Ana Galhoz
| Snapshot Date: 2024-05-06 14:00:02 -0400 (Mon, 06 May 2024) |
| git_url: https://git.bioconductor.org/packages/wppi |
| git_branch: RELEASE_3_19 |
| git_last_commit: 1ad2e46 |
| git_last_commit_date: 2024-04-30 11:33:03 -0400 (Tue, 30 Apr 2024) |
| Back to Mac ARM64 build report for BioC 3.19 |
|
This page was generated on 2024-05-07 11:32:49 -0400 (Tue, 07 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
| 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 2282/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| wppi 1.12.0 (landing page) Ana Galhoz
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the wppi package: - 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: 1.12.0 |
| 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_1.12.0.tar.gz |
| StartedAt: 2024-05-07 01:48:41 -0400 (Tue, 07 May 2024) |
| EndedAt: 2024-05-07 01:50:33 -0400 (Tue, 07 May 2024) |
| EllapsedTime: 112.3 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_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/wppi.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘wppi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wppi’ version ‘1.12.0’
* 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 ... 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
[2024-05-07 01:48:52] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-07 01:48:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-07 01:48:52] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-07 01:48:52] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-05-07 01:48:52] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-07 01:48:52] [TRACE] [OmnipathR] Contains 1 files.
[2024-05-07 01:48:52] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-05-07 01:48:52] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-07 01:48:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-07 01:48:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-07 01:48:52] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2024-05-07 01:48:52] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-07 01:48:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-07 01:48:52] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-07 01:48:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-07 01:48:52] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-07 01:48:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-07 01:48:52] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-07 01:48:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-07 01:48:52] [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
[2024-05-07 01:48:57] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-07 01:48:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-07 01:48:57] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-07 01:48:57] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-05-07 01:48:57] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-07 01:48:57] [TRACE] [OmnipathR] Contains 1 files.
[2024-05-07 01:48:57] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-05-07 01:48:57] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-07 01:48:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-07 01:48:57] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-07 01:48:57] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2024-05-07 01:48:57] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-07 01:48:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-07 01:48:57] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-07 01:48:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-07 01:48:57] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-07 01:48:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-07 01:48:57] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-07 01:48:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-07 01:48:57] [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 9.209 0.236 9.454
common_neighbors 2.171 0.085 38.174
* 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
‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/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/4.4-arm64/Resources/library’ * installing *source* package ‘wppi’ ... ** using staged installation ** R ** byte-compile and prepare package for lazy loading [2024-05-06 15:40:03] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-06 15:40:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 15:40:03] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-06 15:40:03] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-06 15:40:03] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-06 15:40:03] [TRACE] [OmnipathR] Contains 1 files. [2024-05-06 15:40:03] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-06 15:40:03] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-06 15:40:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 15:40:03] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-06 15:40:03] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2024-05-06 15:40:03] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-06 15:40:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 15:40:03] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-06 15:40:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 15:40:03] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-06 15:40:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 15:40:03] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-06 15:40:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 15:40:03] [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 [2024-05-06 15:40:04] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-06 15:40:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 15:40:04] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-06 15:40:04] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-06 15:40:04] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-06 15:40:04] [TRACE] [OmnipathR] Contains 1 files. [2024-05-06 15:40:04] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-06 15:40:04] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-06 15:40:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 15:40:04] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-06 15:40:04] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2024-05-06 15:40:04] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-06 15:40:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 15:40:04] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-06 15:40:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 15:40:04] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-06 15:40:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 15:40:04] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-06 15:40:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 15:40:04] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-05-06 15:40:05] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-06 15:40:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 15:40:05] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-06 15:40:05] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-06 15:40:05] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-06 15:40:05] [TRACE] [OmnipathR] Contains 1 files. [2024-05-06 15:40:05] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-06 15:40:05] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-06 15:40:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 15:40:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-05-06 15:40:05] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2024-05-06 15:40:05] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-06 15:40:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 15:40:05] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-06 15:40:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 15:40:05] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-06 15:40:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 15:40:05] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-06 15:40:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-06 15:40:05] [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 | 2.171 | 0.085 | 38.174 | |
| count_genes | 3.522 | 0.162 | 4.021 | |
| filter_annot_with_network | 2.211 | 0.048 | 2.260 | |
| functional_annot | 0.858 | 0.069 | 2.294 | |
| graph_from_op | 1.144 | 0.030 | 1.174 | |
| in_omnipath | 1.099 | 0.014 | 1.113 | |
| prioritization_genes | 4.846 | 0.128 | 4.980 | |
| process_annot | 0.344 | 0.008 | 0.352 | |
| random_walk | 4.706 | 0.109 | 4.815 | |
| score_candidate_genes_from_PPI | 4.827 | 0.096 | 4.923 | |
| subgraph_op | 1.070 | 0.013 | 1.084 | |
| weighted_adj | 3.661 | 0.074 | 3.736 | |
| wppi | 9.209 | 0.236 | 9.454 | |
| wppi_data | 2.558 | 0.053 | 2.611 | |
| wppi_go_data | 1.200 | 0.036 | 1.237 | |
| wppi_hpo_data | 0.280 | 0.005 | 0.285 | |
| wppi_omnipath_data | 1.221 | 0.023 | 1.243 | |