Christina Schmidt
| Snapshot Date: 2026-04-09 13:40 -0400 (Thu, 09 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/MetaProViz |
| git_branch: devel |
| git_last_commit: 47b2175 |
| git_last_commit_date: 2026-03-27 04:09:49 -0400 (Fri, 27 Mar 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-10 11:35 -0400 (Fri, 10 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4917 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-26 r89717) -- "Unsuffered Consequences" | 4629 |
| 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 1271/2388 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MetaProViz 3.99.50 (landing page) Christina Schmidt
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
| 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: 3.99.50 |
| 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_3.99.50.tar.gz |
| StartedAt: 2026-04-10 01:39:03 -0400 (Fri, 10 Apr 2026) |
| EndedAt: 2026-04-10 01:53:01 -0400 (Fri, 10 Apr 2026) |
| EllapsedTime: 837.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MetaProViz.Rcheck |
| Warnings: 0 |
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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_3.99.50.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/MetaProViz.Rcheck’
* using R version 4.6.0 alpha (2026-04-05 r89794)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-10 05:39:03 UTC
* checking for file ‘MetaProViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MetaProViz’ version ‘3.99.50’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 39 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MetaProViz’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2026-04-10 01:40:56] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-10 01:40:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-10 01:40:56] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-04-10 01:40:56] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-04-10 01:40:56] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-04-09
[2026-04-10 01:40:56] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-04-09 19:11:52 UTC; unix
[2026-04-10 01:40:56] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.12
[2026-04-10 01:40:56] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-04-10 01:40:57] [INFO] [OmnipathR] Session info: [version=R version 4.6.0 alpha (2026-04-05 r89794); 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=2026-04-10; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2026-04-10 01:40:57] [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]
[2026-04-10 01:40:57] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); 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 3.6.6(2026-04-09); colorspace 2.1-2(2025-09-22); ComplexUpset 1.3.3(2021-12-11); crayon 1.5.3(2024-06-20); curl 7.0.0(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 1.2.1(2026-04-03); EnhancedVolcano 1.29.1(2026-04-09); 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 2.2.3(2026-04-07); 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 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); MetaProViz 3.99.50(2026-04-09); OmnipathR 3.19.12(2026-04-09); 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 3.8.7(2026-04-01); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.2(2026-03-31); 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 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); 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 0.7.2(2026-03-21); websocket 1.4.4(2025-04-10); 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)
[2026-04-10 01:40:57] [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
[2026-04-10 01:40:57] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-04-10 01:40:57] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-04-10 01:40:57] [TRACE] [OmnipathR] Contains 1 files.
[2026-04-10 01:40:57] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-04-10 01:40:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-10 01:40:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-10 01:40:57] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-04-10 01:40:57] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2026-04-10 01:40:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-04-10 01:40:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-10 01:40:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-04-10 01:40:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-10 01:40:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-04-10 01:40:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-10 01:40:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-04-10 01:40:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-10 01:40:57] [TRACE] [OmnipathR] Cache locked: FALSE
It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2026-04-10 01:42:14] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-10 01:42:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-10 01:42:14] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-04-10 01:42:14] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-04-10 01:42:14] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-04-09
[2026-04-10 01:42:14] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-04-09 19:11:52 UTC; unix
[2026-04-10 01:42:14] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.12
[2026-04-10 01:42:14] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-04-10 01:42:18] [INFO] [OmnipathR] Session info: [version=R version 4.6.0 alpha (2026-04-05 r89794); 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=2026-04-10; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2026-04-10 01:42:18] [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]
[2026-04-10 01:42:18] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); 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 3.6.6(2026-04-09); colorspace 2.1-2(2025-09-22); ComplexUpset 1.3.3(2021-12-11); crayon 1.5.3(2024-06-20); curl 7.0.0(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 1.2.1(2026-04-03); EnhancedVolcano 1.29.1(2026-04-09); 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 2.2.3(2026-04-07); 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 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); MetaProViz 3.99.50(2026-04-09); OmnipathR 3.19.12(2026-04-09); 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 3.8.7(2026-04-01); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.2(2026-03-31); 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 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); 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 0.7.2(2026-03-21); websocket 1.4.4(2025-04-10); 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)
[2026-04-10 01:42:18] [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
[2026-04-10 01:42:18] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-04-10 01:42:18] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-04-10 01:42:18] [TRACE] [OmnipathR] Contains 1 files.
