty=TRUE, original=0points]
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Setting heights[1] to 0cm [name=title, offset=-2, empty=FALSE, original=5.5points]
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Setting heights[2] to 0cm [name=title, offset=-1, empty=TRUE, original=0points]
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Parsing unit from `0.25cm`
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Setting heights[3] to 0.25cm [name=title, offset=0, empty=FALSE, original=1grobheight]
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Setting heights[4] to 0cm [name=subtitle, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Setting heights[5] to 0cm [name=guide-box-top, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Setting heights[6] to 0cm [name=xlab-t, offset=-1, empty=TRUE, original=0points]
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Setting heights[3] to 0.5cm [name=title, main, offset=0, empty=FALSE, original=0.25cm]
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Parsing unit from `0.5cm`
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Setting heights[4] to 0.5cm [name=subtitle, main, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Parsing unit from `-2.45cm`
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Setting widths[11] to max(-2.45cm, 1cm) [name=guide-box-right, legend, offset=0, empty=FALSE, original=1cm]
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Adding sum(max(2.6cm, -2.45cm, 1cm), -1*max(-2.45cm, 1cm)) to the total width of the gtable, growing it from 12cm to sum(12cm, max(2.6cm, -2.45cm, 1cm), -1*max(-2.45cm, 1cm)).
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Setting widths[11] to max(2.6cm, -2.45cm, 1cm) [name=guide-box-right, offset=0, empty=FALSE, original=max(-2.45cm, 1cm)]
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Sum of heights: 12.00, sum of widths: 13.60
[2026-03-18 01:25:53] [INFO] [MetaProViz] There are possible outlier samples in the data
[2026-03-18 01:25:53] [INFO] [MetaProViz] Filtering round 1 Outlier Samples: MS55_29
[2026-03-18 01:25:53] [INFO] [MetaProViz] viz_pca: PCA plot visualization
[2026-03-18 01:25:53] [INFO] [MetaProViz] character(0)
[2026-03-18 01:25:53] [INFO] [MetaProViz] viz_pca colour: #88CCEE, #DDCC77, #661100, #332288, #AA4499, #999933, #44AA99, #882215, #6699CC, #117733, #888888, #CC6677, black, gold1, darkorchid4, red, orange, blue
[2026-03-18 01:25:53] [INFO] [MetaProViz] viz_pca shape: 15, 17, 16, 18, 6, 7, 8, 11, 12
[2026-03-18 01:25:53] [INFO] [MetaProViz] viz_pca scale_color: discrete
[2026-03-18 01:25:53] [TRACE] [MetaProViz] The plot has legend, adjusting layout to accommodate it.
[2026-03-18 01:25:53] [TRACE] [MetaProViz] Sections: color, shape
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Legend nchar: 2.50cm, Legend width: 4.90cm
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Parsing unit from `4.90cm`
[2026-03-18 01:25:54] [TRACE] [MetaProViz] The plot has title, adjusting layout to accommodate it.
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Parsing unit from `0.5cm`
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Parsing unit from `12`
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Parsing unit from `11`
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Parsing unit from `8cm`
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Setting widths[7] to 8cm [name=axis-b, offset=0, empty=FALSE, original=1null]
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Setting widths[1] to 0cm [name=ylab-l, offset=-4, empty=FALSE, original=5.5points]
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Setting widths[6] to 1cm [name=axis-l, offset=0, empty=FALSE, original=sum(0cm, 1null, 0.70406615677321cm, 0null, max(0points, -0.0966514459665145cm), 0.0966514459665145cm)]
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Setting widths[5] to 1cm [name=ylab-l, offset=0, empty=FALSE, original=1grobwidth]
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Setting widths[3] to 0cm [name=guide-box-left, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Setting widths[8] to 0cm [name=axis-r, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Setting widths[9] to 0cm [name=ylab-r, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Setting widths[4] to 1cm [name=ylab-l, offset=-1, empty=TRUE, original=0points]
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Setting widths[11] to 1cm [name=guide-box-right, offset=0, empty=FALSE, original=sum(0.5null, 0points, 4.94426367579909cm, 0points, 0.5null)]
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Parsing unit from `8cm`
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Setting heights[9] to 8cm [name=axis-l, offset=0, empty=FALSE, original=1null]
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Setting heights[10] to 1cm [name=axis-b, offset=0, empty=FALSE, original=sum(0.0966514459665145cm, max(0points, -0.0966514459665145cm), 0null, 0.375136156773213cm, 1null, 0cm)]
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Parsing unit from `.5cm`
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Setting heights[11] to 0.5cm [name=xlab-b, offset=0, empty=FALSE, original=1grobheight]
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Setting heights[12] to 1cm [name=xlab-b, offset=1, empty=TRUE, original=0points]
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Setting heights[1] to 0cm [name=title, offset=-2, empty=FALSE, original=5.5points]
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Setting heights[2] to 0cm [name=title, offset=-1, empty=TRUE, original=0points]
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Parsing unit from `0.25cm`
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Setting heights[3] to 0.25cm [name=title, offset=0, empty=FALSE, original=1grobheight]
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Setting heights[4] to 0cm [name=subtitle, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Setting heights[5] to 0cm [name=guide-box-top, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Setting heights[6] to 0cm [name=xlab-t, offset=-1, empty=TRUE, original=0points]
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Setting heights[3] to 0.5cm [name=title, main, offset=0, empty=FALSE, original=0.25cm]
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Parsing unit from `0.5cm`
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Setting heights[4] to 0.5cm [name=subtitle, main, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Parsing unit from `3.30cm`
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Setting widths[11] to max(3.3cm, 1cm) [name=guide-box-right, legend, offset=0, empty=FALSE, original=1cm]
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Adding sum(max(4.9cm, 3.3cm, 1cm), -1*max(3.3cm, 1cm)) to the total width of the gtable, growing it from 15.3cm to sum(15.3cm, max(4.9cm, 3.3cm, 1cm), -1*max(3.3cm, 1cm)).
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Setting widths[11] to max(4.9cm, 3.3cm, 1cm) [name=guide-box-right, offset=0, empty=FALSE, original=max(3.3cm, 1cm)]
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Sum of heights: 12.00, sum of widths: 16.90
[2026-03-18 01:25:54] [INFO] [MetaProViz] viz_pca: PCA plot visualization
[2026-03-18 01:25:54] [INFO] [MetaProViz] character(0)
[2026-03-18 01:25:54] [INFO] [MetaProViz] viz_pca colour: #88CCEE, #DDCC77, #661100, #332288, #AA4499, #999933, #44AA99, #882215, #6699CC, #117733, #888888, #CC6677, black, gold1, darkorchid4, red, orange, blue
[2026-03-18 01:25:54] [INFO] [MetaProViz] viz_pca shape: 15, 17, 16, 18, 6, 7, 8, 11, 12
[2026-03-18 01:25:54] [INFO] [MetaProViz] viz_pca scale_color: discrete
[2026-03-18 01:25:54] [TRACE] [MetaProViz] The plot has legend, adjusting layout to accommodate it.
