Ana Galhoz
| Snapshot Date: 2025-08-11 13:40 -0400 (Mon, 11 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/wppi |
| git_branch: RELEASE_3_21 |
| git_last_commit: c49fef6 |
| git_last_commit_date: 2025-04-15 12:26:01 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-08-14 11:48 -0400 (Thu, 14 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4566 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4604 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4545 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
| 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 2318/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| wppi 1.16.0 (landing page) Ana Galhoz
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the wppi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/wppi.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: wppi |
| Version: 1.16.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings wppi_1.16.0.tar.gz |
| StartedAt: 2025-08-12 15:06:05 -0000 (Tue, 12 Aug 2025) |
| EndedAt: 2025-08-12 15:13:59 -0000 (Tue, 12 Aug 2025) |
| EllapsedTime: 474.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: wppi.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings wppi_1.16.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/wppi.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘wppi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wppi’ version ‘1.16.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘wppi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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
[2025-08-12 15:06:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-12 15:06:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-12 15:06:53] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-08-12 15:06:53] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-12 15:06:53] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-11
[2025-08-12 15:06:53] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-08-11 20:19:58 UTC; unix
[2025-08-12 15:06:53] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-08-12 15:06:53] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-08-12 15:06:53] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-08-12; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2025-08-12 15:06:53] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0]
[2025-08-12 15:06:54] [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 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.0(2025-03-21); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); Matrix 1.7-3(2025-03-11); memoise 2.0.1(2021-11-26); OmnipathR 3.16.0(2025-08-11); pillar 1.10.2(2025-04-05); 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 1.3.2(2024-11-28); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); wppi 1.16.0(2025-08-11); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-08-12 15:06:54] [INFO] [OmnipathR] CURL: version: 8.12.1; headers: 8.4.0; ssl_version: OpenSSL/3.4.1; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-08-12 15:06:54] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-08-12 15:06:54] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-08-12 15:06:54] [TRACE] [OmnipathR] Contains 1 files.
[2025-08-12 15:06:54] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-08-12 15:06:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-12 15:06:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-12 15:06:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-08-12 15:06:54] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2025-08-12 15:06:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-12 15:06:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-12 15:06:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-12 15:06:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-12 15:06:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-12 15:06:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-12 15:06:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-12 15:06:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-12 15:06:54] [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
[2025-08-12 15:07:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-12 15:07:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-12 15:07:19] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-08-12 15:07:19] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-12 15:07:19] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-11
[2025-08-12 15:07:19] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-08-11 20:19:58 UTC; unix
[2025-08-12 15:07:19] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-08-12 15:07:19] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-08-12 15:07:19] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-08-12; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2025-08-12 15:07:19] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0]
[2025-08-12 15:07:20] [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 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.0(2025-03-21); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); Matrix 1.7-3(2025-03-11); memoise 2.0.1(2021-11-26); OmnipathR 3.16.0(2025-08-11); pillar 1.10.2(2025-04-05); 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 1.3.2(2024-11-28); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); wppi 1.16.0(2025-08-11); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-08-12 15:07:20] [INFO] [OmnipathR] CURL: version: 8.12.1; headers: 8.4.0; ssl_version: OpenSSL/3.4.1; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-08-12 15:07:20] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-08-12 15:07:20] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-08-12 15:07:20] [TRACE] [OmnipathR] Contains 1 files.
[2025-08-12 15:07:20] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-08-12 15:07:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-12 15:07:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-12 15:07:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-08-12 15:07:20] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2025-08-12 15:07:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-12 15:07:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-12 15:07:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-12 15:07:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-12 15:07:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-12 15:07:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-12 15:07:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-12 15:07:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-12 15:07:20] [TRACE] [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
wppi 71.692 6.418 79.066
prioritization_genes 37.141 2.689 39.937
random_walk 36.707 2.432 39.375
score_candidate_genes_from_PPI 36.178 2.663 39.068
weighted_adj 30.025 2.036 32.289
common_neighbors 19.929 1.764 25.735
count_genes 16.111 0.700 27.417
wppi_data 11.199 0.492 11.751
filter_annot_with_network 10.332 0.156 10.498
wppi_omnipath_data 5.184 0.368 5.601
subgraph_op 5.074 0.443 5.536
in_omnipath 4.894 0.186 5.102
functional_annot 3.407 0.596 23.422
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/wppi.Rcheck/00check.log’
for details.
