Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:33 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
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 |
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
Package 2189/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
wppi 1.7.0 (landing page) Ana Galhoz
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
Package: wppi |
Version: 1.7.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings wppi_1.7.0.tar.gz |
StartedAt: 2023-04-12 00:26:03 -0400 (Wed, 12 Apr 2023) |
EndedAt: 2023-04-12 00:30:17 -0400 (Wed, 12 Apr 2023) |
EllapsedTime: 253.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: wppi.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings wppi_1.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/wppi.Rcheck’ * using R version 4.3.0 alpha (2023-04-03 r84154) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.2 LTS * using session charset: UTF-8 * checking for file ‘wppi/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘wppi’ version ‘1.7.0’ * 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 ... OK * 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 loading without being on the library search path ... OK * checking startup messages can be suppressed ... NOTE [2023-04-12 00:26:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-12 00:26:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 00:26:28] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2023-04-12 00:26:28] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-04-12 00:26:28] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2023-04-12 00:26:28] [TRACE] [OmnipathR] Contains 1 files. [2023-04-12 00:26:28] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-04-12 00:26:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-12 00:26:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 00:26:28] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2023-04-12 00:26:28] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-04-12 00:26:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-04-12 00:26:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 00:26:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-04-12 00:26:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 00:26:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-04-12 00:26:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 00:26:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-04-12 00:26:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 00:26:29] [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 [2023-04-12 00:26:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-12 00:26:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 00:26:42] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2023-04-12 00:26:42] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-04-12 00:26:42] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2023-04-12 00:26:42] [TRACE] [OmnipathR] Contains 1 files. [2023-04-12 00:26:42] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-04-12 00:26:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-12 00:26:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 00:26:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2023-04-12 00:26:42] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-04-12 00:26:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-04-12 00:26:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 00:26:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-04-12 00:26:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 00:26:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-04-12 00:26:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 00:26:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-04-12 00:26:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-12 00:26:42] [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 30.132 0.212 30.345 score_candidate_genes_from_PPI 15.995 0.181 16.176 random_walk 15.531 0.152 15.684 prioritization_genes 15.203 0.185 15.389 weighted_adj 11.496 0.052 11.549 count_genes 8.036 0.547 8.174 wppi_data 6.589 0.048 6.637 common_neighbors 5.603 0.359 8.536 filter_annot_with_network 5.844 0.116 5.962 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘wppi_workflow.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/wppi.Rcheck/00check.log’ for details.
wppi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL wppi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘wppi’ ... ** using staged installation ** R ** byte-compile and prepare package for lazy loading [2023-04-11 15:24:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-11 15:24:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 15:24:46] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2023-04-11 15:24:46] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-04-11 15:24:46] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2023-04-11 15:24:46] [TRACE] [OmnipathR] Contains 1 files. [2023-04-11 15:24:46] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-04-11 15:24:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-11 15:24:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 15:24:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2023-04-11 15:24:46] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-04-11 15:24:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-04-11 15:24:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 15:24:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-04-11 15:24:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 15:24:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-04-11 15:24:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 15:24:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-04-11 15:24:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 15:24:47] [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 [2023-04-11 15:24:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-11 15:24:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 15:24:49] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2023-04-11 15:24:49] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-04-11 15:24:49] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2023-04-11 15:24:49] [TRACE] [OmnipathR] Contains 1 files. [2023-04-11 15:24:49] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-04-11 15:24:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-11 15:24:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 15:24:49] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2023-04-11 15:24:49] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-04-11 15:24:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-04-11 15:24:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 15:24:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-04-11 15:24:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 15:24:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-04-11 15:24:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 15:24:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-04-11 15:24:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 15:24:50] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2023-04-11 15:24:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-11 15:24:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 15:24:52] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2023-04-11 15:24:52] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-04-11 15:24:52] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2023-04-11 15:24:52] [TRACE] [OmnipathR] Contains 1 files. [2023-04-11 15:24:52] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-04-11 15:24:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-11 15:24:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 15:24:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2023-04-11 15:24:52] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-04-11 15:24:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-04-11 15:24:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 15:24:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-04-11 15:24:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 15:24:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-04-11 15:24:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 15:24:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-04-11 15:24:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 15:24:52] [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 | 5.603 | 0.359 | 8.536 | |
count_genes | 8.036 | 0.547 | 8.174 | |
filter_annot_with_network | 5.844 | 0.116 | 5.962 | |
functional_annot | 1.333 | 0.110 | 2.488 | |
graph_from_op | 3.284 | 0.084 | 3.368 | |
in_omnipath | 3.231 | 0.013 | 3.243 | |
prioritization_genes | 15.203 | 0.185 | 15.389 | |
process_annot | 0.556 | 0.000 | 0.556 | |
random_walk | 15.531 | 0.152 | 15.684 | |
score_candidate_genes_from_PPI | 15.995 | 0.181 | 16.176 | |
subgraph_op | 3.050 | 0.004 | 3.055 | |
weighted_adj | 11.496 | 0.052 | 11.549 | |
wppi | 30.132 | 0.212 | 30.345 | |
wppi_data | 6.589 | 0.048 | 6.637 | |
wppi_go_data | 2.213 | 0.024 | 2.238 | |
wppi_hpo_data | 0.409 | 0.008 | 0.417 | |
wppi_omnipath_data | 3.352 | 0.056 | 3.410 | |