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 12:09 -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: 2025-01-14 11:24:05 -0500 (Tue, 14 Jan 2025) |
| EndedAt: 2025-01-14 11:32:39 -0500 (Tue, 14 Jan 2025) |
| EllapsedTime: 514.4 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
[2025-01-14 11:25:07] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-14 11:25:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-14 11:25:07] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-14 11:25:07] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-14 11:25:07] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-14 11:25:07] [TRACE] [OmnipathR] Contains 1 files.
[2025-01-14 11:25:07] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-14 11:25:07] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-14 11:25:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-14 11:25:07] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-14 11:25:07] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-14 11:25:07] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-14 11:25:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-14 11:25:07] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-14 11:25:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-14 11:25:07] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-14 11:25:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-14 11:25:08] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-14 11:25:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-14 11:25:08] [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
[2025-01-14 11:25:46] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-14 11:25:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-14 11:25:46] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-14 11:25:46] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-14 11:25:46] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-14 11:25:46] [TRACE] [OmnipathR] Contains 1 files.
[2025-01-14 11:25:46] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-14 11:25:46] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-14 11:25:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-14 11:25:47] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-14 11:25:47] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-14 11:25:47] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-14 11:25:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-14 11:25:47] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-14 11:25:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-14 11:25:47] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-14 11:25:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-14 11:25:47] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-14 11:25:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-14 11:25:47] [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 71.149 0.623 74.095
score_candidate_genes_from_PPI 37.142 0.492 41.203
prioritization_genes 35.699 0.444 36.733
random_walk 35.035 0.378 36.630
weighted_adj 27.352 0.373 30.288
count_genes 17.140 1.471 20.349
filter_annot_with_network 15.421 0.256 15.948
common_neighbors 15.029 0.565 21.407
wppi_data 14.542 0.128 14.687
in_omnipath 9.044 0.052 9.290
subgraph_op 9.025 0.054 9.957
graph_from_op 9.011 0.046 9.231
wppi_omnipath_data 8.004 0.045 7.939
wppi_go_data 5.645 0.121 5.773
* 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 [2025-01-13 16:00:23] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-13 16:00:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 16:00:23] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-13 16:00:23] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-13 16:00:23] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-13 16:00:23] [TRACE] [OmnipathR] Contains 1 files. [2025-01-13 16:00:23] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-13 16:00:23] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-13 16:00:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 16:00:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-13 16:00:24] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-01-13 16:00:24] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-13 16:00:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 16:00:24] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-13 16:00:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 16:00:24] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-13 16:00:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 16:00:24] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-13 16:00:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 16:00:24] [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 16:00:33] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-13 16:00:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 16:00:33] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-13 16:00:33] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-13 16:00:33] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-13 16:00:33] [TRACE] [OmnipathR] Contains 1 files. [2025-01-13 16:00:33] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-13 16:00:33] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-13 16:00:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 16:00:33] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-13 16:00:33] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-01-13 16:00:33] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-13 16:00:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 16:00:33] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-13 16:00:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 16:00:33] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-13 16:00:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 16:00:33] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-13 16:00:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 16:00:33] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-01-13 16:00:41] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-13 16:00:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 16:00:41] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-13 16:00:41] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-13 16:00:41] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-13 16:00:41] [TRACE] [OmnipathR] Contains 1 files. [2025-01-13 16:00:41] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-13 16:00:41] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-13 16:00:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 16:00:41] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-01-13 16:00:41] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-01-13 16:00:41] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-13 16:00:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 16:00:41] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-13 16:00:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 16:00:41] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-13 16:00:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 16:00:41] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-13 16:00:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-13 16:00:41] [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 | 15.029 | 0.565 | 21.407 | |
| count_genes | 17.140 | 1.471 | 20.349 | |
| filter_annot_with_network | 15.421 | 0.256 | 15.948 | |
| functional_annot | 3.631 | 0.488 | 4.134 | |
| graph_from_op | 9.011 | 0.046 | 9.231 | |
| in_omnipath | 9.044 | 0.052 | 9.290 | |
| prioritization_genes | 35.699 | 0.444 | 36.733 | |
| process_annot | 1.707 | 0.010 | 1.744 | |
| random_walk | 35.035 | 0.378 | 36.630 | |
| score_candidate_genes_from_PPI | 37.142 | 0.492 | 41.203 | |
| subgraph_op | 9.025 | 0.054 | 9.957 | |
| weighted_adj | 27.352 | 0.373 | 30.288 | |
| wppi | 71.149 | 0.623 | 74.095 | |
| wppi_data | 14.542 | 0.128 | 14.687 | |
| wppi_go_data | 5.645 | 0.121 | 5.773 | |
| wppi_hpo_data | 1.254 | 0.007 | 1.303 | |
| wppi_omnipath_data | 8.004 | 0.045 | 7.939 | |