Ana Galhoz
| Snapshot Date: 2025-01-03 13:40 -0500 (Fri, 03 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/wppi |
| git_branch: devel |
| git_last_commit: 321e17d |
| git_last_commit_date: 2024-10-29 10:58:10 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-04 11:47 -0500 (Sat, 04 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4756 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4475 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4435 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4390 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4383 |
| 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 2255/2275 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| wppi 1.15.0 (landing page) Ana Galhoz
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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: 1.15.0 |
| 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_1.15.0.tar.gz |
| StartedAt: 2025-01-04 11:59:57 -0000 (Sat, 04 Jan 2025) |
| EndedAt: 2025-01-04 12:06:57 -0000 (Sat, 04 Jan 2025) |
| EllapsedTime: 420.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: wppi.Rcheck |
| Warnings: 5 |
##############################################################################
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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_1.15.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/wppi.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* 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)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘wppi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wppi’ version ‘1.15.0’
* 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 ... WARNING
Found the following significant warnings:
Warning: program compiled against libxml 212 using older 211
See ‘/home/biocbuild/bbs-3.21-bioc/meat/wppi.Rcheck/00install.out’ for details.
* 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 ...Warning: program compiled against libxml 212 using older 211
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 ... NOTE
Warning: program compiled against libxml 212 using older 211
[2025-01-04 12:00:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-04 12:00:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 12:00:27] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-04 12:00:27] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-04 12:00:27] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-04 12:00:27] [TRACE] [OmnipathR] Contains 1 files.
[2025-01-04 12:00:27] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-04 12:00:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-04 12:00:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 12:00:27] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-04 12:00:27] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2025-01-04 12:00:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-04 12:00:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 12:00:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-04 12:00:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 12:00:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-04 12:00:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 12:00:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-04 12:00:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 12:00:28] [TRACE] [OmnipathR] Cache locked: FALSE
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* 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
Warning: program compiled against libxml 212 using older 211
[2025-01-04 12:00:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-04 12:00:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 12:00:48] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-04 12:00:48] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-04 12:00:48] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-04 12:00:48] [TRACE] [OmnipathR] Contains 1 files.
[2025-01-04 12:00:48] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-04 12:00:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-04 12:00:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 12:00:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-04 12:00:48] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2025-01-04 12:00:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-04 12:00:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 12:00:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-04 12:00:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 12:00:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-04 12:00:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 12:00:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-04 12:00:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 12:00:48] [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 ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking S3 generic/method consistency ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
[2025-01-04 12:01:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-04 12:01:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 12:01:10] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-04 12:01:10] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-04 12:01:10] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-04 12:01:10] [TRACE] [OmnipathR] Contains 1 files.
[2025-01-04 12:01:10] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-04 12:01:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-04 12:01:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 12:01:10] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-04 12:01:10] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2025-01-04 12:01:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-04 12:01:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 12:01:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-04 12:01:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 12:01:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-04 12:01:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 12:01:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-04 12:01:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 12:01:11] [TRACE] [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Warning: program compiled against libxml 212 using older 211
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... NOTE
Warning: program compiled against libxml 212 using older 211
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 58.482 0.786 62.657
score_candidate_genes_from_PPI 30.796 0.052 35.976
prioritization_genes 29.988 0.126 33.665
random_walk 29.266 0.089 33.371
weighted_adj 24.100 0.167 26.406
common_neighbors 16.508 0.304 24.350
count_genes 12.866 0.228 23.604
wppi_data 8.431 0.235 9.010
filter_annot_with_network 8.323 0.095 9.620
in_omnipath 4.577 0.000 5.021
subgraph_op 4.537 0.032 5.335
graph_from_op 4.439 0.000 5.025
functional_annot 2.333 0.037 17.731
* 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: 5 WARNINGs, 7 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-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘wppi’ ... ** using staged installation ** R ** byte-compile and prepare package for lazy loading Warning: program compiled against libxml 212 using older 211 [2025-01-03 20:08:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-03 20:08:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 20:08:21] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-01-03 20:08:22] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-03 20:08:22] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-01-03 20:08:22] [TRACE] [OmnipathR] Contains 1 files. [2025-01-03 20:08:22] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-03 20:08:22] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-03 20:08:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 20:08:22] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-01-03 20:08:22] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-01-03 20:08:22] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-03 20:08:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 20:08:22] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-03 20:08:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 20:08:22] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-03 20:08:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 20:08:22] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-03 20:08:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 20:08:22] [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 Warning: program compiled against libxml 212 using older 211 [2025-01-03 20:08:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-03 20:08:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 20:08:27] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-01-03 20:08:27] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-03 20:08:27] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-01-03 20:08:27] [TRACE] [OmnipathR] Contains 1 files. [2025-01-03 20:08:27] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-03 20:08:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-03 20:08:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 20:08:27] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-01-03 20:08:27] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-01-03 20:08:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-03 20:08:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 20:08:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-03 20:08:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 20:08:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-03 20:08:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 20:08:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-03 20:08:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 20:08:27] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location Warning: program compiled against libxml 212 using older 211 [2025-01-03 20:08:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-03 20:08:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 20:08:32] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-01-03 20:08:32] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-03 20:08:32] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-01-03 20:08:32] [TRACE] [OmnipathR] Contains 1 files. [2025-01-03 20:08:32] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-03 20:08:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-03 20:08:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 20:08:32] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-01-03 20:08:32] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-01-03 20:08:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-03 20:08:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 20:08:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-03 20:08:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 20:08:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-03 20:08:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 20:08:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-03 20:08:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 20:08:32] [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 | 16.508 | 0.304 | 24.350 | |
| count_genes | 12.866 | 0.228 | 23.604 | |
| filter_annot_with_network | 8.323 | 0.095 | 9.620 | |
| functional_annot | 2.333 | 0.037 | 17.731 | |
| graph_from_op | 4.439 | 0.000 | 5.025 | |
| in_omnipath | 4.577 | 0.000 | 5.021 | |
| prioritization_genes | 29.988 | 0.126 | 33.665 | |
| process_annot | 1.091 | 0.028 | 1.206 | |
| random_walk | 29.266 | 0.089 | 33.371 | |
| score_candidate_genes_from_PPI | 30.796 | 0.052 | 35.976 | |
| subgraph_op | 4.537 | 0.032 | 5.335 | |
| weighted_adj | 24.100 | 0.167 | 26.406 | |
| wppi | 58.482 | 0.786 | 62.657 | |
| wppi_data | 8.431 | 0.235 | 9.010 | |
| wppi_go_data | 3.594 | 0.098 | 3.826 | |
| wppi_hpo_data | 0.758 | 0.019 | 0.807 | |
| wppi_omnipath_data | 4.345 | 0.094 | 4.601 | |