[ Started: 2026-03-25 22:47:08 CET ]
[ MetaProViz v3.99.40 for BioC-3.23 from https://github.com/saezlab/MetaProViz@devel (1b6f20a 2026-03-25 22:19:59) ]

* checking for file ‘./DESCRIPTION’ ... OK
* preparing ‘MetaProViz’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘quick-start.Rmd’ using rmarkdown
Warning in png(..., res = dpi, units = "in") :
  unable to open connection to X11 display ''
[2026-03-25 22:47:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-25 22:47:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-25 22:47:46] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-03-25 22:47:46] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-03-25 21:41:40 UTC; omnipath
[2026-03-25 22:47:46] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-03-25 22:47:46] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-25 21:41:42 UTC; unix
[2026-03-25 22:47:46] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.11
[2026-03-25 22:47:46] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-03-25 22:47:46] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-23 r89685); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-03-25; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-03-25 22:47:46] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=2.13.2/2.15.0; pango=; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; 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=/opt/R-devel/lib/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-03-25 22:47:47] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocStyle 2.39.0(2025-10-30); 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(2025-12-03); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); 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(2026-03-25); OmnipathR 3.19.11(2026-03-25); 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 0.7.2(2026-03-21); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-25 22:47:47] [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
[2026-03-25 22:47:47] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-03-25 22:47:47] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-03-25 22:47:47] [TRACE]   [OmnipathR] Contains 1 files.
[2026-03-25 22:47:47] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-03-25 22:47:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-25 22:47:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-25 22:47:47] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-03-25 22:47:47] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-03-25 22:47:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-25 22:47:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-25 22:47:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-25 22:47:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-25 22:47:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-25 22:47:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-25 22:47:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.6-3.23/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-25 22:47:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-25 22:47:47] [TRACE]   [OmnipathR] Cache locked: FALSE
[2026-03-25 22:47:54] [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
[2026-03-25 22:47:54] [INFO]    [MetaProViz] 3 metabolites where removed: AICAR, FAICAR, SAICAR
[2026-03-25 22:47:54] [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
[2026-03-25 22:47:56] [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
[2026-03-25 22:48:00] [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
[2026-03-25 22:48:00] [INFO]    [MetaProViz] viz_pca: PCA plot visualization
[2026-03-25 22:48:00] [INFO]    [MetaProViz] character(0)
[2026-03-25 22:48:00] [INFO]    [MetaProViz] viz_pca colour: #88CCEE, #DDCC77, #661100, #332288, #AA4499, #999933, #44AA99, #882215, #6699CC, #117733, #888888, #CC6677, black, gold1, darkorchid4, red, orange, blue
[2026-03-25 22:48:00] [INFO]    [MetaProViz] viz_pca shape: 15, 17, 16, 18, 6, 7, 8, 11, 12
[2026-03-25 22:48:00] [INFO]    [MetaProViz] viz_pca scale_color: discrete
[2026-03-25 22:48:00] [TRACE]   [MetaProViz] The plot has legend, adjusting layout to accommodate it.
[2026-03-25 22:48:00] [TRACE]   [MetaProViz] Sections: color, shape
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Legend nchar: 2.50cm, Legend width: 2.60cm
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Parsing unit from `2.60cm`
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] The plot has title, adjusting layout to accommodate it.
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Parsing unit from `0.5cm`
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Parsing unit from `12`
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Parsing unit from `11`
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Parsing unit from `8cm`
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Setting widths[7] to 8cm [name=axis-b, offset=0, empty=FALSE, original=1null]
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Setting widths[1] to 0cm [name=ylab-l, offset=-4, empty=FALSE, original=5.5points]
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Parsing unit from `1cm`
[2026-03-25 22:48:01] [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)]
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Parsing unit from `1cm`
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Setting widths[5] to 1cm [name=ylab-l, offset=0, empty=FALSE, original=1grobwidth]
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Setting widths[3] to 0cm [name=guide-box-left, offset=0, empty=FALSE, original=0cm]
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Setting widths[8] to 0cm [name=axis-r, offset=0, empty=FALSE, original=0cm]
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Setting widths[9] to 0cm [name=ylab-r, offset=0, empty=FALSE, original=0cm]
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Parsing unit from `1cm`
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Setting widths[4] to 1cm [name=ylab-l, offset=-1, empty=TRUE, original=0points]
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Parsing unit from `1cm`
[2026-03-25 22:48:01] [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)]
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Parsing unit from `8cm`
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Setting heights[9] to 8cm [name=axis-l, offset=0, empty=FALSE, original=1null]
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Parsing unit from `1cm`
[2026-03-25 22:48:01] [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)]
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Parsing unit from `.5cm`
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Setting heights[11] to 0.5cm [name=xlab-b, offset=0, empty=FALSE, original=1grobheight]
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Parsing unit from `1cm`
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Setting heights[12] to 1cm [name=xlab-b, offset=1, empty=TRUE, original=0points]
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Setting heights[1] to 0cm [name=title, offset=-2, empty=FALSE, original=5.5points]
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Setting heights[2] to 0cm [name=title, offset=-1, empty=TRUE, original=0points]
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Parsing unit from `0.25cm`
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Setting heights[3] to 0.25cm [name=title, offset=0, empty=FALSE, original=1grobheight]
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Setting heights[4] to 0cm [name=subtitle, offset=0, empty=FALSE, original=0cm]
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Setting heights[5] to 0cm [name=guide-box-top, offset=0, empty=FALSE, original=0cm]
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Setting heights[6] to 0cm [name=xlab-t, offset=-1, empty=TRUE, original=0points]
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Setting heights[3] to 0.5cm [name=title, main, offset=0, empty=FALSE, original=0.25cm]
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Parsing unit from `0.5cm`
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Setting heights[4] to 0.5cm [name=subtitle, main, offset=0, empty=FALSE, original=0cm]
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Parsing unit from `-2.45cm`
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Setting widths[11] to max(-2.45cm, 1cm) [name=guide-box-right, legend, offset=0, empty=FALSE, original=1cm]
[2026-03-25 22:48:01] [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)).