[2026-03-18 01:25:54] [TRACE] [MetaProViz] Sections: color, shape
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Legend nchar: 5.25cm, Legend width: 5.25cm
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Parsing unit from `5.25cm`
[2026-03-18 01:25:55] [TRACE] [MetaProViz] The plot has title, adjusting layout to accommodate it.
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Parsing unit from `0.5cm`
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Parsing unit from `12`
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Parsing unit from `11`
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Parsing unit from `8cm`
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Setting widths[7] to 8cm [name=axis-b, offset=0, empty=FALSE, original=1null]
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Setting widths[1] to 0cm [name=ylab-l, offset=-4, empty=FALSE, original=5.5points]
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Setting widths[6] to 1cm [name=axis-l, offset=0, empty=FALSE, original=sum(0cm, 1null, 0.70406615677321cm, 0null, max(0points, -0.0966514459665145cm), 0.0966514459665145cm)]
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Setting widths[5] to 1cm [name=ylab-l, offset=0, empty=FALSE, original=1grobwidth]
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Setting widths[3] to 0cm [name=guide-box-left, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Setting widths[8] to 0cm [name=axis-r, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Setting widths[9] to 0cm [name=ylab-r, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Setting widths[4] to 1cm [name=ylab-l, offset=-1, empty=TRUE, original=0points]
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Setting widths[11] to 1cm [name=guide-box-right, offset=0, empty=FALSE, original=sum(0.5null, 0points, 4.0742977283105cm, 0points, 0.5null)]
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Parsing unit from `8cm`
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Setting heights[9] to 8cm [name=axis-l, offset=0, empty=FALSE, original=1null]
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Setting heights[10] to 1cm [name=axis-b, offset=0, empty=FALSE, original=sum(0.0966514459665145cm, max(0points, -0.0966514459665145cm), 0null, 0.375136156773213cm, 1null, 0cm)]
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Parsing unit from `.5cm`
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Setting heights[11] to 0.5cm [name=xlab-b, offset=0, empty=FALSE, original=1grobheight]
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Setting heights[12] to 1cm [name=xlab-b, offset=1, empty=TRUE, original=0points]
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Setting heights[1] to 0cm [name=title, offset=-2, empty=FALSE, original=5.5points]
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Setting heights[2] to 0cm [name=title, offset=-1, empty=TRUE, original=0points]
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Parsing unit from `0.25cm`
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Setting heights[3] to 0.25cm [name=title, offset=0, empty=FALSE, original=1grobheight]
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Setting heights[4] to 0cm [name=subtitle, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Setting heights[5] to 0cm [name=guide-box-top, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Setting heights[6] to 0cm [name=xlab-t, offset=-1, empty=TRUE, original=0points]
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Setting heights[3] to 0.5cm [name=title, main, offset=0, empty=FALSE, original=0.25cm]
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Parsing unit from `0.5cm`
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Setting heights[4] to 0.5cm [name=subtitle, main, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Parsing unit from `-0.70cm`
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Setting widths[11] to max(-0.7cm, 1cm) [name=guide-box-right, legend, offset=0, empty=FALSE, original=1cm]
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Adding sum(max(5.25cm, -0.7cm, 1cm), -1*max(-0.7cm, 1cm)) to the total width of the gtable, growing it from 12cm to sum(12cm, max(5.25cm, -0.7cm, 1cm), -1*max(-0.7cm, 1cm)).
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Setting widths[11] to max(5.25cm, -0.7cm, 1cm) [name=guide-box-right, offset=0, empty=FALSE, original=max(-0.7cm, 1cm)]
[2026-03-18 01:25:55] [TRACE] [MetaProViz] Sum of heights: 12.00, sum of widths: 16.25
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/MetaProViz.Rcheck/vign_test/MetaProViz/vignettes/quick-start_files/figure-html/processing-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/MetaProViz.Rcheck/vign_test/MetaProViz/vignettes/quick-start_files/figure-html/processing-2.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/MetaProViz.Rcheck/vign_test/MetaProViz/vignettes/quick-start_files/figure-html/processing-3.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/MetaProViz.Rcheck/vign_test/MetaProViz/vignettes/quick-start_files/figure-html/processing-4.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/MetaProViz.Rcheck/vign_test/MetaProViz/vignettes/quick-start_files/figure-html/processing-5.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/MetaProViz.Rcheck/vign_test/MetaProViz/vignettes/quick-start_files/figure-html/processing-6.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/MetaProViz.Rcheck/vign_test/MetaProViz/vignettes/quick-start_files/figure-html/processing-7.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/MetaProViz.Rcheck/vign_test/MetaProViz/vignettes/quick-start_files/figure-html/processing-8.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/MetaProViz.Rcheck/vign_test/MetaProViz/vignettes/quick-start_files/figure-html/processing-9.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/MetaProViz.Rcheck/vign_test/MetaProViz/vignettes/quick-start_files/figure-html/processing-10.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/MetaProViz.Rcheck/vign_test/MetaProViz/vignettes/quick-start_files/figure-html/processing-11.png" but not available.
[2026-03-18 01:26:12] [INFO] [MetaProViz] viz_pca: PCA plot visualization
[2026-03-18 01:26:12] [INFO] [MetaProViz] viz_pca results saved at /home/biocbuild/bbs-3.23-bioc/meat/MetaProViz.Rcheck/vign_test/MetaProViz/vignettes/MetaProViz_Results/PCAPlots
[2026-03-18 01:26:12] [INFO] [MetaProViz] viz_pca colour: #88CCEE, #DDCC77, #661100, #332288, #AA4499, #999933, #44AA99, #882215, #6699CC, #117733, #888888, #CC6677, black, gold1, darkorchid4, red, orange, blue
[2026-03-18 01:26:12] [INFO] [MetaProViz] viz_pca shape: 15, 17, 16, 18, 6, 7, 8, 11, 12
[2026-03-18 01:26:13] [INFO] [MetaProViz] viz_pca scale_color: discrete
[2026-03-18 01:26:13] [TRACE] [MetaProViz] The plot has legend, adjusting layout to accommodate it.
