| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:53 -0000 (Wed, 01 Mar 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" | 4266 |
| 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 2154/2171 | 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: 2023-02-28 18:46:01 -0000 (Tue, 28 Feb 2023) |
| EndedAt: 2023-02-28 18:52:54 -0000 (Tue, 28 Feb 2023) |
| EllapsedTime: 413.5 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
[2023-02-28 18:46:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-28 18:46:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-28 18:46:40] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-02-28 18:46:40] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-02-28 18:46:40] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-02-28 18:46:40] [TRACE] [OmnipathR] Contains 1 files.
[2023-02-28 18:46:40] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-02-28 18:46:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-02-28 18:46:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-28 18:46:40] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-02-28 18:46:40] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-02-28 18:46:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-02-28 18:46:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-28 18:46:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-02-28 18:46:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-28 18:46:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-02-28 18:46:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-28 18:46:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-02-28 18:46:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-02-28 18:46:40] [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 42.254 0.132 42.386
score_candidate_genes_from_PPI 22.711 0.124 22.835
random_walk 21.775 0.204 21.979
prioritization_genes 21.517 0.328 21.846
weighted_adj 16.505 0.040 16.545
count_genes 10.817 1.074 19.026
wppi_data 9.390 0.088 9.479
filter_annot_with_network 8.304 0.081 8.385
common_neighbors 7.809 0.317 10.302
functional_annot 3.018 0.349 18.710
* 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 [2023-02-27 10:03:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-02-27 10:03:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-27 10:03:23] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2023-02-27 10:03:23] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-02-27 10:03:23] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2023-02-27 10:03:23] [TRACE] [OmnipathR] Contains 1 files. [2023-02-27 10:03:23] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-02-27 10:03:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-02-27 10:03:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-27 10:03:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2023-02-27 10:03:23] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2023-02-27 10:03:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-02-27 10:03:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-27 10:03:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-02-27 10:03:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-27 10:03:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-02-27 10:03:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-27 10:03:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-02-27 10:03:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-27 10:03:23] [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 [2023-02-27 10:03:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-02-27 10:03:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-27 10:03:27] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2023-02-27 10:03:27] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-02-27 10:03:27] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2023-02-27 10:03:27] [TRACE] [OmnipathR] Contains 1 files. [2023-02-27 10:03:27] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-02-27 10:03:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-02-27 10:03:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-27 10:03:27] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2023-02-27 10:03:27] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2023-02-27 10:03:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-02-27 10:03:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-27 10:03:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-02-27 10:03:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-27 10:03:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-02-27 10:03:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-27 10:03:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-02-27 10:03:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-27 10:03:28] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2023-02-27 10:03:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-02-27 10:03:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-27 10:03:31] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2023-02-27 10:03:31] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-02-27 10:03:31] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2023-02-27 10:03:31] [TRACE] [OmnipathR] Contains 1 files. [2023-02-27 10:03:31] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-02-27 10:03:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-02-27 10:03:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-27 10:03:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2023-02-27 10:03:31] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2023-02-27 10:03:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-02-27 10:03:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-27 10:03:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-02-27 10:03:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-27 10:03:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-02-27 10:03:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-27 10:03:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-02-27 10:03:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-02-27 10:03:31] [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 | 7.809 | 0.317 | 10.302 | |
| count_genes | 10.817 | 1.074 | 19.026 | |
| filter_annot_with_network | 8.304 | 0.081 | 8.385 | |
| functional_annot | 3.018 | 0.349 | 18.710 | |
| graph_from_op | 4.621 | 0.068 | 4.689 | |
| in_omnipath | 4.769 | 0.031 | 4.800 | |
| prioritization_genes | 21.517 | 0.328 | 21.846 | |
| process_annot | 1.433 | 0.028 | 1.462 | |
| random_walk | 21.775 | 0.204 | 21.979 | |
| score_candidate_genes_from_PPI | 22.711 | 0.124 | 22.835 | |
| subgraph_op | 4.663 | 0.024 | 4.688 | |
| weighted_adj | 16.505 | 0.040 | 16.545 | |
| wppi | 42.254 | 0.132 | 42.386 | |
| wppi_data | 9.390 | 0.088 | 9.479 | |
| wppi_go_data | 2.810 | 0.012 | 2.821 | |
| wppi_hpo_data | 1.219 | 0.012 | 1.231 | |
| wppi_omnipath_data | 4.601 | 0.000 | 4.600 | |