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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MetaProViz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MetaProViz_3.99.40.tar.gz |
| StartedAt: 2026-03-17 19:20:44 -0400 (Tue, 17 Mar 2026) |
| EndedAt: 2026-03-17 19:29:37 -0400 (Tue, 17 Mar 2026) |
| EllapsedTime: 532.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MetaProViz.Rcheck |
| Warnings: 0 |
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###
### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MetaProViz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MetaProViz_3.99.40.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/MetaProViz.Rcheck’
* using R Under development (unstable) (2026-03-01 r89506)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Sonoma 14.8.3
* using session charset: UTF-8
* current time: 2026-03-17 23:20:45 UTC
* using option ‘--no-vignettes’
* 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 whether startup messages can be suppressed ... NOTE
[2026-03-17 19:22:29] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-17 19:22:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-17 19:22:29] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-03-17 19:22:29] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-03-17 19:22:29] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-03-17
[2026-03-17 19:22:29] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-17 19:04:47 UTC; unix
[2026-03-17 19:22:29] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.7
[2026-03-17 19:22:29] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-03-17 19:22:29] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-01 r89506); os=macOS Sonoma 14.8.3; system=aarch64, darwin23; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-17; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-03-17 19:22:29] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=2.13.2/2.14.2; pango=; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.7.0; tcl=8.6; curl=8.7.1; zlib=1.2.12; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib; readline=5.2; BLAS=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2026-03-17 19:22:29] [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 19:22:29] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2026-03-17 19:22:29] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-03-17 19:22:29] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-03-17 19:22:29] [TRACE] [OmnipathR] Contains 1 files.
[2026-03-17 19:22:29] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-03-17 19:22:29] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-17 19:22:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-17 19:22:29] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-03-17 19:22:29] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2026-03-17 19:22:29] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-17 19:22:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-17 19:22:29] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-17 19:22:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-17 19:22:29] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-17 19:22:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-17 19:22:29] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-17 19:22:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-17 19:22:29] [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
[2026-03-17 19:24:14] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-17 19:24:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-17 19:24:14] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-03-17 19:24:14] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-03-17 19:24:14] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-03-17
[2026-03-17 19:24:14] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-17 19:04:47 UTC; unix
[2026-03-17 19:24:14] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.7
[2026-03-17 19:24:14] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-03-17 19:24:14] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-01 r89506); os=macOS Sonoma 14.8.3; system=aarch64, darwin23; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-17; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-03-17 19:24:14] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=2.13.2/2.14.2; pango=; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.7.0; tcl=8.6; curl=8.7.1; zlib=1.2.12; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib; readline=5.2; BLAS=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2026-03-17 19:24:14] [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 19:24:14] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2026-03-17 19:24:14] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-03-17 19:24:14] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-03-17 19:24:14] [TRACE] [OmnipathR] Contains 1 files.
[2026-03-17 19:24:14] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-03-17 19:24:14] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-17 19:24:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-17 19:24:14] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-03-17 19:24:14] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2026-03-17 19:24:14] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-17 19:24:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-17 19:24:14] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-17 19:24:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-17 19:24:14] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-17 19:24:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-17 19:24:14] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-17 19:24:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-17 19:24:14] [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 23.714 4.354 39.533
dma 7.607 2.180 15.596
processing 5.511 1.773 7.990
cluster_ora 3.927 0.904 26.791
mca_2cond 3.904 0.885 5.962
pool_estimation 3.560 0.972 5.202
metsigdb_metalinks 1.287 0.416 10.975
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.23-bioc/meat/MetaProViz.Rcheck/00check.log’
for details.
