Ana Galhoz
| Snapshot Date: 2024-03-03 14:05:05 -0500 (Sun, 03 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/wppi |
| git_branch: RELEASE_3_18 |
| git_last_commit: dc6b662 |
| git_last_commit_date: 2023-10-24 11:31:51 -0500 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-04 11:38:00 -0500 (Mon, 04 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" | 4692 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.2 (2023-10-31 ucrt) -- "Eye Holes" | 4445 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" | 4466 |
| 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 2248/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| wppi 1.10.0 (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 | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / 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: 1.10.0 |
| 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_1.10.0.tar.gz |
| StartedAt: 2024-03-04 00:12:52 -0500 (Mon, 04 Mar 2024) |
| EndedAt: 2024-03-04 00:16:53 -0500 (Mon, 04 Mar 2024) |
| EllapsedTime: 240.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: wppi.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/wppi.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘wppi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wppi’ version ‘1.10.0’
* 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
[2024-03-04 00:13:24] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-04 00:13:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-04 00:13:24] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-04 00:13:24] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-03-04 00:13:24] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-04 00:13:24] [TRACE] [OmnipathR] Contains 1 files.
[2024-03-04 00:13:24] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-03-04 00:13:24] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-04 00:13:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-04 00:13:24] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-04 00:13:24] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-03-04 00:13:24] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-04 00:13:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-04 00:13:24] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-04 00:13:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-04 00:13:24] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-04 00:13:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-04 00:13:24] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-04 00:13:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-04 00:13:24] [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
[2024-03-04 00:13:42] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-04 00:13:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-04 00:13:42] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-04 00:13:42] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-03-04 00:13:42] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-04 00:13:42] [TRACE] [OmnipathR] Contains 1 files.
[2024-03-04 00:13:42] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-03-04 00:13:42] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-04 00:13:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-04 00:13:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-04 00:13:43] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-03-04 00:13:43] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-04 00:13:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-04 00:13:43] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-04 00:13:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-04 00:13:43] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-04 00:13:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-04 00:13:43] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-04 00:13:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-04 00:13:43] [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 29.069 0.802 30.123
prioritization_genes 16.402 0.444 16.959
random_walk 16.156 0.488 16.819
score_candidate_genes_from_PPI 16.142 0.402 16.701
weighted_adj 11.379 0.383 11.868
count_genes 9.369 0.982 9.814
filter_annot_with_network 7.422 0.217 7.676
common_neighbors 7.144 0.359 16.129
wppi_data 6.214 0.151 6.419
* 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-3.18-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 [2024-03-03 15:27:44] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-03 15:27:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-03 15:27:45] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-03 15:27:45] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-03 15:27:45] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-03 15:27:45] [TRACE] [OmnipathR] Contains 1 files. [2024-03-03 15:27:45] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-03 15:27:45] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-03 15:27:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-03 15:27:45] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-03 15:27:45] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-03-03 15:27:45] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-03 15:27:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-03 15:27:45] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-03 15:27:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-03 15:27:45] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-03 15:27:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-03 15:27:45] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-03 15:27:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-03 15:27:45] [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 [2024-03-03 15:27:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-03 15:27:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-03 15:27:50] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-03 15:27:50] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-03 15:27:50] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-03 15:27:50] [TRACE] [OmnipathR] Contains 1 files. [2024-03-03 15:27:50] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-03 15:27:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-03 15:27:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-03 15:27:50] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-03 15:27:50] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-03-03 15:27:50] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-03 15:27:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-03 15:27:50] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-03 15:27:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-03 15:27:50] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-03 15:27:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-03 15:27:50] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-03 15:27:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-03 15:27:50] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-03-03 15:27:54] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-03 15:27:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-03 15:27:54] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-03 15:27:54] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-03 15:27:54] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-03 15:27:54] [TRACE] [OmnipathR] Contains 1 files. [2024-03-03 15:27:54] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-03 15:27:54] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-03 15:27:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-03 15:27:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-03 15:27:55] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-03-03 15:27:55] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-03 15:27:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-03 15:27:55] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-03 15:27:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-03 15:27:55] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-03 15:27:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-03 15:27:55] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-03 15:27:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-03 15:27:55] [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 | 7.144 | 0.359 | 16.129 | |
| count_genes | 9.369 | 0.982 | 9.814 | |
| filter_annot_with_network | 7.422 | 0.217 | 7.676 | |
| functional_annot | 2.120 | 0.298 | 3.540 | |
| graph_from_op | 3.789 | 0.065 | 3.875 | |
| in_omnipath | 3.770 | 0.066 | 3.855 | |
| prioritization_genes | 16.402 | 0.444 | 16.959 | |
| process_annot | 1.001 | 0.019 | 1.028 | |
| random_walk | 16.156 | 0.488 | 16.819 | |
| score_candidate_genes_from_PPI | 16.142 | 0.402 | 16.701 | |
| subgraph_op | 3.519 | 0.120 | 3.666 | |
| weighted_adj | 11.379 | 0.383 | 11.868 | |
| wppi | 29.069 | 0.802 | 30.123 | |
| wppi_data | 6.214 | 0.151 | 6.419 | |
| wppi_go_data | 2.177 | 0.045 | 2.246 | |
| wppi_hpo_data | 0.734 | 0.055 | 0.798 | |
| wppi_omnipath_data | 3.073 | 0.050 | 3.142 | |