[2026-04-10 01:42:18] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-04-10 01:42:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-10 01:42:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-10 01:42:18] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-04-10 01:42:18] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2026-04-10 01:42:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-04-10 01:42:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-10 01:42:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-04-10 01:42:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-10 01:42:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-04-10 01:42:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-10 01:42:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-04-10 01:42:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-10 01:42:18] [TRACE] [OmnipathR] Cache locked: FALSE
build_seed_neighbors: no visible binding for global variable ‘type1’
build_seed_neighbors: no visible binding for global variable ‘id1’
build_seed_neighbors: no visible binding for global variable ‘type2’
build_seed_neighbors: no visible binding for global variable ‘id2’
Undefined global functions or variables:
id1 id2 type1 type2
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'reexports.Rd':
‘[magrittr:pipe]{%>%}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
cluster_ora 77.245 12.481 115.344
traverse_ids 38.961 3.849 42.229
dma 20.730 1.452 21.948
mca_2cond 12.115 1.066 13.128
equivalent_id 10.446 1.537 11.934
processing 10.508 1.159 11.542
pool_estimation 8.868 0.907 9.672
metadata_analysis 5.163 0.232 5.343
metsigdb_metalinks 3.996 1.263 14.368
* 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 ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.23-bioc/meat/MetaProViz.Rcheck/00check.log’
for details.
MetaProViz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/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 ‘3.99.50’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading [2026-04-09 15:25:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-09 15:25:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-09 15:25:18] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2026-04-09 15:25:18] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-04-09 15:25:18] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-04-09 [2026-04-09 15:25:18] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-04-09 19:11:52 UTC; unix [2026-04-09 15:25:18] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.12 [2026-04-09 15:25:18] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2026-04-09 15:25:18] [INFO] [OmnipathR] Session info: [version=R version 4.6.0 alpha (2026-04-05 r89794); 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=2026-04-09; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2026-04-09 15:25:18] [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] [2026-04-09 15:25:18] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); 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 3.6.6(2026-04-09); colorspace 2.1-2(2025-09-22); ComplexUpset 1.3.3(2021-12-11); crayon 1.5.3(2024-06-20); curl 7.0.0(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 1.2.1(2026-04-03); EnhancedVolcano 1.29.1(2026-04-09); 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 2.2.3(2026-04-07); 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 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); MetaProViz 3.99.50(2026-04-09); OmnipathR 3.19.12(2026-04-09); 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 3.8.7(2026-04-01); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.2(2026-03-31); 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 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); 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 0.7.2(2026-03-21); websocket 1.4.4(2025-04-10); 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) [2026-04-09 15:25:18] [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 [2026-04-09 15:25:18] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-09 15:25:18] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2026-04-09 15:25:18] [TRACE] [OmnipathR] Contains 1 files. [2026-04-09 15:25:18] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-09 15:25:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-09 15:25:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-09 15:25:18] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2026-04-09 15:25:18] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2026-04-09 15:25:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-09 15:25:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-09 15:25:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-09 15:25:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-09 15:25:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-09 15:25:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-09 15:25:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-09 15:25:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-09 15:25:18] [TRACE] [OmnipathR] Cache locked: FALSE ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2026-04-09 15:25:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-09 15:25:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-09 15:25:43] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2026-04-09 15:25:43] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-04-09 15:25:43] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-04-09 [2026-04-09 15:25:43] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-04-09 19:11:52 UTC; unix [2026-04-09 15:25:43] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.12 [2026-04-09 15:25:43] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2026-04-09 15:25:44] [INFO] [OmnipathR] Session info: [version=R version 4.6.0 alpha (2026-04-05 r89794); 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=2026-04-09; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2026-04-09 15:25:44] [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] [2026-04-09 15:25:44] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); 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 3.6.6(2026-04-09); colorspace 2.1-2(2025-09-22); ComplexUpset 1.3.3(2021-12-11); crayon 1.5.3(2024-06-20); curl 7.0.0(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 1.2.1(2026-04-03); EnhancedVolcano 1.29.1(2026-04-09); 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 2.2.3(2026-04-07); 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 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); MetaProViz 3.99.50(2026-04-09); OmnipathR 3.19.12(2026-04-09); 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 3.8.7(2026-04-01); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.2(2026-03-31); 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 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); 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 0.7.2(2026-03-21); websocket 1.4.4(2025-04-10); 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) [2026-04-09 15:25:44] [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 [2026-04-09 15:25:44] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-09 15:25:44] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2026-04-09 