Ana Galhoz
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/wppi |
| git_branch: RELEASE_3_17 |
| git_last_commit: 284601d |
| git_last_commit_date: 2023-04-25 11:28:27 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:35:53 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 2212/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| wppi 1.8.0 (landing page) Ana Galhoz
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
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: 1.8.0 |
| 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_1.8.0.tar.gz |
| StartedAt: 2023-10-16 02:07:18 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 02:11:31 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 253.7 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/site-library --timings wppi_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/wppi.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘wppi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wppi’ version ‘1.8.0’
* 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
[2023-10-16 02:07:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-16 02:07:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-16 02:07:42] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-10-16 02:07:42] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-10-16 02:07:42] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-10-16 02:07:42] [TRACE] [OmnipathR] Contains 1 files.
[2023-10-16 02:07:42] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-10-16 02:07:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-16 02:07:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-16 02:07:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-10-16 02:07:42] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2023-10-16 02:07:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-10-16 02:07:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-16 02:07:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-10-16 02:07:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-16 02:07:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-10-16 02:07:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-16 02:07:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-10-16 02:07:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-16 02:07:42] [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
[2023-10-16 02:07:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-16 02:07:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-16 02:07:54] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-10-16 02:07:54] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-10-16 02:07:54] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-10-16 02:07:54] [TRACE] [OmnipathR] Contains 1 files.
[2023-10-16 02:07:54] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-10-16 02:07:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-16 02:07:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-16 02:07:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-10-16 02:07:54] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2023-10-16 02:07:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-10-16 02:07:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-16 02:07:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-10-16 02:07:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-16 02:07:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-10-16 02:07:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-16 02:07:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-10-16 02:07:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-16 02:07:55] [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 30.946 0.204 31.150
random_walk 15.646 0.233 15.878
prioritization_genes 15.569 0.180 15.751
score_candidate_genes_from_PPI 15.549 0.104 15.654
weighted_adj 11.584 0.088 11.673
count_genes 8.223 0.550 8.248
wppi_data 7.486 0.128 7.615
filter_annot_with_network 5.958 0.141 6.099
common_neighbors 5.420 0.406 8.597
* 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 [2023-10-15 15:30:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-10-15 15:30:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:30:17] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2023-10-15 15:30:17] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-10-15 15:30:17] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2023-10-15 15:30:17] [TRACE] [OmnipathR] Contains 1 files. [2023-10-15 15:30:17] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-10-15 15:30:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-10-15 15:30:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:30:17] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2023-10-15 15:30:17] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-10-15 15:30:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-10-15 15:30:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:30:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-10-15 15:30:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:30:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-10-15 15:30:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:30:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-10-15 15:30:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:30:17] [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 [2023-10-15 15:30:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-10-15 15:30:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:30:20] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2023-10-15 15:30:20] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-10-15 15:30:20] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2023-10-15 15:30:20] [TRACE] [OmnipathR] Contains 1 files. [2023-10-15 15:30:20] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-10-15 15:30:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-10-15 15:30:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:30:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2023-10-15 15:30:20] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-10-15 15:30:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-10-15 15:30:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:30:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-10-15 15:30:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:30:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-10-15 15:30:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:30:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-10-15 15:30:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:30:20] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2023-10-15 15:30:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-10-15 15:30:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:30:23] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2023-10-15 15:30:23] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-10-15 15:30:23] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2023-10-15 15:30:23] [TRACE] [OmnipathR] Contains 1 files. [2023-10-15 15:30:23] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-10-15 15:30:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-10-15 15:30:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:30:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2023-10-15 15:30:23] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-10-15 15:30:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-10-15 15:30:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:30:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-10-15 15:30:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:30:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-10-15 15:30:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:30:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-10-15 15:30:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:30:23] [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 | 5.420 | 0.406 | 8.597 | |
| count_genes | 8.223 | 0.550 | 8.248 | |
| filter_annot_with_network | 5.958 | 0.141 | 6.099 | |
| functional_annot | 2.085 | 0.184 | 3.635 | |
| graph_from_op | 3.308 | 0.041 | 3.347 | |
| in_omnipath | 3.056 | 0.008 | 3.064 | |
| prioritization_genes | 15.569 | 0.180 | 15.751 | |
| process_annot | 0.833 | 0.040 | 0.873 | |
| random_walk | 15.646 | 0.233 | 15.878 | |
| score_candidate_genes_from_PPI | 15.549 | 0.104 | 15.654 | |
| subgraph_op | 3.128 | 0.040 | 3.168 | |
| weighted_adj | 11.584 | 0.088 | 11.673 | |
| wppi | 30.946 | 0.204 | 31.150 | |
| wppi_data | 7.486 | 0.128 | 7.615 | |
| wppi_go_data | 2.254 | 0.008 | 2.262 | |
| wppi_hpo_data | 0.803 | 0.008 | 0.811 | |
| wppi_omnipath_data | 3.079 | 0.004 | 3.084 | |