Ana Galhoz
| Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/wppi |
| git_branch: RELEASE_3_18 |
| git_last_commit: dc6b662 |
| git_last_commit_date: 2023-10-24 11:31:51 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:38:23 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 2248/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| wppi 1.10.0 (landing page) Ana Galhoz
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.10.0 |
| 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_1.10.0.tar.gz |
| StartedAt: 2024-04-16 10:30:45 -0400 (Tue, 16 Apr 2024) |
| EndedAt: 2024-04-16 10:39:32 -0400 (Tue, 16 Apr 2024) |
| EllapsedTime: 527.1 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_1.10.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/wppi.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘wppi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wppi’ version ‘1.10.0’
* 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 ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 startup messages can be suppressed ... NOTE
[2024-04-16 10:31:41] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-16 10:31:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-04-16 10:31:41] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-04-16 10:31:41] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-04-16 10:31:41] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-04-16 10:31:41] [TRACE] [OmnipathR] Contains 1 files.
[2024-04-16 10:31:41] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-04-16 10:31:41] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-16 10:31:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-04-16 10:31:41] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-04-16 10:31:41] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-04-16 10:31:41] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-04-16 10:31:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-04-16 10:31:41] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-04-16 10:31:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-04-16 10:31:41] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-04-16 10:31:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-04-16 10:31:41] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-04-16 10:31:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-04-16 10:31:41] [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
[2024-04-16 10:32:14] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-16 10:32:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-04-16 10:32:14] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-04-16 10:32:14] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-04-16 10:32:14] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-04-16 10:32:14] [TRACE] [OmnipathR] Contains 1 files.
[2024-04-16 10:32:14] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-04-16 10:32:14] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-16 10:32:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-04-16 10:32:14] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-04-16 10:32:14] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-04-16 10:32:14] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-04-16 10:32:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-04-16 10:32:14] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-04-16 10:32:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-04-16 10:32:14] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-04-16 10:32:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-04-16 10:32:14] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-04-16 10:32:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-04-16 10:32:14] [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 61.281 0.593 62.640
score_candidate_genes_from_PPI 33.568 0.434 36.713
random_walk 32.815 0.377 36.429
prioritization_genes 32.414 0.388 34.506
weighted_adj 24.486 0.260 26.231
count_genes 13.898 1.486 14.573
common_neighbors 14.343 0.565 89.276
filter_annot_with_network 13.977 0.223 14.800
wppi_data 13.264 0.127 13.416
in_omnipath 8.854 0.092 9.350
subgraph_op 8.748 0.052 9.543
graph_from_op 8.531 0.058 9.170
wppi_omnipath_data 6.442 0.046 6.501
functional_annot 3.564 0.427 6.402
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.18-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/4.3-x86_64/Resources/library’ * installing *source* package ‘wppi’ ... ** using staged installation ** R ** byte-compile and prepare package for lazy loading [2024-04-15 15:59:13] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-15 15:59:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-15 15:59:13] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-04-15 15:59:13] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-04-15 15:59:13] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-04-15 15:59:13] [TRACE] [OmnipathR] Contains 1 files. [2024-04-15 15:59:13] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-04-15 15:59:13] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-15 15:59:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-15 15:59:13] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-04-15 15:59:13] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-04-15 15:59:13] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-04-15 15:59:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-15 15:59:13] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-04-15 15:59:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-15 15:59:13] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-04-15 15:59:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-15 15:59:13] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-04-15 15:59:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-15 15:59:13] [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 [2024-04-15 15:59:21] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-15 15:59:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-15 15:59:21] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-04-15 15:59:21] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-04-15 15:59:21] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-04-15 15:59:21] [TRACE] [OmnipathR] Contains 1 files. [2024-04-15 15:59:21] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-04-15 15:59:21] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-15 15:59:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-15 15:59:21] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-04-15 15:59:21] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-04-15 15:59:21] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-04-15 15:59:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-15 15:59:21] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-04-15 15:59:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-15 15:59:21] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-04-15 15:59:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-15 15:59:21] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-04-15 15:59:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-15 15:59:21] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-04-15 15:59:27] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-15 15:59:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-15 15:59:27] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-04-15 15:59:27] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-04-15 15:59:27] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-04-15 15:59:27] [TRACE] [OmnipathR] Contains 1 files. [2024-04-15 15:59:27] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-04-15 15:59:27] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-04-15 15:59:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-15 15:59:27] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-04-15 15:59:27] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-04-15 15:59:27] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-04-15 15:59:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-15 15:59:27] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-04-15 15:59:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-15 15:59:27] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-04-15 15:59:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-15 15:59:27] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-04-15 15:59:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-04-15 15:59:27] [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 | 14.343 | 0.565 | 89.276 | |
| count_genes | 13.898 | 1.486 | 14.573 | |
| filter_annot_with_network | 13.977 | 0.223 | 14.800 | |
| functional_annot | 3.564 | 0.427 | 6.402 | |
| graph_from_op | 8.531 | 0.058 | 9.170 | |
| in_omnipath | 8.854 | 0.092 | 9.350 | |
| prioritization_genes | 32.414 | 0.388 | 34.506 | |
| process_annot | 1.798 | 0.032 | 2.034 | |
| random_walk | 32.815 | 0.377 | 36.429 | |
| score_candidate_genes_from_PPI | 33.568 | 0.434 | 36.713 | |
| subgraph_op | 8.748 | 0.052 | 9.543 | |
| weighted_adj | 24.486 | 0.260 | 26.231 | |
| wppi | 61.281 | 0.593 | 62.640 | |
| wppi_data | 13.264 | 0.127 | 13.416 | |
| wppi_go_data | 4.241 | 0.076 | 4.326 | |
| wppi_hpo_data | 1.102 | 0.014 | 1.118 | |
| wppi_omnipath_data | 6.442 | 0.046 | 6.501 | |