15:25:44] [TRACE] [OmnipathR] Contains 1 files. [2026-04-09 15:25:44] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-09 15:25:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-09 15:25:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-09 15:25:44] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2026-04-09 15:25:44] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2026-04-09 15:25:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-09 15:25:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-09 15:25:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-09 15:25:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-09 15:25:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-09 15:25:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-09 15:25:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-09 15:25:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-09 15:25:44] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2026-04-09 15:25:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-09 15:25:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-09 15:25:58] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2026-04-09 15:25:58] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-04-09 15:25:58] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-04-09 [2026-04-09 15:25:58] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-04-09 19:11:52 UTC; unix [2026-04-09 15:25:58] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.12 [2026-04-09 15:25:58] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2026-04-09 15:25:58] [INFO] [OmnipathR] Session info: [version=R version 4.6.0 alpha (2026-04-05 r89794); 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=2026-04-09; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2026-04-09 15:25:58] [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] [2026-04-09 15:25:58] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); 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 3.6.6(2026-04-09); colorspace 2.1-2(2025-09-22); ComplexUpset 1.3.3(2021-12-11); crayon 1.5.3(2024-06-20); curl 7.0.0(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 1.2.1(2026-04-03); EnhancedVolcano 1.29.1(2026-04-09); 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 2.2.3(2026-04-07); 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 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); MetaProViz 3.99.50(2026-04-09); OmnipathR 3.19.12(2026-04-09); 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 3.8.7(2026-04-01); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.2(2026-03-31); 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 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); 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 0.7.2(2026-03-21); websocket 1.4.4(2025-04-10); 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) [2026-04-09 15:25:58] [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 [2026-04-09 15:25:58] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-04-09 15:25:58] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2026-04-09 15:25:58] [TRACE] [OmnipathR] Contains 1 files. [2026-04-09 15:25:58] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-04-09 15:25:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-04-09 15:25:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-09 15:25:58] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2026-04-09 15:25:58] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2026-04-09 15:25:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-04-09 15:25:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-09 15:25:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-04-09 15:25:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-09 15:25:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-04-09 15:25:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-09 15:25:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-04-09 15:25:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-04-09 15:25:59] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (MetaProViz)
MetaProViz.Rcheck/tests/testthat.Rout
R version 4.6.0 alpha (2026-04-05 r89794)
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.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(MetaProViz)
[2026-04-10 01:49:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-10 01:49:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-10 01:49:23] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-04-10 01:49:23] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-04-10 01:49:23] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-04-09
[2026-04-10 01:49:23] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-04-09 19:11:52 UTC; unix
[2026-04-10 01:49:23] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.12
[2026-04-10 01:49:23] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-04-10 01:49:24] [INFO] [OmnipathR] Session info: [version=R version 4.6.0 alpha (2026-04-05 r89794); 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=2026-04-10; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2026-04-10 01:49:24] [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]
[2026-04-10 01:49:24] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); 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 3.6.6(2026-04-09); colorspace 2.1-2(2025-09-22); ComplexUpset 1.3.3(2021-12-11); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); EnhancedVolcano 1.29.1(2026-04-09); 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 2.2.3(2026-04-07); 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 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); MetaProViz 3.99.50(2026-04-09); OmnipathR 3.19.12(2026-04-09); 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 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); 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 0.7.2(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)
[2026-04-10 01:49:24] [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
[2026-04-10 01:49:24] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-04-10 01:49:24] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-04-10 01:49:24] [TRACE] [OmnipathR] Contains 23 files.
[2026-04-10 01:49:24] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-04-10 01:49:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-04-10 01:49:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-10 01:49:24] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-04-10 01:49:24] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2026-04-10 01:49:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-04-10 01:49:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-10 01:49:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-04-10 01:49:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-10 01:49:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-04-10 01:49:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-10 01:49:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-04-10 01:49:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-04-10 01:49:24] [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%.
[2026-04-10 01:49:36] [TRACE] [MetaProViz] Error The HMDB column selected as InpuID in metadata_info was not found in data. Please check your input.