MetaProViz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MetaProViz ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/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 15:10:22] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-17 15:10:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:10:22] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-03-17 15:10:22] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-03-17 15:10:22] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-03-17 [2026-03-17 15:10:22] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-17 19:04:47 UTC; unix [2026-03-17 15:10:22] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.7 [2026-03-17 15:10:22] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2026-03-17 15:10:22] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-01 r89506); os=macOS Sonoma 14.8.3; system=aarch64, darwin23; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-17; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2026-03-17 15:10:22] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=2.13.2/2.14.2; pango=; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.7.0; tcl=8.6; curl=8.7.1; zlib=1.2.12; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib; readline=5.2; BLAS=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2026-03-17 15:10:22] [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 15:10:22] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2026-03-17 15:10:22] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-17 15:10:22] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-03-17 15:10:22] [TRACE] [OmnipathR] Contains 1 files. [2026-03-17 15:10:22] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-17 15:10:22] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-17 15:10:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:10:22] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-03-17 15:10:22] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2026-03-17 15:10:22] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-17 15:10:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:10:22] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-17 15:10:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:10:22] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-17 15:10:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:10:22] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-17 15:10:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:10:22] [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 15:10:33] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-17 15:10:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:10:33] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-03-17 15:10:33] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-03-17 15:10:33] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-03-17 [2026-03-17 15:10:33] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-17 19:04:47 UTC; unix [2026-03-17 15:10:33] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.7 [2026-03-17 15:10:33] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2026-03-17 15:10:33] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-01 r89506); os=macOS Sonoma 14.8.3; system=aarch64, darwin23; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-17; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2026-03-17 15:10:33] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=2.13.2/2.14.2; pango=; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.7.0; tcl=8.6; curl=8.7.1; zlib=1.2.12; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib; readline=5.2; BLAS=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2026-03-17 15:10:33] [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 15:10:33] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2026-03-17 15:10:33] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-17 15:10:33] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-03-17 15:10:33] [TRACE] [OmnipathR] Contains 1 files. [2026-03-17 15:10:33] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-17 15:10:33] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-17 15:10:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:10:33] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-03-17 15:10:33] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2026-03-17 15:10:33] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-17 15:10:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:10:33] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-17 15:10:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:10:33] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-17 15:10:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:10:33] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-17 15:10:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:10:33] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2026-03-17 15:10:39] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-17 15:10:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:10:39] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-03-17 15:10:39] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-03-17 15:10:39] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-03-17 [2026-03-17 15:10:39] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-17 19:04:47 UTC; unix [2026-03-17 15:10:39] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.7 [2026-03-17 15:10:39] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2026-03-17 15:10:39] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-01 r89506); os=macOS Sonoma 14.8.3; system=aarch64, darwin23; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-17; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2026-03-17 15:10:39] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=2.13.2/2.14.2; pango=; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.7.0; tcl=8.6; curl=8.7.1; zlib=1.2.12; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib; readline=5.2; BLAS=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2026-03-17 15:10:39] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(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 15:10:39] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2026-03-17 15:10:39] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-17 15:10:39] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-03-17 15:10:39] [TRACE] [OmnipathR] Contains 1 files. [2026-03-17 15:10:39] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-17 15:10:39] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-17 15:10:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:10:39] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-03-17 15:10:39] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2026-03-17 15:10:39] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-17 15:10:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:10:39] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-17 15:10:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:10:39] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-17 15:10:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:10:39] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-17 15:10:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-17 15:10:39] [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) (2026-03-01 r89506) -- "Unsuffered Consequences"
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Platform: aarch64-apple-darwin23
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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)
[2026-03-17 19:29:22] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-17 19:29:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-17 19:29:22] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-03-17 19:29:22] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-03-17 19:29:22] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-03-17
[2026-03-17 19:29:22] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-17 19:04:47 UTC; unix
[2026-03-17 19:29:22] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.7
[2026-03-17 19:29:22] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-03-17 19:29:23] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-03-01 r89506); os=macOS Sonoma 14.8.3; system=aarch64, darwin23; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-17; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-03-17 19:29:23] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=2.13.2/2.14.2; pango=; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.7.0; tcl=8.6; curl=8.7.1; zlib=1.2.12; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib; readline=5.2; BLAS=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2026-03-17 19:29:23] [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); 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); 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); 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); 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 19:29:23] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2026-03-17 19:29:23] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-03-17 19:29:23] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-03-17 19:29:23] [TRACE] [OmnipathR] Contains 17 files.
[2026-03-17 19:29:23] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-03-17 19:29:23] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-17 19:29:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-17 19:29:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-03-17 19:29:23] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2026-03-17 19:29:23] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-17 19:29:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-17 19:29:23] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-17 19:29:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-17 19:29:23] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-17 19:29:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-17 19:29:23] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-17 19:29:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-17 19:29:23] [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%.
