| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-23 01:34:35 -0000 (Thu, 23 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4245 |
| 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: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 2147/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| wppi 1.7.0 (landing page) Ana Galhoz
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | 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/library --timings wppi_1.7.0.tar.gz |
| StartedAt: 2023-02-22 15:04:42 -0000 (Wed, 22 Feb 2023) |
| EndedAt: 2023-02-22 15:13:27 -0000 (Wed, 22 Feb 2023) |
| EllapsedTime: 525.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: wppi.Rcheck |
| Warnings: 0 |
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###
### 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/library --timings wppi_1.7.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/wppi.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-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 22.04.1 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 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
[2023-02-22 15:05:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-22 15:05:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-22 15:05:21] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-02-22 15:05:21] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-02-22 15:05:21] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-02-22 15:05:21] [TRACE] [OmnipathR] Contains 1 files.
[2023-02-22 15:05:21] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-02-22 15:05:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-22 15:05:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-22 15:05:21] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-02-22 15:05:21] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-02-22 15:05:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-02-22 15:05:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-22 15:05:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-02-22 15:05:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-22 15:05:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-02-22 15:05:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-22 15:05:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-02-22 15:05:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-22 15:05:21] [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 43.289 0.160 43.451
score_candidate_genes_from_PPI 22.834 0.188 23.025
prioritization_genes 21.903 0.263 22.169
random_walk 21.982 0.160 22.143
weighted_adj 16.919 0.104 17.024
count_genes 10.681 0.917 20.076
wppi_data 9.463 0.056 9.520
filter_annot_with_network 8.224 0.109 8.333
common_neighbors 7.758 0.358 11.155
functional_annot 3.107 0.302 20.417
* 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: 1 NOTE
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/library’ * installing *source* package ‘wppi’ ... ** using staged installation ** R ** byte-compile and prepare package for lazy loading [2023-02-21 17:56:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-02-21 17:56:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-21 17:56:50] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2023-02-21 17:56:50] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-02-21 17:56:50] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2023-02-21 17:56:50] [TRACE] [OmnipathR] Contains 1 files. [2023-02-21 17:56:50] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-02-21 17:56:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-02-21 17:56:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-21 17:56:50] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2023-02-21 17:56:50] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2023-02-21 17:56:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-02-21 17:56:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-21 17:56:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-02-21 17:56:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-21 17:56:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-02-21 17:56:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-21 17:56:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-02-21 17:56:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-21 17:56:50] [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 [2023-02-21 17:56:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-02-21 17:56:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-21 17:56:54] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2023-02-21 17:56:54] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-02-21 17:56:54] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2023-02-21 17:56:54] [TRACE] [OmnipathR] Contains 1 files. [2023-02-21 17:56:54] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-02-21 17:56:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-02-21 17:56:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-21 17:56:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2023-02-21 17:56:54] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2023-02-21 17:56:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-02-21 17:56:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-21 17:56:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-02-21 17:56:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-21 17:56:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-02-21 17:56:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-21 17:56:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-02-21 17:56:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-21 17:56:54] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2023-02-21 17:56:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-02-21 17:56:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-21 17:56:58] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2023-02-21 17:56:58] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-02-21 17:56:58] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2023-02-21 17:56:58] [TRACE] [OmnipathR] Contains 1 files. [2023-02-21 17:56:58] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-02-21 17:56:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-02-21 17:56:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-21 17:56:58] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2023-02-21 17:56:58] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2023-02-21 17:56:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-02-21 17:56:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-21 17:56:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-02-21 17:56:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-21 17:56:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-02-21 17:56:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-21 17:56:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-02-21 17:56:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-21 17:56:58] [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 | 7.758 | 0.358 | 11.155 | |
| count_genes | 10.681 | 0.917 | 20.076 | |
| filter_annot_with_network | 8.224 | 0.109 | 8.333 | |
| functional_annot | 3.107 | 0.302 | 20.417 | |
| graph_from_op | 4.663 | 0.140 | 4.804 | |
| in_omnipath | 4.839 | 0.112 | 4.951 | |
| prioritization_genes | 21.903 | 0.263 | 22.169 | |
| process_annot | 1.443 | 0.036 | 1.479 | |
| random_walk | 21.982 | 0.160 | 22.143 | |
| score_candidate_genes_from_PPI | 22.834 | 0.188 | 23.025 | |
| subgraph_op | 4.716 | 0.032 | 4.749 | |
| weighted_adj | 16.919 | 0.104 | 17.024 | |
| wppi | 43.289 | 0.160 | 43.451 | |
| wppi_data | 9.463 | 0.056 | 9.520 | |
| wppi_go_data | 2.835 | 0.016 | 2.851 | |
| wppi_hpo_data | 1.255 | 0.000 | 1.255 | |
| wppi_omnipath_data | 4.580 | 0.004 | 4.584 | |