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Sections: color, shape
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Legend nchar: 2.00cm, Legend width: 3.70cm
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Parsing unit from `3.70cm`
[2026-03-18 01:26:13] [TRACE] [MetaProViz] The plot has title, adjusting layout to accommodate it.
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Parsing unit from `0.5cm`
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Parsing unit from `12`
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Parsing unit from `11`
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Parsing unit from `8cm`
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Setting widths[7] to 8cm [name=axis-b, offset=0, empty=FALSE, original=1null]
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Setting widths[1] to 0cm [name=ylab-l, offset=-4, empty=FALSE, original=5.5points]
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Setting widths[6] to 1cm [name=axis-l, offset=0, empty=FALSE, original=sum(0cm, 1null, 0.791696156773212cm, 0null, max(0points, -0.0966514459665145cm), 0.0966514459665145cm)]
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Setting widths[5] to 1cm [name=ylab-l, offset=0, empty=FALSE, original=1grobwidth]
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Setting widths[3] to 0cm [name=guide-box-left, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Setting widths[8] to 0cm [name=axis-r, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Setting widths[9] to 0cm [name=ylab-r, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Setting widths[4] to 1cm [name=ylab-l, offset=-1, empty=TRUE, original=0points]
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Setting widths[11] to 1cm [name=guide-box-right, offset=0, empty=FALSE, original=sum(0.5null, 0points, 3.72950867579909cm, 0points, 0.5null)]
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Parsing unit from `8cm`
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Setting heights[9] to 8cm [name=axis-l, offset=0, empty=FALSE, original=1null]
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Setting heights[10] to 1cm [name=axis-b, offset=0, empty=FALSE, original=sum(0.0966514459665145cm, max(0points, -0.0966514459665145cm), 0null, 0.368362823439879cm, 1null, 0cm)]
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Parsing unit from `.5cm`
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Setting heights[11] to 0.5cm [name=xlab-b, offset=0, empty=FALSE, original=1grobheight]
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Setting heights[12] to 1cm [name=xlab-b, offset=1, empty=TRUE, original=0points]
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Setting heights[1] to 0cm [name=title, offset=-2, empty=FALSE, original=5.5points]
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Setting heights[2] to 0cm [name=title, offset=-1, empty=TRUE, original=0points]
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Parsing unit from `0.25cm`
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Setting heights[3] to 0.25cm [name=title, offset=0, empty=FALSE, original=1grobheight]
[2026-03-18 01:26:13] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:14] [TRACE] [MetaProViz] Setting heights[4] to 0cm [name=subtitle, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:26:14] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:14] [TRACE] [MetaProViz] Setting heights[5] to 0cm [name=guide-box-top, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:26:14] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:14] [TRACE] [MetaProViz] Setting heights[6] to 0cm [name=xlab-t, offset=-1, empty=TRUE, original=0points]
[2026-03-18 01:26:14] [TRACE] [MetaProViz] Setting heights[3] to 0.5cm [name=title, main, offset=0, empty=FALSE, original=0.25cm]
[2026-03-18 01:26:14] [TRACE] [MetaProViz] Parsing unit from `0.5cm`
[2026-03-18 01:26:14] [TRACE] [MetaProViz] Setting heights[4] to 0.5cm [name=subtitle, main, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:26:14] [TRACE] [MetaProViz] Parsing unit from `-8.95cm`
[2026-03-18 01:26:14] [TRACE] [MetaProViz] Setting widths[11] to max(-8.95cm, 1cm) [name=guide-box-right, legend, offset=0, empty=FALSE, original=1cm]
[2026-03-18 01:26:14] [TRACE] [MetaProViz] Adding sum(max(3.7cm, -8.95cm, 1cm), -1*max(-8.95cm, 1cm)) to the total width of the gtable, growing it from 12cm to sum(12cm, max(3.7cm, -8.95cm, 1cm), -1*max(-8.95cm, 1cm)).
[2026-03-18 01:26:14] [TRACE] [MetaProViz] Setting widths[11] to max(3.7cm, -8.95cm, 1cm) [name=guide-box-right, offset=0, empty=FALSE, original=max(-8.95cm, 1cm)]
[2026-03-18 01:26:14] [TRACE] [MetaProViz] Sum of heights: 12.00, sum of widths: 14.70
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/MetaProViz.Rcheck/vign_test/MetaProViz/vignettes/quick-start_files/figure-html/pca_plot-1.png" but not available.
[2026-03-18 01:26:15] [TRACE] [MetaProViz] Parsing unit from `12`
[2026-03-18 01:26:15] [TRACE] [MetaProViz] Parsing unit from `11`
[2026-03-18 01:26:15] [TRACE] [MetaProViz] Parsing unit from `2cm`
[2026-03-18 01:26:15] [TRACE] [MetaProViz] Setting widths[5] to 2cm [name=legend, offset=0, empty=FALSE, original=max(1.1grobwidth, sum(12bigpts, 1.32grobwidth))]
[2026-03-18 01:26:15] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:26:15] [TRACE] [MetaProViz] Setting heights[1] to 1cm [name=main, offset=0, empty=FALSE, original=1.5grobheight]
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/MetaProViz.Rcheck/vign_test/MetaProViz/vignettes/quick-start_files/figure-html/heatmap_plot-1.png" but not available.
[2026-03-18 01:26:15] [INFO] [MetaProViz] dma: Differential metabolite analysis.
[2026-03-18 01:26:15] [INFO] [MetaProViz] There are no NA/0 values
[2026-03-18 01:26:16] [INFO] [MetaProViz] For the condition 786-M1A, 94.41 % of the metabolites follow a normal distribution and 5.59 % of the metabolites are not-normally distributed according to the Shapiro-test. You have chosen t.test, which is for parametric hypothesis testing. `shapiro.test` ignores missing values in the calculation.
[2026-03-18 01:26:16] [INFO] [MetaProViz] For the condition HK2, 96.13 % of the metabolites follow a normal distribution and 3.87 % of the metabolites are not-normally distributed according to the Shapiro-test. You have chosen t.test, which is for parametric hypothesis testing. `shapiro.test` ignores missing values in the calculation.
[2026-03-18 01:26:18] [TRACE] [MetaProViz] The plot has title, adjusting layout to accommodate it.