[2026-03-17 19:29:32] [TRACE] [MetaProViz] Error The HMDB column selected as InpuID in metadata_info was not found in data. Please check your input.
[2026-03-17 19:29:33] [TRACE] [MetaProViz] Error The HMDB column selected as InpuID in metadata_info was not found in data. Please check your input.
[2026-03-17 19:29:33] [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
5.927 2.548 11.366
MetaProViz.Rcheck/MetaProViz-Ex.timings
| name | user | system | elapsed | |
| alanine_pathways | 0.020 | 0.011 | 0.042 | |
| biocrates_features | 0.036 | 0.014 | 0.088 | |
| cellular_meta | 0.010 | 0.007 | 0.040 | |
| checkmatch_pk_to_data | 0 | 0 | 0 | |
| cluster_ora | 3.927 | 0.904 | 26.791 | |
| cluster_pk | 0.091 | 0.027 | 0.136 | |
| compare_pk | 0 | 0 | 0 | |
| count_id | 0.632 | 0.284 | 1.367 | |
| dma | 7.607 | 2.180 | 15.596 | |
| equivalent_features | 0.012 | 0.007 | 0.032 | |
| equivalent_id | 23.714 | 4.354 | 39.533 | |
| gaude_pathways | 0.012 | 0.005 | 0.021 | |
| hallmarks | 0.014 | 0.003 | 0.018 | |
| intracell_dma | 0.017 | 0.010 | 0.036 | |
| intracell_raw | 0.034 | 0.020 | 0.061 | |
| intracell_raw_se | 0.097 | 0.007 | 0.123 | |
| make_gene_metab_set | 0.335 | 0.368 | 0.451 | |
| mapping_ambiguity | 0 | 0 | 0 | |
| mca_2cond | 3.904 | 0.885 | 5.962 | |
| mca_core | 0.136 | 0.012 | 0.164 | |
| mca_core_rules | 0.011 | 0.006 | 0.022 | |
| mca_twocond_rules | 0.007 | 0.004 | 0.017 | |
| medium_raw | 0.024 | 0.016 | 0.059 | |
| meta_pk | 0.067 | 0.009 | 0.081 | |
| metadata_analysis | 1.859 | 0.366 | 2.726 | |
| metaproviz_config_path | 0 | 0 | 0 | |
| metaproviz_load_config | 0.001 | 0.001 | 0.001 | |
| metaproviz_log | 0.000 | 0.000 | 0.001 | |
| metaproviz_logfile | 0.001 | 0.000 | 0.000 | |
| metaproviz_reset_config | 0.002 | 0.001 | 0.004 | |
| metaproviz_save_config | 0.002 | 0.001 | 0.008 | |
| metaproviz_set_loglevel | 0.001 | 0.001 | 0.000 | |
| metsigdb_chemicalclass | 0.393 | 0.183 | 0.324 | |
| metsigdb_kegg | 0.715 | 0.086 | 0.906 | |
| metsigdb_metalinks | 1.287 | 0.416 | 10.975 | |
| pool_estimation | 3.560 | 0.972 | 5.202 | |
| processing | 5.511 | 1.773 | 7.990 | |
| replicate_sum | 0.194 | 0.085 | 0.410 | |
| standard_ora | 0.574 | 0.111 | 0.764 | |
| tissue_dma | 0.024 | 0.013 | 0.060 | |
| tissue_dma_old | 0.020 | 0.012 | 0.049 | |
| tissue_dma_young | 0.022 | 0.012 | 0.063 | |
| tissue_meta | 0.017 | 0.010 | 0.039 | |
| tissue_norm | 0.064 | 0.018 | 0.098 | |
| tissue_norm_se | 0.027 | 0.004 | 0.049 | |
| tissue_tvn_proteomics | 0.027 | 0.007 | 0.056 | |
| tissue_tvn_rnaseq | 0.049 | 0.007 | 0.078 | |
| translate_id | 0.000 | 0.000 | 0.001 | |
| viz_graph | 0.253 | 0.058 | 0.376 | |
| viz_heatmap | 0.284 | 0.066 | 0.438 | |
| viz_pca | 1.421 | 0.199 | 1.656 | |
| viz_superplot | 1.734 | 0.451 | 2.236 | |
| viz_volcano | 0.313 | 0.064 | 0.456 | |