[2026-03-25 22:48:01] [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)]
[2026-03-25 22:48:01] [TRACE]   [MetaProViz] Sum of heights: 12.00, sum of widths: 13.60
[2026-03-25 22:48:02] [INFO]    [MetaProViz] viz_pca: PCA plot visualization
[2026-03-25 22:48:02] [INFO]    [MetaProViz] character(0)
[2026-03-25 22:48:02] [INFO]    [MetaProViz] viz_pca colour: #88CCEE, #DDCC77, #661100, #332288, #AA4499, #999933, #44AA99, #882215, #6699CC, #117733, #888888, #CC6677, black, gold1, darkorchid4, red, orange, blue
[2026-03-25 22:48:02] [INFO]    [MetaProViz] viz_pca shape: 15, 17, 16, 18, 6, 7, 8, 11, 12
[2026-03-25 22:48:02] [INFO]    [MetaProViz] viz_pca scale_color: discrete
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] The plot has legend, adjusting layout to accommodate it.
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Sections: color, shape
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Legend nchar: 2.50cm, Legend width: 2.60cm
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Parsing unit from `2.60cm`
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] The plot has title, adjusting layout to accommodate it.
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Parsing unit from `0.5cm`
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Parsing unit from `12`
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Parsing unit from `11`
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Parsing unit from `8cm`
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Setting widths[7] to 8cm [name=axis-b, offset=0, empty=FALSE, original=1null]
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Setting widths[1] to 0cm [name=ylab-l, offset=-4, empty=FALSE, original=5.5points]
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Parsing unit from `1cm`
[2026-03-25 22:48:02] [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)]
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Parsing unit from `1cm`
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Setting widths[5] to 1cm [name=ylab-l, offset=0, empty=FALSE, original=1grobwidth]
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Setting widths[3] to 0cm [name=guide-box-left, offset=0, empty=FALSE, original=0cm]
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Setting widths[8] to 0cm [name=axis-r, offset=0, empty=FALSE, original=0cm]
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Setting widths[9] to 0cm [name=ylab-r, offset=0, empty=FALSE, original=0cm]
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Parsing unit from `1cm`
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Setting widths[4] to 1cm [name=ylab-l, offset=-1, empty=TRUE, original=0points]
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Parsing unit from `1cm`
[2026-03-25 22:48:02] [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)]
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Parsing unit from `8cm`
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Setting heights[9] to 8cm [name=axis-l, offset=0, empty=FALSE, original=1null]
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Parsing unit from `1cm`
[2026-03-25 22:48:02] [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)]
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Parsing unit from `.5cm`
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Setting heights[11] to 0.5cm [name=xlab-b, offset=0, empty=FALSE, original=1grobheight]
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Parsing unit from `1cm`
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Setting heights[12] to 1cm [name=xlab-b, offset=1, empty=TRUE, original=0points]
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Setting heights[1] to 0cm [name=title, offset=-2, empty=FALSE, original=5.5points]
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Setting heights[2] to 0cm [name=title, offset=-1, empty=TRUE, original=0points]
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Parsing unit from `0.25cm`
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Setting heights[3] to 0.25cm [name=title, offset=0, empty=FALSE, original=1grobheight]
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Setting heights[4] to 0cm [name=subtitle, offset=0, empty=FALSE, original=0cm]
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Setting heights[5] to 0cm [name=guide-box-top, offset=0, empty=FALSE, original=0cm]
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Setting heights[6] to 0cm [name=xlab-t, offset=-1, empty=TRUE, original=0points]
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Setting heights[3] to 0.5cm [name=title, main, offset=0, empty=FALSE, original=0.25cm]
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Parsing unit from `0.5cm`
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Setting heights[4] to 0.5cm [name=subtitle, main, offset=0, empty=FALSE, original=0cm]
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Parsing unit from `-2.45cm`
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Setting widths[11] to max(-2.45cm, 1cm) [name=guide-box-right, legend, offset=0, empty=FALSE, original=1cm]
[2026-03-25 22:48:02] [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)).