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Parsing unit from `0.5cm`
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Parsing unit from `12`
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Parsing unit from `11`
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Parsing unit from `6cm`
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Setting widths[7] to 6cm [name=axis-b, offset=0, empty=FALSE, original=1null]
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Setting widths[1] to 0cm [name=ylab-l, offset=-4, empty=FALSE, original=12points]
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Setting widths[6] to 1cm [name=axis-l, offset=0, empty=FALSE, original=sum(0cm, 1null, 0.364845150131451cm, 0null, max(0points, -0.210875882108759cm), 0.210875882108759cm)]
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Setting widths[5] to 1cm [name=ylab-l, offset=0, empty=FALSE, original=1grobwidth]
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Setting widths[3] to 0cm [name=guide-box-left, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Setting widths[8] to 0cm [name=axis-r, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Setting widths[9] to 0cm [name=ylab-r, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Setting widths[4] to 1cm [name=ylab-l, offset=-1, empty=TRUE, original=0points]
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Setting widths[11] to 1cm [name=guide-box-right, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Parsing unit from `8cm`
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Setting heights[9] to 8cm [name=axis-l, offset=0, empty=FALSE, original=1null]
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Parsing unit from `0.75cm`
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Setting heights[10] to 0.75cm [name=axis-b, offset=0, empty=FALSE, original=sum(0.210875882108759cm, max(0points, -0.210875882108759cm), 0null, 0.499606261242562cm, 1null, 0cm)]
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Parsing unit from `0.75cm`
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Setting heights[11] to 0.75cm [name=xlab-b, offset=0, empty=FALSE, original=1grobheight]
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Setting heights[1] to 0cm [name=title, offset=-2, empty=FALSE, original=12points]
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Setting heights[2] to 0cm [name=title, offset=-1, empty=TRUE, original=0points]
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Parsing unit from `0.25cm`
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Setting heights[3] to 0.25cm [name=title, offset=0, empty=FALSE, original=1grobheight]
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Setting heights[4] to 0cm [name=subtitle, offset=0, empty=FALSE, original=1grobheight]
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Setting heights[5] to 0cm [name=guide-box-top, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Setting heights[6] to 0cm [name=xlab-t, offset=-1, empty=TRUE, original=0points]
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Setting heights[3] to 0.5cm [name=title, main, offset=0, empty=FALSE, original=0.25cm]
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Parsing unit from `0.5cm`
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Setting heights[4] to 0.5cm [name=subtitle, main, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Parsing unit from `-0.70cm`
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Setting widths[11] to max(-0.7cm, 1cm) [name=guide-box-right, legend, offset=0, empty=FALSE, original=1cm]
[2026-03-18 01:26:18] [TRACE] [MetaProViz] Sum of heights: 12.00, sum of widths: 12.00
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/MetaProViz.Rcheck/vign_test/MetaProViz/vignettes/quick-start_files/figure-html/dma-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/MetaProViz.Rcheck/vign_test/MetaProViz/vignettes/quick-start_files/figure-html/dma-2.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/MetaProViz.Rcheck/vign_test/MetaProViz/vignettes/quick-start_files/figure-html/dma-3.png" but not available.
[2026-03-18 01:26:21] [INFO] [MetaProViz] Load KEGG.
[2026-03-18 01:26:21] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-03-18 01:26:21] [TRACE] [OmnipathR] Looking up in cache: `https://rest.kegg.jp/link/compound/pathway`.
[2026-03-18 01:26:21] [INFO] [OmnipathR] Cache record does not exist: `https://rest.kegg.jp/link/compound/pathway`
[2026-03-18 01:26:21] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.kegg.jp/link/compound/pathway`.
[2026-03-18 01:26:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-18 01:26:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:26:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-18 01:26:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:26:21] [INFO] [OmnipathR] Cache item `c6ff89c85308605f76b13b8b7eef2efc510fca11` version 1: status changed from `unknown` to `started`.
[2026-03-18 01:26:21] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/c6ff89c85308605f76b13b8b7eef2efc510fca11-1.rds`.
[2026-03-18 01:26:21] [INFO] [OmnipathR] Retrieving URL: `https://rest.kegg.jp/link/compound/pathway`
[2026-03-18 01:26:21] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.kegg.jp/link/compound/pathway`
[2026-03-18 01:26:21] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-18 01:26:21] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-18 01:26:21] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-18 01:26:22] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-03-18 01:26:22] [TRACE] [OmnipathR] Downloaded 11.2 Kb in 0.821237s from rest.kegg.jp (13.6 Kb/s); Redirect: 0s, DNS look up: 0.001971s, Connection: 0.003135s, Pretransfer: 0.55316s, First byte at: 0.821167s
[2026-03-18 01:26:22] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Wed, 18 Mar 2026 05:26:21 GMT; Server: Apache; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked
[2026-03-18 01:26:26] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/c6ff89c85308605f76b13b8b7eef2efc510fca11-1.rds`.
[2026-03-18 01:26:26] [INFO] [OmnipathR] Download ready [key=c6ff89c85308605f76b13b8b7eef2efc510fca11, version=1]
[2026-03-18 01:26:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-18 01:26:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:26:26] [INFO] [OmnipathR] Cache item `c6ff89c85308605f76b13b8b7eef2efc510fca11` version 1: status changed from `started` to `ready`.
[2026-03-18 01:26:26] [SUCCESS] [OmnipathR] KEGG (rest.kegg.jp): downloaded 19564 records
[2026-03-18 01:26:26] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-03-18 01:26:26] [TRACE] [OmnipathR] Looking up in cache: `https://rest.kegg.jp/list/pathway`.
[2026-03-18 01:26:26] [INFO] [OmnipathR] Cache record does not exist: `https://rest.kegg.jp/list/pathway`
[2026-03-18 01:26:26] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.kegg.jp/list/pathway`.
[2026-03-18 01:26:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-18 01:26:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:26:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-18 01:26:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:26:26] [INFO] [OmnipathR] Cache item `0bd054860c052a2ac0d7a3849b304d085f377df0` version 1: status changed from `unknown` to `started`.
[2026-03-18 01:26:26] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/0bd054860c052a2ac0d7a3849b304d085f377df0-1.rds`.
[2026-03-18 01:26:26] [INFO] [OmnipathR] Retrieving URL: `https://rest.kegg.jp/list/pathway`
[2026-03-18 01:26:26] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.kegg.jp/list/pathway`
[2026-03-18 01:26:26] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-18 01:26:26] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-18 01:26:26] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-18 01:26:27] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-03-18 01:26:27] [TRACE] [OmnipathR] Downloaded 9.8 Kb in 0.805847s from rest.kegg.jp (12.1 Kb/s); Redirect: 0s, DNS look up: 0.001976s, Connection: 0.002739s, Pretransfer: 0.546072s, First byte at: 0.805777s
[2026-03-18 01:26:27] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Wed, 18 Mar 2026 05:26:26 GMT; Server: Apache; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked
[2026-03-18 01:26:28] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/0bd054860c052a2ac0d7a3849b304d085f377df0-1.rds`.
