Ana Galhoz
| Snapshot Date: 2024-07-21 14:00 -0400 (Sun, 21 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/wppi |
| git_branch: RELEASE_3_19 |
| git_last_commit: 1ad2e46 |
| git_last_commit_date: 2024-04-30 11:33:03 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-07-24 09:06 -0400 (Wed, 24 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4747 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4467 |
| 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 2282/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| wppi 1.12.0 (landing page) Ana Galhoz
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | 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 | | ||||||||
|
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: 1.12.0 |
| 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_1.12.0.tar.gz |
| StartedAt: 2024-07-22 14:36:40 -0400 (Mon, 22 Jul 2024) |
| EndedAt: 2024-07-22 14:45:24 -0400 (Mon, 22 Jul 2024) |
| EllapsedTime: 524.7 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_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/wppi.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 12.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘wppi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wppi’ version ‘1.12.0’
* 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
[2024-07-22 14:37:36] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-22 14:37:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-22 14:37:36] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-22 14:37:36] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-07-22 14:37:36] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-22 14:37:36] [TRACE] [OmnipathR] Contains 1 files.
[2024-07-22 14:37:36] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-07-22 14:37:36] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-22 14:37:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-22 14:37:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-22 14:37:36] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-22 14:37:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-22 14:37:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-22 14:37:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-22 14:37:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-22 14:37:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-22 14:37:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-22 14:37:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-22 14:37:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-22 14:37:37] [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
[2024-07-22 14:38:10] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-22 14:38:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-22 14:38:10] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-22 14:38:10] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-07-22 14:38:10] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-22 14:38:10] [TRACE] [OmnipathR] Contains 1 files.
[2024-07-22 14:38:10] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-07-22 14:38:10] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-22 14:38:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-22 14:38:10] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-22 14:38:10] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-22 14:38:10] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-22 14:38:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-22 14:38:10] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-22 14:38:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-22 14:38:10] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-22 14:38:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-22 14:38:10] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-22 14:38:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-22 14:38:10] [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 69.735 0.632 80.896
score_candidate_genes_from_PPI 36.005 0.457 41.265
random_walk 35.013 0.425 38.461
prioritization_genes 35.059 0.330 39.529
weighted_adj 26.950 0.343 31.821
count_genes 15.309 1.760 16.835
wppi_data 15.912 0.179 18.008
common_neighbors 15.048 0.550 18.964
filter_annot_with_network 14.743 0.198 16.726
in_omnipath 9.323 0.099 10.737
subgraph_op 9.220 0.078 11.050
graph_from_op 9.157 0.074 10.506
wppi_omnipath_data 8.950 0.070 9.369
wppi_go_data 5.448 0.086 5.779
functional_annot 3.621 0.288 10.507
* 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-3.19-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 [2024-07-21 16:05:17] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-07-21 16:05:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-21 16:05:17] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-07-21 16:05:17] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-07-21 16:05:17] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-07-21 16:05:17] [TRACE] [OmnipathR] Contains 1 files. [2024-07-21 16:05:17] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-07-21 16:05:17] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-07-21 16:05:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-21 16:05:17] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-07-21 16:05:17] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-07-21 16:05:17] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-07-21 16:05:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-21 16:05:17] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-07-21 16:05:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-21 16:05:17] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-07-21 16:05:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-21 16:05:18] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-07-21 16:05:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-21 16:05:18] [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 [2024-07-21 16:05:26] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-07-21 16:05:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-21 16:05:26] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-07-21 16:05:26] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-07-21 16:05:26] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-07-21 16:05:26] [TRACE] [OmnipathR] Contains 1 files. [2024-07-21 16:05:26] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-07-21 16:05:26] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-07-21 16:05:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-21 16:05:26] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-07-21 16:05:26] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-07-21 16:05:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-07-21 16:05:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-21 16:05:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-07-21 16:05:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-21 16:05:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-07-21 16:05:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-21 16:05:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-07-21 16:05:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-21 16:05:26] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-07-21 16:05:32] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-07-21 16:05:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-21 16:05:32] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-07-21 16:05:32] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-07-21 16:05:32] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-07-21 16:05:32] [TRACE] [OmnipathR] Contains 1 files. [2024-07-21 16:05:32] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-07-21 16:05:32] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-07-21 16:05:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-21 16:05:32] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-07-21 16:05:33] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-07-21 16:05:33] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-07-21 16:05:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-21 16:05:33] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-07-21 16:05:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-21 16:05:33] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-07-21 16:05:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-21 16:05:33] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-07-21 16:05:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-21 16:05:33] [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 | 15.048 | 0.550 | 18.964 | |
| count_genes | 15.309 | 1.760 | 16.835 | |
| filter_annot_with_network | 14.743 | 0.198 | 16.726 | |
| functional_annot | 3.621 | 0.288 | 10.507 | |
| graph_from_op | 9.157 | 0.074 | 10.506 | |
| in_omnipath | 9.323 | 0.099 | 10.737 | |
| prioritization_genes | 35.059 | 0.330 | 39.529 | |
| process_annot | 1.794 | 0.022 | 2.015 | |
| random_walk | 35.013 | 0.425 | 38.461 | |
| score_candidate_genes_from_PPI | 36.005 | 0.457 | 41.265 | |
| subgraph_op | 9.220 | 0.078 | 11.050 | |
| weighted_adj | 26.950 | 0.343 | 31.821 | |
| wppi | 69.735 | 0.632 | 80.896 | |
| wppi_data | 15.912 | 0.179 | 18.008 | |
| wppi_go_data | 5.448 | 0.086 | 5.779 | |
| wppi_hpo_data | 1.362 | 0.014 | 1.441 | |
| wppi_omnipath_data | 8.950 | 0.070 | 9.369 | |