Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 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 2269/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
wppi 1.14.0 (landing page) Ana Galhoz
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | 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: 1.14.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:wppi.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings wppi_1.14.0.tar.gz |
StartedAt: 2024-12-20 07:12:03 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 07:16:49 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 286.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: wppi.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:wppi.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings wppi_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/wppi.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'wppi/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'wppi' version '1.14.0' * 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 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 [2024-12-20 07:12:42] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-12-20 07:12:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 07:12:42] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-12-20 07:12:42] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-12-20 07:12:42] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-12-20 07:12:42] [TRACE] [OmnipathR] Contains 1 files. [2024-12-20 07:12:42] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-12-20 07:12:42] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-12-20 07:12:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 07:12:42] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-12-20 07:12:42] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-12-20 07:12:42] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-12-20 07:12:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 07:12:42] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-12-20 07:12:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 07:12:43] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-12-20 07:12:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 07:12:43] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-12-20 07:12:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 07:12:43] [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 [2024-12-20 07:13:05] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-12-20 07:13:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 07:13:05] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-12-20 07:13:05] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-12-20 07:13:05] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-12-20 07:13:05] [TRACE] [OmnipathR] Contains 1 files. [2024-12-20 07:13:05] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-12-20 07:13:05] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-12-20 07:13:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 07:13:05] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-12-20 07:13:05] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-12-20 07:13:05] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-12-20 07:13:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 07:13:05] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-12-20 07:13:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 07:13:05] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-12-20 07:13:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 07:13:05] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-12-20 07:13:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-20 07:13:05] [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 38.17 0.92 39.10 score_candidate_genes_from_PPI 19.68 0.42 20.13 random_walk 19.09 0.24 19.33 prioritization_genes 18.75 0.29 19.05 weighted_adj 14.94 0.33 15.26 count_genes 13.23 0.70 12.56 wppi_data 8.42 0.17 8.59 filter_annot_with_network 8.31 0.15 8.47 common_neighbors 7.55 0.33 10.31 * 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 'F:/biocbuild/bbs-3.20-bioc/meat/wppi.Rcheck/00check.log' for details.
wppi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL wppi ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'wppi' ... ** using staged installation ** R ** byte-compile and prepare package for lazy loading [2024-12-19 16:16:47] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-12-19 16:16:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 16:16:47] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-12-19 16:16:47] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-12-19 16:16:47] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-12-19 16:16:47] [TRACE] [OmnipathR] Contains 1 files. [2024-12-19 16:16:47] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-12-19 16:16:47] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-12-19 16:16:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 16:16:47] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-12-19 16:16:47] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-12-19 16:16:47] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-12-19 16:16:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 16:16:47] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-12-19 16:16:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 16:16:47] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-12-19 16:16:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 16:16:47] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-12-19 16:16:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 16:16:47] [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 [2024-12-19 16:16:55] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-12-19 16:16:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 16:16:55] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-12-19 16:16:55] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-12-19 16:16:55] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-12-19 16:16:55] [TRACE] [OmnipathR] Contains 1 files. [2024-12-19 16:16:55] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-12-19 16:16:55] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-12-19 16:16:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 16:16:55] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-12-19 16:16:55] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-12-19 16:16:55] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-12-19 16:16:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 16:16:55] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-12-19 16:16:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 16:16:55] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-12-19 16:16:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 16:16:55] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-12-19 16:16:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 16:16:55] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-12-19 16:16:59] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-12-19 16:16:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 16:16:59] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-12-19 16:16:59] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-12-19 16:16:59] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-12-19 16:16:59] [TRACE] [OmnipathR] Contains 1 files. [2024-12-19 16:16:59] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-12-19 16:16:59] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-12-19 16:16:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 16:16:59] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-12-19 16:16:59] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-12-19 16:16:59] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-12-19 16:16:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 16:16:59] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-12-19 16:16:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 16:16:59] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-12-19 16:16:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 16:16:59] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-12-19 16:16:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-19 16:16:59] [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 | 7.55 | 0.33 | 10.31 | |
count_genes | 13.23 | 0.70 | 12.56 | |
filter_annot_with_network | 8.31 | 0.15 | 8.47 | |
functional_annot | 2.23 | 0.10 | 2.61 | |
graph_from_op | 4.16 | 0.12 | 4.28 | |
in_omnipath | 3.53 | 0.03 | 3.56 | |
prioritization_genes | 18.75 | 0.29 | 19.05 | |
process_annot | 1.19 | 0.07 | 1.26 | |
random_walk | 19.09 | 0.24 | 19.33 | |
score_candidate_genes_from_PPI | 19.68 | 0.42 | 20.13 | |
subgraph_op | 4.68 | 0.05 | 4.73 | |
weighted_adj | 14.94 | 0.33 | 15.26 | |
wppi | 38.17 | 0.92 | 39.10 | |
wppi_data | 8.42 | 0.17 | 8.59 | |
wppi_go_data | 3.17 | 0.06 | 3.25 | |
wppi_hpo_data | 0.60 | 0.03 | 0.63 | |
wppi_omnipath_data | 4.06 | 0.03 | 4.09 | |