[2026-03-18 01:26:28] [INFO] [OmnipathR] Download ready [key=0bd054860c052a2ac0d7a3849b304d085f377df0, version=1]
[2026-03-18 01:26:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-18 01:26:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:26:28] [INFO] [OmnipathR] Cache item `0bd054860c052a2ac0d7a3849b304d085f377df0` version 1: status changed from `started` to `ready`.
[2026-03-18 01:26:28] [SUCCESS] [OmnipathR] KEGG (rest.kegg.jp): downloaded 585 records
[2026-03-18 01:26:28] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-03-18 01:26:28] [TRACE] [OmnipathR] Looking up in cache: `https://rest.kegg.jp/list/compound`.
[2026-03-18 01:26:28] [INFO] [OmnipathR] Cache record does not exist: `https://rest.kegg.jp/list/compound`
[2026-03-18 01:26:28] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.kegg.jp/list/compound`.
[2026-03-18 01:26:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-18 01:26:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:26:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-18 01:26:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:26:28] [INFO] [OmnipathR] Cache item `855597ce84b494f3ef3ac5750c407848569a7f66` version 1: status changed from `unknown` to `started`.
[2026-03-18 01:26:28] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/855597ce84b494f3ef3ac5750c407848569a7f66-1.rds`.
[2026-03-18 01:26:28] [INFO] [OmnipathR] Retrieving URL: `https://rest.kegg.jp/list/compound`
[2026-03-18 01:26:28] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.kegg.jp/list/compound`
[2026-03-18 01:26:28] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-18 01:26:28] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-18 01:26:28] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-18 01:26:29] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-03-18 01:26:29] [TRACE] [OmnipathR] Downloaded 9.8 Kb in 1.002933s from rest.kegg.jp (9.7 Kb/s); Redirect: 0s, DNS look up: 0.003525s, Connection: 0.004336s, Pretransfer: 0.548835s, First byte at: 1.002881s
[2026-03-18 01:26:29] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Wed, 18 Mar 2026 05:26:29 GMT; Server: Apache; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked
[2026-03-18 01:26:35] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/855597ce84b494f3ef3ac5750c407848569a7f66-1.rds`.
[2026-03-18 01:26:35] [INFO] [OmnipathR] Download ready [key=855597ce84b494f3ef3ac5750c407848569a7f66, version=1]
[2026-03-18 01:26:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-18 01:26:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:26:35] [INFO] [OmnipathR] Cache item `855597ce84b494f3ef3ac5750c407848569a7f66` version 1: status changed from `started` to `ready`.
[2026-03-18 01:26:35] [SUCCESS] [OmnipathR] KEGG (rest.kegg.jp): downloaded 19571 records
[2026-03-18 01:26:35] [INFO] [OmnipathR] Loading database `List of organisms in KEGG`.
[2026-03-18 01:26:35] [TRACE] [OmnipathR] Checking on-disk cache for database `kegg_organisms`.
[2026-03-18 01:26:35] [INFO] [OmnipathR] Cache record does not exist: `db://kegg_organisms`
[2026-03-18 01:26:35] [TRACE] [OmnipathR] Loading database `kegg_organisms` from source.
[2026-03-18 01:26:35] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-03-18 01:26:35] [TRACE] [OmnipathR] Looking up in cache: `https://rest.kegg.jp/list/organism`.
[2026-03-18 01:26:35] [INFO] [OmnipathR] Cache record does not exist: `https://rest.kegg.jp/list/organism`
[2026-03-18 01:26:35] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.kegg.jp/list/organism`.
[2026-03-18 01:26:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-18 01:26:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:26:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-18 01:26:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:26:35] [INFO] [OmnipathR] Cache item `e7c3da8d7f582ca4c3a757f7408df807fbe91b47` version 1: status changed from `unknown` to `started`.
[2026-03-18 01:26:35] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/e7c3da8d7f582ca4c3a757f7408df807fbe91b47-1.rds`.
[2026-03-18 01:26:35] [INFO] [OmnipathR] Retrieving URL: `https://rest.kegg.jp/list/organism`
[2026-03-18 01:26:35] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.kegg.jp/list/organism`
[2026-03-18 01:26:35] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-18 01:26:35] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-18 01:26:35] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-18 01:26:37] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-03-18 01:26:37] [TRACE] [OmnipathR] Downloaded 4.1 Kb in 1.390366s from rest.kegg.jp (2.9 Kb/s); Redirect: 0s, DNS look up: 0.002987s, Connection: 0.003835s, Pretransfer: 1.097046s, First byte at: 1.39031s
[2026-03-18 01:26:37] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Wed, 18 Mar 2026 05:26:36 GMT; Server: Apache; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked
[2026-03-18 01:26:42] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/e7c3da8d7f582ca4c3a757f7408df807fbe91b47-1.rds`.
[2026-03-18 01:26:42] [INFO] [OmnipathR] Download ready [key=e7c3da8d7f582ca4c3a757f7408df807fbe91b47, version=1]
[2026-03-18 01:26:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-18 01:26:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:26:42] [INFO] [OmnipathR] Cache item `e7c3da8d7f582ca4c3a757f7408df807fbe91b47` version 1: status changed from `started` to `ready`.
[2026-03-18 01:26:42] [SUCCESS] [OmnipathR] KEGG (rest.kegg.jp): downloaded 11635 records
[2026-03-18 01:26:42] [TRACE] [OmnipathR] Saving database `kegg_organisms` to on-disk cache.
[2026-03-18 01:26:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-18 01:26:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:26:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-18 01:26:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:26:43] [INFO] [OmnipathR] Cache item `67846511e943f593aa512e9096b2b1e2964deb90` version 1: status changed from `unknown` to `started`.
[2026-03-18 01:26:43] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/67846511e943f593aa512e9096b2b1e2964deb90-1.rds`.
[2026-03-18 01:26:43] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/67846511e943f593aa512e9096b2b1e2964deb90-1.rds`.
[2026-03-18 01:26:43] [INFO] [OmnipathR] Download ready [key=67846511e943f593aa512e9096b2b1e2964deb90, version=1]
[2026-03-18 01:26:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-18 01:26:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:26:43] [INFO] [OmnipathR] Cache item `67846511e943f593aa512e9096b2b1e2964deb90` version 1: status changed from `started` to `ready`.