[2026-03-25 22:48:02] [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)]
[2026-03-25 22:48:02] [TRACE]   [MetaProViz] Sum of heights: 12.00, sum of widths: 13.60
[2026-03-25 22:48:02] [INFO]    [MetaProViz] There are possible outlier samples in the data
[2026-03-25 22:48:02] [INFO]    [MetaProViz] Filtering round  1  Outlier Samples:  MS55_29  
[2026-03-25 22:48:02] [INFO]    [MetaProViz] viz_pca: PCA plot visualization
[2026-03-25 22:48:02] [INFO]    [MetaProViz] character(0)
[2026-03-25 22:48:02] [INFO]    [MetaProViz] viz_pca colour: #88CCEE, #DDCC77, #661100, #332288, #AA4499, #999933, #44AA99, #882215, #6699CC, #117733, #888888, #CC6677, black, gold1, darkorchid4, red, orange, blue
[2026-03-25 22:48:02] [INFO]    [MetaProViz] viz_pca shape: 15, 17, 16, 18, 6, 7, 8, 11, 12
[2026-03-25 22:48:03] [INFO]    [MetaProViz] viz_pca scale_color: discrete
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] The plot has legend, adjusting layout to accommodate it.
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Sections: color, shape
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Legend nchar: 2.50cm, Legend width: 4.90cm
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Parsing unit from `4.90cm`
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] The plot has title, adjusting layout to accommodate it.
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Parsing unit from `0.5cm`
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Parsing unit from `12`
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Parsing unit from `11`
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Parsing unit from `8cm`
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Setting widths[7] to 8cm [name=axis-b, offset=0, empty=FALSE, original=1null]
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Setting widths[1] to 0cm [name=ylab-l, offset=-4, empty=FALSE, original=5.5points]
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Parsing unit from `1cm`
[2026-03-25 22:48:03] [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)]
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Parsing unit from `1cm`
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Setting widths[5] to 1cm [name=ylab-l, offset=0, empty=FALSE, original=1grobwidth]
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Setting widths[3] to 0cm [name=guide-box-left, offset=0, empty=FALSE, original=0cm]
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Setting widths[8] to 0cm [name=axis-r, offset=0, empty=FALSE, original=0cm]
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Setting widths[9] to 0cm [name=ylab-r, offset=0, empty=FALSE, original=0cm]
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Parsing unit from `1cm`
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Setting widths[4] to 1cm [name=ylab-l, offset=-1, empty=TRUE, original=0points]
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Parsing unit from `1cm`
[2026-03-25 22:48:03] [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)]
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Parsing unit from `8cm`
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Setting heights[9] to 8cm [name=axis-l, offset=0, empty=FALSE, original=1null]
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Parsing unit from `1cm`
[2026-03-25 22:48:03] [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)]
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Parsing unit from `.5cm`
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Setting heights[11] to 0.5cm [name=xlab-b, offset=0, empty=FALSE, original=1grobheight]
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Parsing unit from `1cm`
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Setting heights[12] to 1cm [name=xlab-b, offset=1, empty=TRUE, original=0points]
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Setting heights[1] to 0cm [name=title, offset=-2, empty=FALSE, original=5.5points]
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Setting heights[2] to 0cm [name=title, offset=-1, empty=TRUE, original=0points]
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Parsing unit from `0.25cm`
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Setting heights[3] to 0.25cm [name=title, offset=0, empty=FALSE, original=1grobheight]
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Setting heights[4] to 0cm [name=subtitle, offset=0, empty=FALSE, original=0cm]
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Setting heights[5] to 0cm [name=guide-box-top, offset=0, empty=FALSE, original=0cm]
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Setting heights[6] to 0cm [name=xlab-t, offset=-1, empty=TRUE, original=0points]
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Setting heights[3] to 0.5cm [name=title, main, offset=0, empty=FALSE, original=0.25cm]
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Parsing unit from `0.5cm`
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Setting heights[4] to 0.5cm [name=subtitle, main, offset=0, empty=FALSE, original=0cm]
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Parsing unit from `3.30cm`
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Setting widths[11] to max(3.3cm, 1cm) [name=guide-box-right, legend, offset=0, empty=FALSE, original=1cm]
[2026-03-25 22:48:03] [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)).
