Ana Galhoz
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024) |
| 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 2024-12-24 11:44 -0500 (Tue, 24 Dec 2024).
| 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" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
| 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 2254/2274 | 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. |
| Package: wppi |
| Version: 1.15.0 |
| 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_1.15.0.tar.gz |
| StartedAt: 2024-12-23 23:55:02 -0500 (Mon, 23 Dec 2024) |
| EndedAt: 2024-12-23 23:59:52 -0500 (Mon, 23 Dec 2024) |
| EllapsedTime: 289.5 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_1.15.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/wppi.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 ‘1.15.0’
* 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 ... 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
[2024-12-23 23:55:37] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-23 23:55:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-12-23 23:55:37] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-12-23 23:55:37] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-12-23 23:55:37] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-12-23 23:55:37] [TRACE] [OmnipathR] Contains 1 files.
[2024-12-23 23:55:37] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-12-23 23:55:37] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-23 23:55:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-12-23 23:55:37] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-12-23 23:55:37] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-12-23 23:55:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-12-23 23:55:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-12-23 23:55:38] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-12-23 23:55:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-12-23 23:55:38] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-12-23 23:55:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-12-23 23:55:38] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-12-23 23:55:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-12-23 23:55:38] [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
[2024-12-23 23:55:58] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-23 23:55:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-12-23 23:55:58] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-12-23 23:55:58] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-12-23 23:55:58] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-12-23 23:55:58] [TRACE] [OmnipathR] Contains 1 files.
[2024-12-23 23:55:58] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-12-23 23:55:58] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-23 23:55:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-12-23 23:55:58] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-12-23 23:55:58] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-12-23 23:55:58] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-12-23 23:55:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-12-23 23:55:58] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-12-23 23:55:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-12-23 23:55:58] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-12-23 23:55:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-12-23 23:55:58] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-12-23 23:55:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-12-23 23:55:58] [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 36.377 0.537 37.046
score_candidate_genes_from_PPI 22.766 0.368 23.258
random_walk 22.668 0.415 23.238
prioritization_genes 22.721 0.360 23.211
weighted_adj 16.751 0.276 17.117
common_neighbors 12.596 0.340 20.926
count_genes 10.661 0.879 14.082
filter_annot_with_network 7.450 0.191 7.692
wppi_data 6.227 0.091 6.337
* 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-3.21-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/4.5-x86_64/Resources/library’ * installing *source* package ‘wppi’ ... ** using staged installation ** R ** byte-compile and prepare package for lazy loading [2024-12-23 15:28:14] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-23 15:28:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-23 15:28:14] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-12-23 15:28:14] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-12-23 15:28:14] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-12-23 15:28:14] [TRACE] [OmnipathR] Contains 1 files. [2024-12-23 15:28:14] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-12-23 15:28:14] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-23 15:28:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-23 15:28:14] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-12-23 15:28:15] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-12-23 15:28:15] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-12-23 15:28:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-23 15:28:15] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-12-23 15:28:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-23 15:28:15] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-12-23 15:28:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-23 15:28:15] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-12-23 15:28:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-23 15:28:15] [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 [2024-12-23 15:28:20] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-23 15:28:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-23 15:28:20] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-12-23 15:28:20] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-12-23 15:28:20] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-12-23 15:28:20] [TRACE] [OmnipathR] Contains 1 files. [2024-12-23 15:28:20] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-12-23 15:28:20] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-23 15:28:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-23 15:28:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-12-23 15:28:21] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-12-23 15:28:21] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-12-23 15:28:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-23 15:28:21] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-12-23 15:28:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-23 15:28:21] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-12-23 15:28:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-23 15:28:21] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-12-23 15:28:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-23 15:28:21] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-12-23 15:28:25] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-23 15:28:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-23 15:28:25] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-12-23 15:28:25] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-12-23 15:28:25] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-12-23 15:28:25] [TRACE] [OmnipathR] Contains 1 files. [2024-12-23 15:28:25] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-12-23 15:28:25] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-23 15:28:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-23 15:28:25] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-12-23 15:28:26] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-12-23 15:28:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-12-23 15:28:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-23 15:28:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-12-23 15:28:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-23 15:28:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-12-23 15:28:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-23 15:28:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-12-23 15:28:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-23 15:28:26] [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 | 12.596 | 0.340 | 20.926 | |
| count_genes | 10.661 | 0.879 | 14.082 | |
| filter_annot_with_network | 7.450 | 0.191 | 7.692 | |
| functional_annot | 2.045 | 0.323 | 2.597 | |
| graph_from_op | 3.498 | 0.036 | 3.550 | |
| in_omnipath | 3.597 | 0.046 | 3.660 | |
| prioritization_genes | 22.721 | 0.360 | 23.211 | |
| process_annot | 1.038 | 0.014 | 1.061 | |
| random_walk | 22.668 | 0.415 | 23.238 | |
| score_candidate_genes_from_PPI | 22.766 | 0.368 | 23.258 | |
| subgraph_op | 3.175 | 0.033 | 3.223 | |
| weighted_adj | 16.751 | 0.276 | 17.117 | |
| wppi | 36.377 | 0.537 | 37.046 | |
| wppi_data | 6.227 | 0.091 | 6.337 | |
| wppi_go_data | 2.786 | 0.073 | 2.864 | |
| wppi_hpo_data | 0.542 | 0.005 | 0.548 | |
| wppi_omnipath_data | 2.669 | 0.027 | 2.699 | |