[2026-03-18 01:26:43] [INFO] [OmnipathR] Loaded database `List of organisms in KEGG`.
[2026-03-18 01:26:43] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-03-18 01:26:43] [TRACE] [OmnipathR] Looking up in cache: `https://rest.kegg.jp/conv/compound/pubchem`.
[2026-03-18 01:26:43] [INFO] [OmnipathR] Cache record does not exist: `https://rest.kegg.jp/conv/compound/pubchem`
[2026-03-18 01:26:43] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.kegg.jp/conv/compound/pubchem`.
[2026-03-18 01:26:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-18 01:26:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:26:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-18 01:26:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:26:43] [INFO] [OmnipathR] Cache item `df48f267c99a2d8dd3cb7ed031941afbedc22d48` version 1: status changed from `unknown` to `started`.
[2026-03-18 01:26:43] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/df48f267c99a2d8dd3cb7ed031941afbedc22d48-1.rds`.
[2026-03-18 01:26:43] [INFO] [OmnipathR] Retrieving URL: `https://rest.kegg.jp/conv/compound/pubchem`
[2026-03-18 01:26:43] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.kegg.jp/conv/compound/pubchem`
[2026-03-18 01:26:43] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-18 01:26:43] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-18 01:26:43] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-18 01:26:44] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-03-18 01:26:44] [TRACE] [OmnipathR] Downloaded 9.8 Kb in 0.80862s from rest.kegg.jp (12.1 Kb/s); Redirect: 0s, DNS look up: 0.001764s, Connection: 0.002513s, Pretransfer: 0.550225s, First byte at: 0.808559s
[2026-03-18 01:26:44] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Wed, 18 Mar 2026 05:26:43 GMT; Server: Apache; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked
[2026-03-18 01:26:48] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/df48f267c99a2d8dd3cb7ed031941afbedc22d48-1.rds`.
[2026-03-18 01:26:48] [INFO] [OmnipathR] Download ready [key=df48f267c99a2d8dd3cb7ed031941afbedc22d48, version=1]
[2026-03-18 01:26:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-18 01:26:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:26:48] [INFO] [OmnipathR] Cache item `df48f267c99a2d8dd3cb7ed031941afbedc22d48` version 1: status changed from `started` to `ready`.
[2026-03-18 01:26:49] [SUCCESS] [OmnipathR] KEGG (rest.kegg.jp): downloaded 19442 records
[2026-03-18 01:26:50] [TRACE] [MetaProViz] The plot has title, adjusting layout to accommodate it.
[2026-03-18 01:26:50] [TRACE] [MetaProViz] Parsing unit from `0.5cm`
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Parsing unit from `12`
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Parsing unit from `11`
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Parsing unit from `6cm`
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Setting widths[7] to 6cm [name=axis-b, offset=0, empty=FALSE, original=1null]
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Setting widths[1] to 0cm [name=ylab-l, offset=-4, empty=FALSE, original=12points]
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Setting widths[6] to 1cm [name=axis-l, offset=0, empty=FALSE, original=sum(0cm, 1null, 0.367138205687007cm, 0null, max(0points, -0.210875882108759cm), 0.210875882108759cm)]
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Setting widths[5] to 1cm [name=ylab-l, offset=0, empty=FALSE, original=1grobwidth]
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Setting widths[3] to 0cm [name=guide-box-left, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Setting widths[8] to 0cm [name=axis-r, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Setting widths[9] to 0cm [name=ylab-r, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Setting widths[4] to 1cm [name=ylab-l, offset=-1, empty=TRUE, original=0points]
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Setting widths[11] to 1cm [name=guide-box-right, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Parsing unit from `8cm`
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Setting heights[9] to 8cm [name=axis-l, offset=0, empty=FALSE, original=1null]
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Parsing unit from `0.75cm`
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Setting heights[10] to 0.75cm [name=axis-b, offset=0, empty=FALSE, original=sum(0.210875882108759cm, max(0points, -0.210875882108759cm), 0null, 0.512659039020341cm, 1null, 0cm)]
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Parsing unit from `0.75cm`
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Setting heights[11] to 0.75cm [name=xlab-b, offset=0, empty=FALSE, original=1grobheight]
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Setting heights[1] to 0cm [name=title, offset=-2, empty=FALSE, original=12points]
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Setting heights[2] to 0cm [name=title, offset=-1, empty=TRUE, original=0points]
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Parsing unit from `0.25cm`
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Setting heights[3] to 0.25cm [name=title, offset=0, empty=FALSE, original=1grobheight]
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Setting heights[4] to 0cm [name=subtitle, offset=0, empty=FALSE, original=1grobheight]
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Setting heights[5] to 0cm [name=guide-box-top, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Setting heights[6] to 0cm [name=xlab-t, offset=-1, empty=TRUE, original=0points]
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Setting heights[3] to 0.5cm [name=title, main, offset=0, empty=FALSE, original=0.25cm]
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Parsing unit from `0.5cm`
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Setting heights[4] to 0.5cm [name=subtitle, main, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Parsing unit from `-4.20cm`
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Setting widths[11] to max(-4.2cm, 1cm) [name=guide-box-right, legend, offset=0, empty=FALSE, original=1cm]
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Sum of heights: 12.00, sum of widths: 12.00
[2026-03-18 01:26:51] [TRACE] [MetaProViz] The plot has title, adjusting layout to accommodate it.