[2026-03-25 22:48:03] [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)]
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Sum of heights: 12.00, sum of widths: 16.90
[2026-03-25 22:48:03] [INFO]    [MetaProViz] viz_pca: PCA plot visualization
[2026-03-25 22:48:03] [INFO]    [MetaProViz] character(0)
[2026-03-25 22:48:03] [INFO]    [MetaProViz] viz_pca colour: #88CCEE, #DDCC77, #661100, #332288, #AA4499, #999933, #44AA99, #882215, #6699CC, #117733, #888888, #CC6677, black, gold1, darkorchid4, red, orange, blue
[2026-03-25 22:48:03] [INFO]    [MetaProViz] viz_pca shape: 15, 17, 16, 18, 6, 7, 8, 11, 12
[2026-03-25 22:48:03] [INFO]    [MetaProViz] viz_pca scale_color: discrete
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] The plot has legend, adjusting layout to accommodate it.
[2026-03-25 22:48:03] [TRACE]   [MetaProViz] Sections: color, shape
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Legend nchar: 5.25cm, Legend width: 5.25cm
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Parsing unit from `5.25cm`
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] The plot has title, adjusting layout to accommodate it.
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Parsing unit from `0.5cm`
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Parsing unit from `12`
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Parsing unit from `11`
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Parsing unit from `8cm`
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Setting widths[7] to 8cm [name=axis-b, offset=0, empty=FALSE, original=1null]
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Setting widths[1] to 0cm [name=ylab-l, offset=-4, empty=FALSE, original=5.5points]
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Parsing unit from `1cm`
[2026-03-25 22:48:04] [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)]
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Parsing unit from `1cm`
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Setting widths[5] to 1cm [name=ylab-l, offset=0, empty=FALSE, original=1grobwidth]
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Setting widths[3] to 0cm [name=guide-box-left, offset=0, empty=FALSE, original=0cm]
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Setting widths[8] to 0cm [name=axis-r, offset=0, empty=FALSE, original=0cm]
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Setting widths[9] to 0cm [name=ylab-r, offset=0, empty=FALSE, original=0cm]
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Parsing unit from `1cm`
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Setting widths[4] to 1cm [name=ylab-l, offset=-1, empty=TRUE, original=0points]
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Parsing unit from `1cm`
[2026-03-25 22:48:04] [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)]
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Parsing unit from `8cm`
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Setting heights[9] to 8cm [name=axis-l, offset=0, empty=FALSE, original=1null]
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Parsing unit from `1cm`
[2026-03-25 22:48:04] [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)]
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Parsing unit from `.5cm`
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Setting heights[11] to 0.5cm [name=xlab-b, offset=0, empty=FALSE, original=1grobheight]
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Parsing unit from `1cm`
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Setting heights[12] to 1cm [name=xlab-b, offset=1, empty=TRUE, original=0points]
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Setting heights[1] to 0cm [name=title, offset=-2, empty=FALSE, original=5.5points]
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Setting heights[2] to 0cm [name=title, offset=-1, empty=TRUE, original=0points]
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Parsing unit from `0.25cm`
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Setting heights[3] to 0.25cm [name=title, offset=0, empty=FALSE, original=1grobheight]
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Setting heights[4] to 0cm [name=subtitle, offset=0, empty=FALSE, original=0cm]
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Setting heights[5] to 0cm [name=guide-box-top, offset=0, empty=FALSE, original=0cm]
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Parsing unit from `0cm`
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Setting heights[6] to 0cm [name=xlab-t, offset=-1, empty=TRUE, original=0points]
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Setting heights[3] to 0.5cm [name=title, main, offset=0, empty=FALSE, original=0.25cm]
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Parsing unit from `0.5cm`
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Setting heights[4] to 0.5cm [name=subtitle, main, offset=0, empty=FALSE, original=0cm]
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Parsing unit from `-0.70cm`
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Setting widths[11] to max(-0.7cm, 1cm) [name=guide-box-right, legend, offset=0, empty=FALSE, original=1cm]
[2026-03-25 22:48:04] [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)).
[2026-03-25 22:48:04] [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)]
[2026-03-25 22:48:04] [TRACE]   [MetaProViz] Sum of heights: 12.00, sum of widths: 16.25

Quitting from quick-start.Rmd:113-132 [processing]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R: unbalanced graphic context push-pop `graphic-context' @ error/draw.c/RenderMVGContent/3274
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


Quitting from quick-start.Rmd:113-132 [processing]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


Quitting from quick-start.Rmd:113-132 [processing]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'quick-start.Rmd' failed with diagnostics:
R: unbalanced graphic context push-pop `graphic-context' @ error/draw.c/RenderMVGContent/3274
--- failed re-building ‘quick-start.Rmd’

SUMMARY: processing the following file failed:
  ‘quick-start.Rmd’

Error: Vignette re-building failed.
Execution halted
[ Finished: 2026-03-25 22:48:17 CET ]