Ana Galhoz
| Snapshot Date: 2024-12-10 13:40 -0500 (Tue, 10 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 2024-12-11 11:47 -0500 (Wed, 11 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" | 4752 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4464 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4414 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4369 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4277 |
| 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 2253/2273 | 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 | ERROR | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the wppi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]: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: 2024-12-11 06:44:12 -0500 (Wed, 11 Dec 2024) |
| EndedAt: 2024-12-11 06:49:32 -0500 (Wed, 11 Dec 2024) |
| EllapsedTime: 320.1 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_1.15.0.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: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘wppi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wppi’ version ‘1.15.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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
[2024-12-11 06:48:07] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-11 06:48:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-12-11 06:48:07] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-12-11 06:48:07] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-12-11 06:48:07] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-12-11 06:48:07] [TRACE] [OmnipathR] Contains 1 files.
[2024-12-11 06:48:07] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-12-11 06:48:07] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-11 06:48:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-12-11 06:48:07] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-12-11 06:48:07] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2024-12-11 06:48:07] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-12-11 06:48:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-12-11 06:48:07] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-12-11 06:48:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-12-11 06:48:07] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-12-11 06:48:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-12-11 06:48:07] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-12-11 06:48:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-12-11 06:48:07] [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
[2024-12-11 06:48:13] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-11 06:48:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-12-11 06:48:13] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-12-11 06:48:13] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-12-11 06:48:13] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-12-11 06:48:13] [TRACE] [OmnipathR] Contains 1 files.
[2024-12-11 06:48:13] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-12-11 06:48:13] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-11 06:48:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-12-11 06:48:13] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-12-11 06:48:13] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2024-12-11 06:48:13] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-12-11 06:48:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-12-11 06:48:13] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-12-11 06:48:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-12-11 06:48:13] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-12-11 06:48:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-12-11 06:48:13] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-12-11 06:48:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-12-11 06:48:13] [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 12.566 0.183 12.751
score_candidate_genes_from_PPI 6.374 0.116 6.491
prioritization_genes 6.031 0.082 6.113
random_walk 5.857 0.090 5.948
weighted_adj 5.184 0.073 5.262
common_neighbors 3.479 0.083 11.513
* 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-arm64/Resources/library’ * installing *source* package ‘wppi’ ... ** using staged installation ** R ** byte-compile and prepare package for lazy loading [2024-12-10 15:17:23] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-10 15:17:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-10 15:17:23] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-12-10 15:17:23] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-12-10 15:17:23] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-12-10 15:17:23] [TRACE] [OmnipathR] Contains 1 files. [2024-12-10 15:17:23] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-12-10 15:17:23] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-10 15:17:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-10 15:17:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-12-10 15:17:23] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2024-12-10 15:17:23] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-12-10 15:17:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-10 15:17:23] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-12-10 15:17:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-10 15:17:23] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-12-10 15:17:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-10 15:17:23] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-12-10 15:17:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-10 15:17:23] [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 [2024-12-10 15:17:25] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-10 15:17:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-10 15:17:25] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-12-10 15:17:25] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-12-10 15:17:25] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-12-10 15:17:25] [TRACE] [OmnipathR] Contains 1 files. [2024-12-10 15:17:25] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-12-10 15:17:25] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-10 15:17:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-10 15:17:25] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-12-10 15:17:25] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2024-12-10 15:17:25] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-12-10 15:17:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-10 15:17:25] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-12-10 15:17:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-10 15:17:25] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-12-10 15:17:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-10 15:17:25] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-12-10 15:17:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-10 15:17:25] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-12-10 15:17:26] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-10 15:17:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-10 15:17:26] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-12-10 15:17:26] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-12-10 15:17:26] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-12-10 15:17:26] [TRACE] [OmnipathR] Contains 1 files. [2024-12-10 15:17:26] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-12-10 15:17:26] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-10 15:17:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-10 15:17:26] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-12-10 15:17:26] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2024-12-10 15:17:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-12-10 15:17:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-10 15:17:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-12-10 15:17:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-10 15:17:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-12-10 15:17:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-10 15:17:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-12-10 15:17:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-10 15:17:26] [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 | 3.479 | 0.083 | 11.513 | |
| count_genes | 4.388 | 0.173 | 4.462 | |
| filter_annot_with_network | 2.556 | 0.045 | 2.601 | |
| functional_annot | 0.817 | 0.045 | 1.379 | |
| graph_from_op | 1.022 | 0.012 | 1.034 | |
| in_omnipath | 1.051 | 0.014 | 1.065 | |
| prioritization_genes | 6.031 | 0.082 | 6.113 | |
| process_annot | 0.310 | 0.005 | 0.315 | |
| random_walk | 5.857 | 0.090 | 5.948 | |
| score_candidate_genes_from_PPI | 6.374 | 0.116 | 6.491 | |
| subgraph_op | 1.002 | 0.012 | 1.014 | |
| weighted_adj | 5.184 | 0.073 | 5.262 | |
| wppi | 12.566 | 0.183 | 12.751 | |
| wppi_data | 2.876 | 0.045 | 2.921 | |
| wppi_go_data | 1.504 | 0.028 | 1.531 | |
| wppi_hpo_data | 0.272 | 0.004 | 0.276 | |
| wppi_omnipath_data | 1.080 | 0.011 | 1.092 | |