Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-04 11:40:09 -0500 (Mon, 04 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
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 2233/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
wppi 1.11.0 (landing page) Ana Galhoz
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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: 1.11.0 |
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_1.11.0.tar.gz |
StartedAt: 2024-03-02 12:26:14 -0500 (Sat, 02 Mar 2024) |
EndedAt: 2024-03-02 12:35:08 -0500 (Sat, 02 Mar 2024) |
EllapsedTime: 534.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: wppi.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/wppi.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘wppi/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘wppi’ version ‘1.11.0’ * 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 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 whether startup messages can be suppressed ... NOTE [2024-03-02 12:27:10] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-02 12:27:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-02 12:27:10] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-02 12:27:10] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-02 12:27:10] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-02 12:27:10] [TRACE] [OmnipathR] Contains 1 files. [2024-03-02 12:27:10] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-02 12:27:10] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-02 12:27:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-02 12:27:10] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-02 12:27:11] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-03-02 12:27:11] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-02 12:27:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-02 12:27:11] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-02 12:27:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-02 12:27:11] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-02 12:27:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-02 12:27:11] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-02 12:27:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-02 12:27:11] [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 [2024-03-02 12:27:46] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-02 12:27:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-02 12:27:46] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-02 12:27:46] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-02 12:27:46] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-02 12:27:46] [TRACE] [OmnipathR] Contains 1 files. [2024-03-02 12:27:46] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-02 12:27:46] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-02 12:27:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-02 12:27:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-02 12:27:46] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-03-02 12:27:46] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-02 12:27:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-02 12:27:46] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-02 12:27:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-02 12:27:46] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-02 12:27:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-02 12:27:46] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-02 12:27:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-02 12:27:47] [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 66.562 1.035 79.742 score_candidate_genes_from_PPI 34.730 0.578 41.709 prioritization_genes 34.120 0.590 41.337 random_walk 33.543 0.510 40.714 weighted_adj 25.636 0.380 31.473 common_neighbors 14.842 0.644 20.635 wppi_data 15.211 0.235 17.442 count_genes 13.759 1.620 16.211 filter_annot_with_network 14.181 0.274 16.758 subgraph_op 9.224 0.104 11.330 in_omnipath 9.115 0.116 11.412 graph_from_op 9.065 0.109 10.600 wppi_omnipath_data 9.009 0.102 10.109 functional_annot 3.574 0.416 11.858 * 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 [2024-03-01 16:04:20] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-01 16:04:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-01 16:04:20] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-01 16:04:20] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-01 16:04:20] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-01 16:04:20] [TRACE] [OmnipathR] Contains 1 files. [2024-03-01 16:04:20] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-01 16:04:20] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-01 16:04:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-01 16:04:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-01 16:04:20] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-03-01 16:04:20] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-01 16:04:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-01 16:04:20] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-01 16:04:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-01 16:04:20] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-01 16:04:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-01 16:04:20] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-01 16:04:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-01 16:04:20] [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 [2024-03-01 16:04:28] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-01 16:04:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-01 16:04:28] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-01 16:04:28] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-01 16:04:28] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-01 16:04:28] [TRACE] [OmnipathR] Contains 1 files. [2024-03-01 16:04:28] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-01 16:04:28] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-01 16:04:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-01 16:04:28] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-01 16:04:29] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-03-01 16:04:29] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-01 16:04:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-01 16:04:29] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-01 16:04:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-01 16:04:29] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-01 16:04:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-01 16:04:29] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-01 16:04:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-01 16:04:29] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-03-01 16:04:35] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-01 16:04:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-01 16:04:35] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-01 16:04:35] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-01 16:04:35] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-01 16:04:35] [TRACE] [OmnipathR] Contains 1 files. [2024-03-01 16:04:35] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-01 16:04:35] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-01 16:04:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-01 16:04:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-01 16:04:35] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-03-01 16:04:35] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-01 16:04:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-01 16:04:35] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-01 16:04:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-01 16:04:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-01 16:04:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-01 16:04:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-01 16:04:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-01 16:04:36] [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 | 14.842 | 0.644 | 20.635 | |
count_genes | 13.759 | 1.620 | 16.211 | |
filter_annot_with_network | 14.181 | 0.274 | 16.758 | |
functional_annot | 3.574 | 0.416 | 11.858 | |
graph_from_op | 9.065 | 0.109 | 10.600 | |
in_omnipath | 9.115 | 0.116 | 11.412 | |
prioritization_genes | 34.120 | 0.590 | 41.337 | |
process_annot | 1.724 | 0.036 | 2.111 | |
random_walk | 33.543 | 0.510 | 40.714 | |
score_candidate_genes_from_PPI | 34.730 | 0.578 | 41.709 | |
subgraph_op | 9.224 | 0.104 | 11.330 | |
weighted_adj | 25.636 | 0.380 | 31.473 | |
wppi | 66.562 | 1.035 | 79.742 | |
wppi_data | 15.211 | 0.235 | 17.442 | |
wppi_go_data | 4.344 | 0.041 | 4.901 | |
wppi_hpo_data | 1.473 | 0.049 | 1.711 | |
wppi_omnipath_data | 9.009 | 0.102 | 10.109 | |