[2026-03-18 01:26:51] [TRACE] [MetaProViz] Parsing unit from `0.5cm`
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Parsing unit from `12`
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Parsing unit from `11`
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Parsing unit from `6cm`
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Setting widths[7] to 6cm [name=axis-b, offset=0, empty=FALSE, original=1null]
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Setting widths[1] to 0cm [name=ylab-l, offset=-4, empty=FALSE, original=12points]
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Setting widths[6] to 1cm [name=axis-l, offset=0, empty=FALSE, original=sum(0cm, 1null, 0.367138205687007cm, 0null, max(0points, -0.210875882108759cm), 0.210875882108759cm)]
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Setting widths[5] to 1cm [name=ylab-l, offset=0, empty=FALSE, original=1grobwidth]
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Setting widths[3] to 0cm [name=guide-box-left, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Setting widths[8] to 0cm [name=axis-r, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Setting widths[9] to 0cm [name=ylab-r, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Setting widths[4] to 1cm [name=ylab-l, offset=-1, empty=TRUE, original=0points]
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Parsing unit from `1cm`
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Setting widths[11] to 1cm [name=guide-box-right, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Parsing unit from `8cm`
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Setting heights[9] to 8cm [name=axis-l, offset=0, empty=FALSE, original=1null]
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Parsing unit from `0.75cm`
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Setting heights[10] to 0.75cm [name=axis-b, offset=0, empty=FALSE, original=sum(0.210875882108759cm, max(0points, -0.210875882108759cm), 0null, 0.512659039020341cm, 1null, 0cm)]
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Parsing unit from `0.75cm`
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Setting heights[11] to 0.75cm [name=xlab-b, offset=0, empty=FALSE, original=1grobheight]
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Setting heights[1] to 0cm [name=title, offset=-2, empty=FALSE, original=12points]
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Setting heights[2] to 0cm [name=title, offset=-1, empty=TRUE, original=0points]
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Parsing unit from `0.25cm`
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Setting heights[3] to 0.25cm [name=title, offset=0, empty=FALSE, original=1grobheight]
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Setting heights[4] to 0cm [name=subtitle, offset=0, empty=FALSE, original=1grobheight]
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Setting heights[5] to 0cm [name=guide-box-top, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Parsing unit from `0cm`
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Setting heights[6] to 0cm [name=xlab-t, offset=-1, empty=TRUE, original=0points]
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Setting heights[3] to 0.5cm [name=title, main, offset=0, empty=FALSE, original=0.25cm]
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Parsing unit from `0.5cm`
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Setting heights[4] to 0.5cm [name=subtitle, main, offset=0, empty=FALSE, original=0cm]
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Parsing unit from `-1.70cm`
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Setting widths[11] to max(-1.7cm, 1cm) [name=guide-box-right, legend, offset=0, empty=FALSE, original=1cm]
[2026-03-18 01:26:52] [TRACE] [MetaProViz] Sum of heights: 12.00, sum of widths: 12.00
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/MetaProViz.Rcheck/vign_test/MetaProViz/vignettes/quick-start_files/figure-html/volcano_pea-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/MetaProViz.Rcheck/vign_test/MetaProViz/vignettes/quick-start_files/figure-html/volcano_pea-2.png" but not available.
File Hexagon_MetaProViz.png not found in resource path
Error: processing vignette 'quick-start.Rmd' failed with diagnostics:
pandoc document conversion failed with error 99
--- failed re-building ‘quick-start.Rmd’
SUMMARY: processing the following file failed:
‘quick-start.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 3 NOTEs
See
‘/home/biocbuild/bbs-3.23-bioc/meat/MetaProViz.Rcheck/00check.log’
for details.
MetaProViz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL MetaProViz ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘MetaProViz’ ... ** this is package ‘MetaProViz’ version ‘3.99.40’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading [2026-03-17 15:30:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-17 15:30:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:30:35] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2026-03-17 15:30:35] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-03-17 15:30:35] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-03-17 [2026-03-17 15:30:35] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-17 19:09:17 UTC; unix [2026-03-17 15:30:35] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.7 [2026-03-17 15:30:35] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2026-03-17 15:30:35] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-05 r89546); os=Ubuntu 24.04.4 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-17; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2026-03-17 15:30:35] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-03-17 15:30:36] [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 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); colorspace 2.1-2(2025-09-22); ComplexUpset 1.3.3(2021-12-11); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); EnhancedVolcano 1.29.1(2026-03-17); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 1.6.7(2026-03-06); generics 0.1.4(2025-05-09); ggplot2 4.0.2(2026-02-03); ggrepel 0.9.8(2026-03-17); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); MetaProViz 3.99.40(2026-03-17); OmnipathR 3.19.7(2026-03-17); 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 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); scales 1.4.0(2025-04-24); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-03-17 15:30:36] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-03-17 15:30:36] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-17 15:30:36] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2026-03-17 15:30:36] [TRACE] [OmnipathR] Contains 1 files. [2026-03-17 15:30:36] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-17 15:30:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-17 15:30:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:30:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2026-03-17 15:30:36] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2026-03-17 15:30:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-17 15:30:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:30:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-17 15:30:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:30:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-17 15:30:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:30:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-17 15:30:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:30:36] [TRACE] [OmnipathR] Cache locked: FALSE ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2026-03-17 15:31:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-17 15:31:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:31:00] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2026-03-17 15:31:00] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-03-17 15:31:00] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-03-17 [2026-03-17 15:31:00] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-17 19:09:17 UTC; unix [2026-03-17 15:31:00] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.7 [2026-03-17 15:31:00] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2026-03-17 15:31:00] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-05 r89546); os=Ubuntu 24.04.4 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-17; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2026-03-17 15:31:01] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-03-17 15:31:01] [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 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); colorspace 2.1-2(2025-09-22); ComplexUpset 1.3.3(2021-12-11); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); EnhancedVolcano 1.29.1(2026-03-17); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 1.6.7(2026-03-06); generics 0.1.4(2025-05-09); ggplot2 4.0.2(2026-02-03); ggrepel 0.9.8(2026-03-17); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); MetaProViz 3.99.40(2026-03-17); OmnipathR 3.19.7(2026-03-17); 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 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); scales 1.4.0(2025-04-24); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-03-17 15:31:01] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-03-17 15:31:01] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-17 15:31:01] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2026-03-17 15:31:01] [TRACE] [OmnipathR] Contains 1 files. [2026-03-17 15:31:01] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-17 15:31:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-17 15:31:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:31:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2026-03-17 15:31:01] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2026-03-17 15:31:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-17 15:31:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:31:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-17 15:31:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:31:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-17 15:31:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:31:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-17 15:31:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:31:01] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2026-03-17 15:31:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-17 15:31:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:31:15] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2026-03-17 15:31:15] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-03-17 15:31:15] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-03-17 [2026-03-17 15:31:15] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-17 19:09:17 UTC; unix [2026-03-17 15:31:15] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.7 [2026-03-17 15:31:15] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2026-03-17 15:31:15] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-05 r89546); os=Ubuntu 24.04.4 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-17; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2026-03-17 15:31:15] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-03-17 15:31:15] [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 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); colorspace 2.1-2(2025-09-22); ComplexUpset 1.3.3(2021-12-11); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); EnhancedVolcano 1.29.1(2026-03-17); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 1.6.7(2026-03-06); generics 0.1.4(2025-05-09); ggplot2 4.0.2(2026-02-03); ggrepel 0.9.8(2026-03-17); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); MetaProViz 3.99.40(2026-03-17); OmnipathR 3.19.7(2026-03-17); 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 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); scales 1.4.0(2025-04-24); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-03-17 15:31:15] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-03-17 15:31:15] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-17 15:31:15] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2026-03-17 15:31:15] [TRACE] [OmnipathR] Contains 1 files. [2026-03-17 15:31:15] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-17 15:31:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-17 15:31:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:31:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2026-03-17 15:31:15] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2026-03-17 15:31:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-17 15:31:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:31:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-17 15:31:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:31:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-17 15:31:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:31:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-17 15:31:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:31:15] [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) (2026-03-05 r89546) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
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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
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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)
[2026-03-18 01:25:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-18 01:25:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:25:11] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-03-18 01:25:11] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-03-18 01:25:11] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-03-17
[2026-03-18 01:25:11] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-17 19:09:17 UTC; unix
[2026-03-18 01:25:11] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.7
[2026-03-18 01:25:11] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-03-18 01:25:12] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-05 r89546); os=Ubuntu 24.04.4 LTS; system=x86_64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-18; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2026-03-18 01:25:12] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-03-18 01:25:12] [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 1.3.0(2026-01-14); brio 1.1.5(2024-04-24); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); colorspace 2.1-2(2025-09-22); ComplexUpset 1.3.3(2021-12-11); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); EnhancedVolcano 1.29.1(2026-03-17); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 1.6.7(2026-03-06); generics 0.1.4(2025-05-09); ggplot2 4.0.2(2026-02-03); ggrepel 0.9.8(2026-03-17); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); MetaProViz 3.99.40(2026-03-17); OmnipathR 3.19.7(2026-03-17); 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 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); scales 1.4.0(2025-04-24); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); testthat 3.3.2(2026-01-11); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-18 01:25:12] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-03-18 01:25:12] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-03-18 01:25:12] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-03-18 01:25:12] [TRACE] [OmnipathR] Contains 17 files.
