Ana Galhoz
| Snapshot Date: 2025-02-03 13:00 -0500 (Mon, 03 Feb 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 2025-02-06 12:09 -0500 (Thu, 06 Feb 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" | 4753 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4501 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4524 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4476 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4407 |
| 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 | NA | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | 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. |
| 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: 2025-02-04 11:56:03 -0500 (Tue, 04 Feb 2025) |
| EndedAt: 2025-02-04 12:04:31 -0500 (Tue, 04 Feb 2025) |
| EllapsedTime: 507.6 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: x86_64-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 Monterey 12.7.6
* 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
[2025-02-04 11:57:06] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-04 11:57:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-04 11:57:06] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-04 11:57:06] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-02-04 11:57:06] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-04 11:57:06] [TRACE] [OmnipathR] Contains 1 files.
[2025-02-04 11:57:06] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-02-04 11:57:06] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-04 11:57:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-04 11:57:06] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-04 11:57:06] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-02-04 11:57:06] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-04 11:57:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-04 11:57:06] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-04 11:57:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-04 11:57:06] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-04 11:57:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-04 11:57:06] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-04 11:57:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-04 11:57:06] [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
[2025-02-04 11:57:43] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-04 11:57:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-04 11:57:43] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-04 11:57:43] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-02-04 11:57:43] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-04 11:57:43] [TRACE] [OmnipathR] Contains 1 files.
[2025-02-04 11:57:43] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-02-04 11:57:43] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-04 11:57:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-04 11:57:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-04 11:57:43] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-02-04 11:57:43] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-04 11:57:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-04 11:57:43] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-04 11:57:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-04 11:57:43] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-04 11:57:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-04 11:57:43] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-04 11:57:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-04 11:57:43] [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 67.688 0.622 68.919
score_candidate_genes_from_PPI 37.166 0.397 39.586
random_walk 35.578 0.379 38.765
prioritization_genes 35.467 0.420 36.759
weighted_adj 27.388 0.252 28.654
count_genes 16.998 1.864 18.230
filter_annot_with_network 15.536 0.249 16.188
common_neighbors 15.057 0.569 18.149
wppi_data 14.477 0.151 14.686
in_omnipath 9.105 0.053 9.316
graph_from_op 9.047 0.050 9.275
subgraph_op 8.983 0.038 9.389
wppi_omnipath_data 7.403 0.060 7.486
wppi_go_data 5.560 0.084 5.656
functional_annot 3.685 0.378 10.314
* 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-x86_64/Resources/library’ * installing *source* package ‘wppi’ ... ** using staged installation ** R ** byte-compile and prepare package for lazy loading [2025-02-03 16:07:47] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-03 16:07:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 16:07:47] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-03 16:07:47] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-03 16:07:47] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-03 16:07:47] [TRACE] [OmnipathR] Contains 1 files. [2025-02-03 16:07:47] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-03 16:07:47] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-03 16:07:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 16:07:47] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-03 16:07:47] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-02-03 16:07:47] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-03 16:07:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 16:07:47] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-03 16:07:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 16:07:47] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-03 16:07:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 16:07:47] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-03 16:07:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 16:07:47] [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 [2025-02-03 16:07:56] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-03 16:07:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 16:07:56] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-03 16:07:56] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-03 16:07:56] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-03 16:07:56] [TRACE] [OmnipathR] Contains 1 files. [2025-02-03 16:07:56] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-03 16:07:56] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-03 16:07:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 16:07:56] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-03 16:07:56] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-02-03 16:07:56] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-03 16:07:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 16:07:56] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-03 16:07:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 16:07:56] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-03 16:07:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 16:07:56] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-03 16:07:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 16:07:57] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-02-03 16:08:04] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-03 16:08:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 16:08:04] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-03 16:08:04] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-03 16:08:04] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-03 16:08:04] [TRACE] [OmnipathR] Contains 1 files. [2025-02-03 16:08:04] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-03 16:08:04] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-03 16:08:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 16:08:04] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-03 16:08:04] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-02-03 16:08:04] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-03 16:08:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 16:08:04] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-03 16:08:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 16:08:04] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-03 16:08:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 16:08:04] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-03 16:08:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-03 16:08:04] [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 | 15.057 | 0.569 | 18.149 | |
| count_genes | 16.998 | 1.864 | 18.230 | |
| filter_annot_with_network | 15.536 | 0.249 | 16.188 | |
| functional_annot | 3.685 | 0.378 | 10.314 | |
| graph_from_op | 9.047 | 0.050 | 9.275 | |
| in_omnipath | 9.105 | 0.053 | 9.316 | |
| prioritization_genes | 35.467 | 0.420 | 36.759 | |
| process_annot | 1.707 | 0.018 | 1.878 | |
| random_walk | 35.578 | 0.379 | 38.765 | |
| score_candidate_genes_from_PPI | 37.166 | 0.397 | 39.586 | |
| subgraph_op | 8.983 | 0.038 | 9.389 | |
| weighted_adj | 27.388 | 0.252 | 28.654 | |
| wppi | 67.688 | 0.622 | 68.919 | |
| wppi_data | 14.477 | 0.151 | 14.686 | |
| wppi_go_data | 5.560 | 0.084 | 5.656 | |
| wppi_hpo_data | 1.249 | 0.008 | 1.260 | |
| wppi_omnipath_data | 7.403 | 0.060 | 7.486 | |