Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-28 11:41:30 -0400 (Thu, 28 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
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 2252/2270 | 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 | |||||||||
lconway | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: wppi |
Version: 1.11.0 |
Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings wppi_1.11.0.tar.gz |
StartedAt: 2024-03-28 10:47:43 -0000 (Thu, 28 Mar 2024) |
EndedAt: 2024-03-28 10:52:34 -0000 (Thu, 28 Mar 2024) |
EllapsedTime: 291.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: wppi.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings wppi_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/wppi.Rcheck’ * using R Under development (unstable) (2024-03-19 r86153) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * 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 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... NOTE [2024-03-28 10:48:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-28 10:48:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-28 10:48:19] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-03-28 10:48:19] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-28 10:48:19] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-03-28 10:48:19] [TRACE] [OmnipathR] Contains 1 files. [2024-03-28 10:48:19] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-28 10:48:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-28 10:48:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-28 10:48:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-03-28 10:48:19] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2024-03-28 10:48:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-28 10:48:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-28 10:48:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-28 10:48:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-28 10:48:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-28 10:48:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-28 10:48:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-28 10:48:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-28 10:48:20] [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 [2024-03-28 10:48:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-28 10:48:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-28 10:48:37] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-03-28 10:48:37] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-28 10:48:37] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-03-28 10:48:37] [TRACE] [OmnipathR] Contains 1 files. [2024-03-28 10:48:37] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-28 10:48:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-28 10:48:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-28 10:48:37] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-03-28 10:48:37] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2024-03-28 10:48:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-28 10:48:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-28 10:48:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-28 10:48:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-28 10:48:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-28 10:48:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-28 10:48:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-28 10:48:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-28 10:48:38] [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 38.856 0.139 39.068 score_candidate_genes_from_PPI 20.520 0.163 20.726 random_walk 19.922 0.084 20.046 prioritization_genes 19.775 0.159 19.973 weighted_adj 14.289 0.140 14.454 count_genes 10.325 0.448 17.415 wppi_data 8.816 0.048 8.880 common_neighbors 8.410 0.241 12.906 filter_annot_with_network 7.952 0.043 8.010 functional_annot 2.451 0.182 21.076 * 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 ‘/home/biocbuild/bbs-3.19-bioc/meat/wppi.Rcheck/00check.log’ for details.
wppi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL wppi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’ * installing *source* package ‘wppi’ ... ** using staged installation ** R ** byte-compile and prepare package for lazy loading [2024-03-27 20:05:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-27 20:05:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-27 20:05:26] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-03-27 20:05:26] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-27 20:05:26] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-03-27 20:05:26] [TRACE] [OmnipathR] Contains 1 files. [2024-03-27 20:05:26] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-27 20:05:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-27 20:05:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-27 20:05:26] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-03-27 20:05:26] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2024-03-27 20:05:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-27 20:05:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-27 20:05:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-27 20:05:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-27 20:05:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-27 20:05:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-27 20:05:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-27 20:05:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-27 20:05:27] [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 [2024-03-27 20:05:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-27 20:05:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-27 20:05:31] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-03-27 20:05:31] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-27 20:05:31] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-03-27 20:05:31] [TRACE] [OmnipathR] Contains 1 files. [2024-03-27 20:05:31] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-27 20:05:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-27 20:05:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-27 20:05:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-03-27 20:05:31] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2024-03-27 20:05:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-27 20:05:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-27 20:05:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-27 20:05:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-27 20:05:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-27 20:05:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-27 20:05:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-27 20:05:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-27 20:05:31] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-03-27 20:05:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-27 20:05:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-27 20:05:35] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-03-27 20:05:35] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-27 20:05:35] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-03-27 20:05:35] [TRACE] [OmnipathR] Contains 1 files. [2024-03-27 20:05:35] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-27 20:05:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-27 20:05:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-27 20:05:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-03-27 20:05:35] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2024-03-27 20:05:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-27 20:05:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-27 20:05:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-27 20:05:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-27 20:05:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-27 20:05:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-27 20:05:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-27 20:05:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-27 20:05:35] [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 | 8.410 | 0.241 | 12.906 | |
count_genes | 10.325 | 0.448 | 17.415 | |
filter_annot_with_network | 7.952 | 0.043 | 8.010 | |
functional_annot | 2.451 | 0.182 | 21.076 | |
graph_from_op | 4.436 | 0.044 | 4.489 | |
in_omnipath | 4.626 | 0.023 | 4.660 | |
prioritization_genes | 19.775 | 0.159 | 19.973 | |
process_annot | 1.076 | 0.008 | 1.085 | |
random_walk | 19.922 | 0.084 | 20.046 | |
score_candidate_genes_from_PPI | 20.520 | 0.163 | 20.726 | |
subgraph_op | 4.661 | 0.036 | 4.708 | |
weighted_adj | 14.289 | 0.140 | 14.454 | |
wppi | 38.856 | 0.139 | 39.068 | |
wppi_data | 8.816 | 0.048 | 8.880 | |
wppi_go_data | 2.561 | 0.008 | 2.571 | |
wppi_hpo_data | 0.924 | 0.020 | 0.945 | |
wppi_omnipath_data | 4.358 | 0.012 | 4.378 | |