wppi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL wppi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘wppi’ ... ** this is package ‘wppi’ version ‘1.16.0’ ** using staged installation ** R ** byte-compile and prepare package for lazy loading [2025-08-11 20:20:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-11 20:20:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-11 20:20:41] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-08-11 20:20:41] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-08-11 20:20:41] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-11 [2025-08-11 20:20:41] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-08-11 20:19:58 UTC; unix [2025-08-11 20:20:41] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0 [2025-08-11 20:20:41] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-08-11 20:20:42] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-08-11; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto] [2025-08-11 20:20:42] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0] [2025-08-11 20:20:42] [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 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.0(2025-03-21); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); Matrix 1.7-3(2025-03-11); memoise 2.0.1(2021-11-26); OmnipathR 3.16.0(2025-08-11); pillar 1.10.2(2025-04-05); 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 1.3.2(2024-11-28); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); wppi 1.16.0(2025-08-11); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-08-11 20:20:42] [INFO] [OmnipathR] CURL: version: 8.12.1; headers: 8.4.0; ssl_version: OpenSSL/3.4.1; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2025-08-11 20:20:42] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-11 20:20:42] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-08-11 20:20:42] [TRACE] [OmnipathR] Contains 1 files. [2025-08-11 20:20:42] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-11 20:20:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-11 20:20:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-11 20:20:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-08-11 20:20:42] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-08-11 20:20:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-08-11 20:20:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-11 20:20:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-08-11 20:20:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-11 20:20:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-11 20:20:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-11 20:20:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-08-11 20:20:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-11 20:20:43] [TRACE] [OmnipathR] Cache locked: FALSE Note: wrong number of arguments to '/' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2025-08-11 20:20:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-11 20:20:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-11 20:20:48] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-08-11 20:20:48] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-08-11 20:20:48] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-11 [2025-08-11 20:20:48] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-08-11 20:19:58 UTC; unix [2025-08-11 20:20:48] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0 [2025-08-11 20:20:48] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-08-11 20:20:48] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-08-11; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto] [2025-08-11 20:20:48] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0] [2025-08-11 20:20:49] [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 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.0(2025-03-21); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); Matrix 1.7-3(2025-03-11); memoise 2.0.1(2021-11-26); OmnipathR 3.16.0(2025-08-11); pillar 1.10.2(2025-04-05); 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 1.3.2(2024-11-28); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); wppi 1.16.0(2025-08-11); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-08-11 20:20:49] [INFO] [OmnipathR] CURL: version: 8.12.1; headers: 8.4.0; ssl_version: OpenSSL/3.4.1; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2025-08-11 20:20:49] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-11 20:20:49] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-08-11 20:20:49] [TRACE] [OmnipathR] Contains 1 files. [2025-08-11 20:20:49] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-11 20:20:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-11 20:20:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-11 20:20:49] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-08-11 20:20:49] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-08-11 20:20:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-08-11 20:20:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-11 20:20:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-08-11 20:20:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-11 20:20:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-11 20:20:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-11 20:20:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-08-11 20:20:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-11 20:20:49] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-08-11 20:20:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-11 20:20:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-11 20:20:53] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-08-11 20:20:53] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-08-11 20:20:53] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-11 [2025-08-11 20:20:53] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-08-11 20:19:58 UTC; unix [2025-08-11 20:20:53] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0 [2025-08-11 20:20:53] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-08-11 20:20:54] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-08-11; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto] [2025-08-11 20:20:54] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0] [2025-08-11 20:20:54] [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 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.0(2025-03-21); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); Matrix 1.7-3(2025-03-11); memoise 2.0.1(2021-11-26); OmnipathR 3.16.0(2025-08-11); pillar 1.10.2(2025-04-05); 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 1.3.2(2024-11-28); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); wppi 1.16.0(2025-08-11); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-08-11 20:20:54] [INFO] [OmnipathR] CURL: version: 8.12.1; headers: 8.4.0; ssl_version: OpenSSL/3.4.1; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2025-08-11 20:20:54] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-11 20:20:54] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-08-11 20:20:54] [TRACE] [OmnipathR] Contains 1 files. [2025-08-11 20:20:54] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-11 20:20:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-11 20:20:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-11 20:20:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-08-11 20:20:54] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-08-11 20:20:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-08-11 20:20:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-11 20:20:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-08-11 20:20:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-11 20:20:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-11 20:20:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-11 20:20:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-08-11 20:20:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-11 20:20:54] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (wppi)
wppi.Rcheck/wppi-Ex.timings
| name | user | system | elapsed | |
| common_neighbors | 19.929 | 1.764 | 25.735 | |
| count_genes | 16.111 | 0.700 | 27.417 | |
| filter_annot_with_network | 10.332 | 0.156 | 10.498 | |
| functional_annot | 3.407 | 0.596 | 23.422 | |
| graph_from_op | 4.611 | 0.209 | 4.830 | |
| in_omnipath | 4.894 | 0.186 | 5.102 | |
| prioritization_genes | 37.141 | 2.689 | 39.937 | |
| process_annot | 1.250 | 0.025 | 1.279 | |
| random_walk | 36.707 | 2.432 | 39.375 | |
| score_candidate_genes_from_PPI | 36.178 | 2.663 | 39.068 | |
| subgraph_op | 5.074 | 0.443 | 5.536 | |
| weighted_adj | 30.025 | 2.036 | 32.289 | |
| wppi | 71.692 | 6.418 | 79.066 | |
| wppi_data | 11.199 | 0.492 | 11.751 | |
| wppi_go_data | 3.881 | 0.188 | 4.081 | |
| wppi_hpo_data | 1.156 | 0.048 | 1.206 | |
| wppi_omnipath_data | 5.184 | 0.368 | 5.601 | |