[2026-03-18 01:25:12] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-03-18 01:25:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-18 01:25:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:25:12] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-03-18 01:25:12] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2026-03-18 01:25:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-18 01:25:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:25:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-18 01:25:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:25:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-18 01:25:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:25:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-18 01:25:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-18 01:25:12] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check("MetaProViz")
Attaching package: 'dplyr'
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%.
[2026-03-18 01:25:24] [TRACE] [MetaProViz] Error The HMDB column selected as InpuID in metadata_info was not found in data. Please check your input.
[2026-03-18 01:25:24] [TRACE] [MetaProViz] Error The HMDB column selected as InpuID in metadata_info was not found in data. Please check your input.
[2026-03-18 01:25:24] [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 1 | PASS 9 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1):
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 9 ]
>
> proc.time()
user system elapsed
13.372 2.704 16.038
MetaProViz.Rcheck/MetaProViz-Ex.timings
| name | user | system | elapsed | |
| alanine_pathways | 0.045 | 0.006 | 0.050 | |
| biocrates_features | 0.070 | 0.020 | 0.089 | |
| cellular_meta | 0.029 | 0.001 | 0.030 | |
| checkmatch_pk_to_data | 0.000 | 0.001 | 0.001 | |
| cluster_ora | 9.542 | 1.221 | 30.702 | |
| cluster_pk | 0.225 | 0.015 | 0.237 | |
| compare_pk | 0.001 | 0.000 | 0.000 | |
| count_id | 1.563 | 0.193 | 1.707 | |
| dma | 20.447 | 2.267 | 22.428 | |
| equivalent_features | 0.028 | 0.002 | 0.031 | |
| equivalent_id | 55.058 | 8.122 | 69.061 | |
| gaude_pathways | 0.021 | 0.005 | 0.025 | |
| hallmarks | 0.027 | 0.004 | 0.031 | |
| intracell_dma | 0.043 | 0.019 | 0.062 | |
| intracell_raw | 0.087 | 0.014 | 0.100 | |
| intracell_raw_se | 0.048 | 0.004 | 0.052 | |
| make_gene_metab_set | 0.640 | 0.915 | 1.244 | |
| mapping_ambiguity | 0.001 | 0.000 | 0.000 | |
| mca_2cond | 9.900 | 1.012 | 10.761 | |
| mca_core | 0.153 | 0.007 | 0.159 | |
| mca_core_rules | 0.028 | 0.006 | 0.034 | |
| mca_twocond_rules | 0.022 | 0.003 | 0.024 | |
| medium_raw | 0.067 | 0.008 | 0.074 | |
| meta_pk | 0.138 | 0.013 | 0.149 | |
| metadata_analysis | 4.996 | 0.476 | 5.410 | |
| metaproviz_config_path | 0.001 | 0.000 | 0.001 | |
| metaproviz_load_config | 0.001 | 0.002 | 0.003 | |
| metaproviz_log | 0 | 0 | 0 | |
| metaproviz_logfile | 0.002 | 0.000 | 0.001 | |
| metaproviz_reset_config | 0.006 | 0.001 | 0.007 | |
| metaproviz_save_config | 0.005 | 0.002 | 0.006 | |
| metaproviz_set_loglevel | 0.002 | 0.000 | 0.002 | |
| metsigdb_chemicalclass | 0.638 | 0.389 | 0.683 | |
| metsigdb_kegg | 1.351 | 0.089 | 1.431 | |
| metsigdb_metalinks | 2.462 | 1.070 | 12.340 | |
| pool_estimation | 7.780 | 0.626 | 8.308 | |
| processing | 9.930 | 1.280 | 11.065 | |
| replicate_sum | 0.473 | 0.060 | 0.523 | |
| standard_ora | 3.962 | 0.730 | 5.760 | |
| tissue_dma | 0.060 | 0.016 | 0.075 | |
| tissue_dma_old | 0.057 | 0.008 | 0.065 | |
| tissue_dma_young | 0.048 | 0.021 | 0.069 | |
| tissue_meta | 0.052 | 0.006 | 0.058 | |
| tissue_norm | 0.149 | 0.024 | 0.172 | |
| tissue_norm_se | 0.058 | 0.003 | 0.060 | |
| tissue_tvn_proteomics | 0.068 | 0.011 | 0.077 | |
| tissue_tvn_rnaseq | 0.103 | 0.019 | 0.120 | |
| translate_id | 0.000 | 0.000 | 0.001 | |
| viz_graph | 0.502 | 0.072 | 0.569 | |
| viz_heatmap | 1.075 | 0.235 | 1.305 | |
| viz_pca | 3.503 | 0.299 | 3.776 | |
| viz_superplot | 3.355 | 0.596 | 3.912 | |
| viz_volcano | 0.709 | 0.103 | 0.802 | |