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 11:37:41 -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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:wppi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings wppi_1.8.0.tar.gz |
| StartedAt: 2023-10-16 08:35:18 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 08:43:47 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 509.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: wppi.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:wppi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings wppi_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/wppi.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘wppi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wppi’ version ‘1.8.0’
* 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 startup messages can be suppressed ... NOTE
[2023-10-16 08:36:14] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-16 08:36:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-16 08:36:14] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-16 08:36:14] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-10-16 08:36:14] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-16 08:36:14] [TRACE] [OmnipathR] Contains 1 files.
[2023-10-16 08:36:14] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-10-16 08:36:14] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-16 08:36:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-16 08:36:14] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-16 08:36:14] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2023-10-16 08:36:14] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-10-16 08:36:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-16 08:36:14] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-10-16 08:36:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-16 08:36:15] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-10-16 08:36:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-16 08:36:15] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-10-16 08:36:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-16 08:36:15] [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 08:36:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-16 08:36:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-16 08:36:50] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-16 08:36:50] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-10-16 08:36:50] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-16 08:36:50] [TRACE] [OmnipathR] Contains 1 files.
[2023-10-16 08:36:50] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-10-16 08:36:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-16 08:36:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-16 08:36:50] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-16 08:36:50] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2023-10-16 08:36:50] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-10-16 08:36:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-16 08:36:50] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-10-16 08:36:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-16 08:36:51] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-10-16 08:36:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-16 08:36:51] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-10-16 08:36:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-16 08:36:51] [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 68.233 0.481 70.556
score_candidate_genes_from_PPI 36.631 0.307 41.925
prioritization_genes 36.368 0.420 45.525
random_walk 35.567 0.320 41.674
weighted_adj 27.552 0.249 30.353
count_genes 13.951 1.546 17.240
filter_annot_with_network 13.886 0.219 17.857
common_neighbors 13.209 0.528 17.874
wppi_data 12.546 0.117 12.720
graph_from_op 8.743 0.070 11.093
in_omnipath 8.700 0.058 11.175
subgraph_op 8.566 0.046 9.738
wppi_omnipath_data 7.031 0.048 7.086
functional_annot 3.561 0.278 6.303
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc/meat/wppi.Rcheck/00check.log’
for details.
wppi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL wppi ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘wppi’ ... ** using staged installation ** R ** byte-compile and prepare package for lazy loading [2023-10-15 15:51:17] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2023-10-15 15:51:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:51:17] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-10-15 15:51:17] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-10-15 15:51:17] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-10-15 15:51:17] [TRACE] [OmnipathR] Contains 1 files. [2023-10-15 15:51:17] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-10-15 15:51:17] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2023-10-15 15:51:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:51:17] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-10-15 15:51:17] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-10-15 15:51:17] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-10-15 15:51:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:51:17] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-10-15 15:51:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:51:17] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-10-15 15:51:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:51:17] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-10-15 15:51:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:51:17] [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 15:51:27] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2023-10-15 15:51:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:51:27] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-10-15 15:51:27] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-10-15 15:51:27] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-10-15 15:51:27] [TRACE] [OmnipathR] Contains 1 files. [2023-10-15 15:51:27] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-10-15 15:51:28] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2023-10-15 15:51:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:51:28] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-10-15 15:51:28] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-10-15 15:51:28] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-10-15 15:51:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:51:28] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-10-15 15:51:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:51:28] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-10-15 15:51:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:51:28] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-10-15 15:51:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:51:28] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2023-10-15 15:51:36] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2023-10-15 15:51:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:51:36] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-10-15 15:51:36] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-10-15 15:51:36] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-10-15 15:51:36] [TRACE] [OmnipathR] Contains 1 files. [2023-10-15 15:51:36] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-10-15 15:51:36] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2023-10-15 15:51:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:51:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-10-15 15:51:36] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-10-15 15:51:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-10-15 15:51:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:51:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-10-15 15:51:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:51:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-10-15 15:51:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:51:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-10-15 15:51:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 15:51:37] [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 | 13.209 | 0.528 | 17.874 | |
| count_genes | 13.951 | 1.546 | 17.240 | |
| filter_annot_with_network | 13.886 | 0.219 | 17.857 | |
| functional_annot | 3.561 | 0.278 | 6.303 | |
| graph_from_op | 8.743 | 0.070 | 11.093 | |
| in_omnipath | 8.700 | 0.058 | 11.175 | |
| prioritization_genes | 36.368 | 0.420 | 45.525 | |
| process_annot | 1.703 | 0.017 | 2.103 | |
| random_walk | 35.567 | 0.320 | 41.674 | |
| score_candidate_genes_from_PPI | 36.631 | 0.307 | 41.925 | |
| subgraph_op | 8.566 | 0.046 | 9.738 | |
| weighted_adj | 27.552 | 0.249 | 30.353 | |
| wppi | 68.233 | 0.481 | 70.556 | |
| wppi_data | 12.546 | 0.117 | 12.720 | |
| wppi_go_data | 4.631 | 0.078 | 4.715 | |
| wppi_hpo_data | 1.092 | 0.021 | 1.114 | |
| wppi_omnipath_data | 7.031 | 0.048 | 7.086 | |