Ana Galhoz
| Snapshot Date: 2024-07-10 14:00 -0400 (Wed, 10 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 2024-07-12 17:41 -0400 (Fri, 12 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" | 4741 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4483 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4512 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
| 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 12.7.4 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: 2024-07-11 13:43:21 -0400 (Thu, 11 Jul 2024) |
| EndedAt: 2024-07-11 13:52:07 -0400 (Thu, 11 Jul 2024) |
| EllapsedTime: 525.7 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
[2024-07-11 13:44:18] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-11 13:44:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-11 13:44:18] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-11 13:44:18] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-07-11 13:44:18] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-11 13:44:19] [TRACE] [OmnipathR] Contains 1 files.
[2024-07-11 13:44:19] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-07-11 13:44:19] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-11 13:44:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-11 13:44:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-11 13:44:19] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-11 13:44:19] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-11 13:44:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-11 13:44:19] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-11 13:44:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-11 13:44:19] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-11 13:44:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-11 13:44:19] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-11 13:44:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-11 13:44:19] [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
[2024-07-11 13:44:53] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-11 13:44:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-11 13:44:53] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-11 13:44:53] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-07-11 13:44:53] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-11 13:44:54] [TRACE] [OmnipathR] Contains 1 files.
[2024-07-11 13:44:54] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-07-11 13:44:54] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-11 13:44:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-11 13:44:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-11 13:44:54] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-11 13:44:54] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-11 13:44:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-11 13:44:54] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-11 13:44:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-11 13:44:54] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-11 13:44:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-11 13:44:54] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-11 13:44:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-07-11 13:44:54] [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 70.554 0.710 77.308
score_candidate_genes_from_PPI 36.925 0.580 44.157
random_walk 35.600 0.487 40.235
prioritization_genes 35.628 0.451 39.794
weighted_adj 27.472 0.359 31.980
count_genes 15.307 1.776 16.942
wppi_data 16.047 0.171 16.276
common_neighbors 15.266 0.609 25.685
filter_annot_with_network 15.281 0.237 17.552
in_omnipath 9.595 0.121 10.716
subgraph_op 9.359 0.068 10.686
graph_from_op 9.334 0.088 10.485
wppi_omnipath_data 7.889 0.047 8.184
wppi_go_data 5.602 0.090 5.718
* 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 [2024-07-10 16:07:28] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-07-10 16:07:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-10 16:07:28] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-07-10 16:07:28] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-07-10 16:07:28] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-07-10 16:07:28] [TRACE] [OmnipathR] Contains 1 files. [2024-07-10 16:07:28] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-07-10 16:07:28] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-07-10 16:07:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-10 16:07:28] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-07-10 16:07:28] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-07-10 16:07:28] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-07-10 16:07:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-10 16:07:28] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-07-10 16:07:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-10 16:07:28] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-07-10 16:07:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-10 16:07:28] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-07-10 16:07:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-10 16:07:28] [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 [2024-07-10 16:07:37] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-07-10 16:07:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-10 16:07:37] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-07-10 16:07:37] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-07-10 16:07:37] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-07-10 16:07:37] [TRACE] [OmnipathR] Contains 1 files. [2024-07-10 16:07:37] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-07-10 16:07:37] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-07-10 16:07:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-10 16:07:37] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-07-10 16:07:37] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-07-10 16:07:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-07-10 16:07:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-10 16:07:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-07-10 16:07:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-10 16:07:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-07-10 16:07:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-10 16:07:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-07-10 16:07:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-10 16:07:37] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-07-10 16:07:43] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-07-10 16:07:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-10 16:07:43] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-07-10 16:07:43] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-07-10 16:07:43] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-07-10 16:07:43] [TRACE] [OmnipathR] Contains 1 files. [2024-07-10 16:07:43] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-07-10 16:07:43] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-07-10 16:07:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-10 16:07:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-07-10 16:07:44] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-07-10 16:07:44] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-07-10 16:07:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-10 16:07:44] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-07-10 16:07:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-10 16:07:44] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-07-10 16:07:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-10 16:07:44] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-07-10 16:07:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-10 16:07:44] [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 | 15.266 | 0.609 | 25.685 | |
| count_genes | 15.307 | 1.776 | 16.942 | |
| filter_annot_with_network | 15.281 | 0.237 | 17.552 | |
| functional_annot | 3.645 | 0.394 | 4.490 | |
| graph_from_op | 9.334 | 0.088 | 10.485 | |
| in_omnipath | 9.595 | 0.121 | 10.716 | |
| prioritization_genes | 35.628 | 0.451 | 39.794 | |
| process_annot | 1.901 | 0.030 | 2.227 | |
| random_walk | 35.600 | 0.487 | 40.235 | |
| score_candidate_genes_from_PPI | 36.925 | 0.580 | 44.157 | |
| subgraph_op | 9.359 | 0.068 | 10.686 | |
| weighted_adj | 27.472 | 0.359 | 31.980 | |
| wppi | 70.554 | 0.710 | 77.308 | |
| wppi_data | 16.047 | 0.171 | 16.276 | |
| wppi_go_data | 5.602 | 0.090 | 5.718 | |
| wppi_hpo_data | 1.385 | 0.010 | 1.401 | |
| wppi_omnipath_data | 7.889 | 0.047 | 8.184 | |