Ana Galhoz
| Snapshot Date: 2024-05-29 11:04:14 -0400 (Wed, 29 May 2024) |
| git_url: https://git.bioconductor.org/packages/wppi |
| git_branch: devel |
| git_last_commit: 65eba9a |
| git_last_commit_date: 2024-04-30 11:33:03 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-05-30 12:36:31 -0400 (Thu, 30 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4669 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4404 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4431 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4384 |
| 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 2215/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| wppi 1.13.0 (landing page) Ana Galhoz
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
|
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: 1.13.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:wppi.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings wppi_1.13.0.tar.gz |
| StartedAt: 2024-05-30 03:16:58 -0400 (Thu, 30 May 2024) |
| EndedAt: 2024-05-30 03:20:58 -0400 (Thu, 30 May 2024) |
| EllapsedTime: 240.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: wppi.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:wppi.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings wppi_1.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/wppi.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'wppi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'wppi' version '1.13.0'
* 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 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 whether startup messages can be suppressed ... NOTE
[2024-05-30 03:17:30] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 03:17:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:17:30] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-30 03:17:30] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-05-30 03:17:30] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-30 03:17:30] [TRACE] [OmnipathR] Contains 1 files.
[2024-05-30 03:17:30] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-05-30 03:17:30] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 03:17:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:17:30] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-30 03:17:30] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-30 03:17:30] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-30 03:17:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:17:30] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-30 03:17:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:17:30] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-30 03:17:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:17:30] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-30 03:17:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:17:30] [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
[2024-05-30 03:17:49] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 03:17:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:17:49] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-30 03:17:49] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-05-30 03:17:49] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-30 03:17:49] [TRACE] [OmnipathR] Contains 1 files.
[2024-05-30 03:17:49] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-05-30 03:17:49] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 03:17:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:17:49] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-30 03:17:49] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-30 03:17:49] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-30 03:17:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:17:49] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-30 03:17:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:17:49] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-30 03:17:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:17:49] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-30 03:17:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:17:49] [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 31.93 0.68 32.64
score_candidate_genes_from_PPI 16.02 0.56 16.59
prioritization_genes 16.03 0.30 16.33
random_walk 15.80 0.36 16.16
weighted_adj 12.80 0.38 13.20
count_genes 10.12 0.69 9.75
filter_annot_with_network 7.47 0.08 7.54
common_neighbors 7.28 0.22 10.14
wppi_data 6.66 0.10 6.75
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
'F:/biocbuild/bbs-3.20-bioc/meat/wppi.Rcheck/00check.log'
for details.
wppi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL wppi ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'wppi' ... ** using staged installation ** R ** byte-compile and prepare package for lazy loading [2024-05-29 13:18:09] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-29 13:18:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 13:18:09] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-05-29 13:18:09] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-29 13:18:09] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-05-29 13:18:09] [TRACE] [OmnipathR] Contains 1 files. [2024-05-29 13:18:09] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-29 13:18:09] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-29 13:18:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 13:18:09] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-05-29 13:18:09] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-05-29 13:18:09] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-29 13:18:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 13:18:09] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-29 13:18:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 13:18:09] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-29 13:18:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 13:18:09] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-29 13:18:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 13:18:09] [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 [2024-05-29 13:18:14] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-29 13:18:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 13:18:14] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-05-29 13:18:14] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-29 13:18:14] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-05-29 13:18:14] [TRACE] [OmnipathR] Contains 1 files. [2024-05-29 13:18:14] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-29 13:18:14] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-29 13:18:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 13:18:14] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-05-29 13:18:15] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-05-29 13:18:15] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-29 13:18:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 13:18:15] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-29 13:18:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 13:18:15] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-29 13:18:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 13:18:15] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-29 13:18:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 13:18:15] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-05-29 13:18:18] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-29 13:18:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 13:18:18] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-05-29 13:18:18] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-29 13:18:18] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-05-29 13:18:18] [TRACE] [OmnipathR] Contains 1 files. [2024-05-29 13:18:18] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-29 13:18:18] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2024-05-29 13:18:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 13:18:18] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2024-05-29 13:18:19] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-05-29 13:18:19] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-29 13:18:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 13:18:19] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-29 13:18:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 13:18:19] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-29 13:18:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 13:18:19] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-29 13:18:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-29 13:18:19] [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 | 7.28 | 0.22 | 10.14 | |
| count_genes | 10.12 | 0.69 | 9.75 | |
| filter_annot_with_network | 7.47 | 0.08 | 7.54 | |
| functional_annot | 2.26 | 0.20 | 2.67 | |
| graph_from_op | 3.52 | 0.09 | 3.61 | |
| in_omnipath | 3.78 | 0.05 | 3.83 | |
| prioritization_genes | 16.03 | 0.30 | 16.33 | |
| process_annot | 0.67 | 0.03 | 0.70 | |
| random_walk | 15.80 | 0.36 | 16.16 | |
| score_candidate_genes_from_PPI | 16.02 | 0.56 | 16.59 | |
| subgraph_op | 3.95 | 0.06 | 4.02 | |
| weighted_adj | 12.80 | 0.38 | 13.20 | |
| wppi | 31.93 | 0.68 | 32.64 | |
| wppi_data | 6.66 | 0.10 | 6.75 | |
| wppi_go_data | 2.98 | 0.06 | 3.05 | |
| wppi_hpo_data | 0.72 | 0.03 | 0.75 | |
| wppi_omnipath_data | 4.13 | 0.05 | 4.17 | |