Ana Galhoz
| Snapshot Date: 2025-01-13 13:00 -0500 (Mon, 13 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/wppi |
| git_branch: RELEASE_3_20 |
| git_last_commit: 240f65a |
| git_last_commit_date: 2024-10-29 10:58:10 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-16 12:10 -0500 (Thu, 16 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4746 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4489 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4517 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4469 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4387 |
| 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 2269/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| wppi 1.14.0 (landing page) Ana Galhoz
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | 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 | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
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. |
| Package: wppi |
| Version: 1.14.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:wppi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings wppi_1.14.0.tar.gz |
| StartedAt: 2025-01-15 13:18:00 -0500 (Wed, 15 Jan 2025) |
| EndedAt: 2025-01-15 13:22:31 -0500 (Wed, 15 Jan 2025) |
| EllapsedTime: 270.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: wppi.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:wppi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings wppi_1.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/wppi.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘wppi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wppi’ version ‘1.14.0’
* 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 whether startup messages can be suppressed ... NOTE
[2025-01-15 13:18:36] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-15 13:18:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-15 13:18:36] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-15 13:18:36] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-15 13:18:36] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-15 13:18:36] [TRACE] [OmnipathR] Contains 1 files.
[2025-01-15 13:18:36] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-15 13:18:36] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-15 13:18:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-15 13:18:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-15 13:18:36] [TRACE] [OmnipathR] Pandoc version: `3.1.2`.
[2025-01-15 13:18:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-15 13:18:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-15 13:18:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-15 13:18:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-15 13:18:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-15 13:18:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-15 13:18:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-15 13:18:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-15 13:18:36] [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
[2025-01-15 13:18:57] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-15 13:18:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-15 13:18:57] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-15 13:18:57] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-15 13:18:57] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-15 13:18:57] [TRACE] [OmnipathR] Contains 1 files.
[2025-01-15 13:18:57] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-15 13:18:57] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-15 13:18:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-15 13:18:57] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-15 13:18:57] [TRACE] [OmnipathR] Pandoc version: `3.1.2`.
[2025-01-15 13:18:57] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-15 13:18:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-15 13:18:57] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-15 13:18:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-15 13:18:58] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-15 13:18:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-15 13:18:58] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-15 13:18:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-15 13:18:58] [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 34.974 0.520 35.750
score_candidate_genes_from_PPI 18.332 0.357 18.782
prioritization_genes 16.935 0.355 17.567
random_walk 16.842 0.294 17.222
weighted_adj 13.765 0.204 14.014
count_genes 12.565 0.470 12.983
wppi_data 9.327 0.150 9.510
filter_annot_with_network 8.790 0.184 9.009
common_neighbors 6.491 0.269 10.143
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/wppi.Rcheck/00check.log’
for details.
wppi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL wppi ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘wppi’ ... ** using staged installation ** R ** byte-compile and prepare package for lazy loading [2025-01-13 17:05:39] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-13 17:05:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 17:05:39] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-13 17:05:39] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-13 17:05:39] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-13 17:05:39] [TRACE] [OmnipathR] Contains 1 files. [2025-01-13 17:05:39] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-13 17:05:39] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-13 17:05:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 17:05:39] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-13 17:05:39] [TRACE] [OmnipathR] Pandoc version: `3.1.2`. [2025-01-13 17:05:39] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-13 17:05:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 17:05:39] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-13 17:05:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 17:05:39] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-13 17:05:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 17:05:39] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-13 17:05:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 17:05:39] [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 [2025-01-13 17:05:44] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-13 17:05:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 17:05:44] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-13 17:05:44] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-13 17:05:44] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-13 17:05:44] [TRACE] [OmnipathR] Contains 1 files. [2025-01-13 17:05:44] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-13 17:05:44] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-13 17:05:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 17:05:44] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-13 17:05:44] [TRACE] [OmnipathR] Pandoc version: `3.1.2`. [2025-01-13 17:05:44] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-13 17:05:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 17:05:44] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-13 17:05:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 17:05:44] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-13 17:05:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 17:05:44] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-13 17:05:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 17:05:44] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-01-13 17:05:48] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-13 17:05:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 17:05:48] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-13 17:05:48] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-13 17:05:48] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-13 17:05:48] [TRACE] [OmnipathR] Contains 1 files. [2025-01-13 17:05:48] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-13 17:05:48] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-13 17:05:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 17:05:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-13 17:05:48] [TRACE] [OmnipathR] Pandoc version: `3.1.2`. [2025-01-13 17:05:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-13 17:05:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 17:05:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-13 17:05:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 17:05:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-13 17:05:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 17:05:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-13 17:05:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 17:05:48] [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 | 6.491 | 0.269 | 10.143 | |
| count_genes | 12.565 | 0.470 | 12.983 | |
| filter_annot_with_network | 8.790 | 0.184 | 9.009 | |
| functional_annot | 2.333 | 0.147 | 3.692 | |
| graph_from_op | 3.704 | 0.055 | 3.815 | |
| in_omnipath | 3.668 | 0.058 | 3.779 | |
| prioritization_genes | 16.935 | 0.355 | 17.567 | |
| process_annot | 1.065 | 0.030 | 1.099 | |
| random_walk | 16.842 | 0.294 | 17.222 | |
| score_candidate_genes_from_PPI | 18.332 | 0.357 | 18.782 | |
| subgraph_op | 3.686 | 0.038 | 3.743 | |
| weighted_adj | 13.765 | 0.204 | 14.014 | |
| wppi | 34.974 | 0.520 | 35.750 | |
| wppi_data | 9.327 | 0.150 | 9.510 | |
| wppi_go_data | 4.713 | 0.114 | 4.843 | |
| wppi_hpo_data | 0.899 | 0.017 | 0.919 | |
| wppi_omnipath_data | 3.625 | 0.029 | 3.676 | |