Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-03 10:19 -0400 (Wed, 03 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4480 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4511 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4469 |
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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings wppi_1.12.0.tar.gz |
StartedAt: 2024-07-01 05:04:44 -0400 (Mon, 01 Jul 2024) |
EndedAt: 2024-07-01 05:08:58 -0400 (Mon, 01 Jul 2024) |
EllapsedTime: 254.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: wppi.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings wppi_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/wppi.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... NOTE [2024-07-01 05:05:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-07-01 05:05:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-01 05:05:10] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-07-01 05:05:10] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-07-01 05:05:10] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-07-01 05:05:10] [TRACE] [OmnipathR] Contains 1 files. [2024-07-01 05:05:10] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-07-01 05:05:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-07-01 05:05:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-01 05:05:10] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-07-01 05:05:10] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-07-01 05:05:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-07-01 05:05:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-01 05:05:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-07-01 05:05:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-01 05:05:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-07-01 05:05:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-01 05:05:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-07-01 05:05:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-01 05:05:10] [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 [2024-07-01 05:05:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-07-01 05:05:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-01 05:05:24] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-07-01 05:05:24] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-07-01 05:05:24] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-07-01 05:05:24] [TRACE] [OmnipathR] Contains 1 files. [2024-07-01 05:05:24] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-07-01 05:05:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-07-01 05:05:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-01 05:05:24] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-07-01 05:05:24] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-07-01 05:05:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-07-01 05:05:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-01 05:05:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-07-01 05:05:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-01 05:05:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-07-01 05:05:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-01 05:05:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-07-01 05:05:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-07-01 05:05:24] [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 27.343 0.192 27.536 score_candidate_genes_from_PPI 14.229 0.108 14.337 prioritization_genes 14.080 0.188 14.269 random_walk 13.721 0.149 13.870 weighted_adj 10.613 0.060 10.673 count_genes 9.472 0.704 10.281 common_neighbors 6.531 0.329 11.171 filter_annot_with_network 6.318 0.136 6.456 wppi_data 6.397 0.016 6.413 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * 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/bbs-3.19-bioc/R/bin/R CMD INSTALL wppi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘wppi’ ... ** using staged installation ** R ** byte-compile and prepare package for lazy loading [2024-06-30 15:38:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-06-30 15:38:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-30 15:38:02] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-06-30 15:38:02] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-06-30 15:38:02] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-06-30 15:38:02] [TRACE] [OmnipathR] Contains 1 files. [2024-06-30 15:38:02] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-06-30 15:38:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-06-30 15:38:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-30 15:38:02] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-06-30 15:38:02] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-06-30 15:38:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-06-30 15:38:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-30 15:38:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-06-30 15:38:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-30 15:38:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-06-30 15:38:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-30 15:38:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-06-30 15:38:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-30 15:38:02] [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 [2024-06-30 15:38:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-06-30 15:38:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-30 15:38:05] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-06-30 15:38:05] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-06-30 15:38:05] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-06-30 15:38:05] [TRACE] [OmnipathR] Contains 1 files. [2024-06-30 15:38:05] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-06-30 15:38:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-06-30 15:38:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-30 15:38:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-06-30 15:38:05] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-06-30 15:38:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-06-30 15:38:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-30 15:38:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-06-30 15:38:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-30 15:38:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-06-30 15:38:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-30 15:38:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-06-30 15:38:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-30 15:38:05] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-06-30 15:38:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-06-30 15:38:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-30 15:38:07] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-06-30 15:38:08] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-06-30 15:38:08] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-06-30 15:38:08] [TRACE] [OmnipathR] Contains 1 files. [2024-06-30 15:38:08] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-06-30 15:38:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-06-30 15:38:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-30 15:38:08] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-06-30 15:38:08] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-06-30 15:38:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-06-30 15:38:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-30 15:38:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-06-30 15:38:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-30 15:38:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-06-30 15:38:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-30 15:38:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-06-30 15:38:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-06-30 15:38:08] [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 | 6.531 | 0.329 | 11.171 | |
count_genes | 9.472 | 0.704 | 10.281 | |
filter_annot_with_network | 6.318 | 0.136 | 6.456 | |
functional_annot | 2.079 | 0.168 | 3.394 | |
graph_from_op | 3.176 | 0.025 | 3.200 | |
in_omnipath | 3.064 | 0.040 | 3.105 | |
prioritization_genes | 14.080 | 0.188 | 14.269 | |
process_annot | 0.859 | 0.068 | 0.927 | |
random_walk | 13.721 | 0.149 | 13.870 | |
score_candidate_genes_from_PPI | 14.229 | 0.108 | 14.337 | |
subgraph_op | 2.896 | 0.048 | 2.944 | |
weighted_adj | 10.613 | 0.060 | 10.673 | |
wppi | 27.343 | 0.192 | 27.536 | |
wppi_data | 6.397 | 0.016 | 6.413 | |
wppi_go_data | 3.029 | 0.044 | 3.072 | |
wppi_hpo_data | 0.644 | 0.004 | 0.648 | |
wppi_omnipath_data | 3.057 | 0.012 | 3.069 | |