[2026-04-10 01:49:36] [TRACE] [MetaProViz] Error The HMDB column selected as InpuID in metadata_info was not found in data. Please check your input.
[2026-04-10 01:49:36] [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
13.780 2.668 16.426
MetaProViz.Rcheck/MetaProViz-Ex.timings
| name | user | system | elapsed | |
| alanine_pathways | 0.043 | 0.008 | 0.051 | |
| biocrates_features | 0.079 | 0.014 | 0.090 | |
| cellular_meta | 0.023 | 0.007 | 0.030 | |
| checkmatch_pk_to_data | 0.001 | 0.000 | 0.000 | |
| cluster_ora | 77.245 | 12.481 | 115.344 | |
| cluster_pk | 0.224 | 0.024 | 0.247 | |
| compare_pk | 0.000 | 0.001 | 0.001 | |
| count_id | 1.656 | 0.339 | 1.946 | |
| dma | 20.730 | 1.452 | 21.948 | |
| equivalent_features | 0.029 | 0.002 | 0.031 | |
| equivalent_id | 10.446 | 1.537 | 11.934 | |
| gaude_pathways | 0.024 | 0.000 | 0.024 | |
| get_exclusion_metabolites | 0.000 | 0.001 | 0.000 | |
| hallmarks | 0.030 | 0.001 | 0.030 | |
| intracell_dma | 0.041 | 0.009 | 0.050 | |
| intracell_raw | 0.086 | 0.008 | 0.095 | |
| intracell_raw_se | 0.043 | 0.004 | 0.046 | |
| make_gene_metab_set | 1.889 | 0.883 | 2.424 | |
| mapping_ambiguity | 0 | 0 | 0 | |
| mca_2cond | 12.115 | 1.066 | 13.128 | |
| mca_core | 0.137 | 0.009 | 0.143 | |
| mca_core_rules | 0.026 | 0.006 | 0.031 | |
| mca_twocond_rules | 0.021 | 0.003 | 0.023 | |
| medium_raw | 0.063 | 0.012 | 0.074 | |
| meta_pk | 0.147 | 0.006 | 0.152 | |
| metadata_analysis | 5.163 | 0.232 | 5.343 | |
| metaproviz_config_path | 0.000 | 0.000 | 0.001 | |
| metaproviz_load_config | 0.003 | 0.000 | 0.003 | |
| metaproviz_log | 0.001 | 0.000 | 0.000 | |
| metaproviz_logfile | 0.000 | 0.001 | 0.002 | |
| metaproviz_reset_config | 0.009 | 0.000 | 0.008 | |
| metaproviz_save_config | 0.007 | 0.001 | 0.008 | |
| metaproviz_set_loglevel | 0.003 | 0.001 | 0.003 | |
| metsigdb_chemicalclass | 1.953 | 0.532 | 2.104 | |
| metsigdb_kegg | 1.877 | 0.112 | 1.973 | |
| metsigdb_metalinks | 3.996 | 1.263 | 14.368 | |
| metsigdb_reactome | 0 | 0 | 0 | |
| pool_estimation | 8.868 | 0.907 | 9.672 | |
| processing | 10.508 | 1.159 | 11.542 | |
| replicate_sum | 0.528 | 0.075 | 0.594 | |
| standard_ora | 1.979 | 0.152 | 2.101 | |
| tissue_dma | 0.062 | 0.009 | 0.070 | |
| tissue_dma_old | 0.064 | 0.006 | 0.069 | |
| tissue_dma_young | 0.060 | 0.011 | 0.070 | |
| tissue_meta | 0.048 | 0.008 | 0.055 | |
| tissue_norm | 0.154 | 0.018 | 0.171 | |
| tissue_norm_se | 0.058 | 0.002 | 0.059 | |
| tissue_tvn_proteomics | 0.070 | 0.002 | 0.072 | |
| tissue_tvn_rnaseq | 0.117 | 0.011 | 0.127 | |
| translate_id | 0.000 | 0.000 | 0.001 | |
| traverse_ids | 38.961 | 3.849 | 42.229 | |
| viz_graph | 0.473 | 0.035 | 0.504 | |
| viz_heatmap | 0.642 | 0.045 | 0.682 | |
| viz_pca | 3.477 | 0.113 | 3.571 | |
| viz_superplot | 3.119 | 0.221 | 3.312 | |
| viz_volcano | 0.717 | 0.042 | 0.750 | |