Ana Galhoz
| Snapshot Date: 2024-05-07 14:00:20 -0400 (Tue, 07 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 Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-05-08 11:41:33 -0400 (Wed, 08 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4707 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4484 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4514 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4480 |
| 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
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
| kjohnson3 | macOS 13.6.5 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: wppi |
| Version: 1.12.0 |
| Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings wppi_1.12.0.tar.gz |
| StartedAt: 2024-05-08 13:09:02 -0000 (Wed, 08 May 2024) |
| EndedAt: 2024-05-08 13:13:50 -0000 (Wed, 08 May 2024) |
| EllapsedTime: 288.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: wppi.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings wppi_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/wppi.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2024-05-08 13:09:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-08 13:09:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-08 13:09:37] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-08 13:09:37] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-05-08 13:09:37] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-08 13:09:37] [TRACE] [OmnipathR] Contains 1 files.
[2024-05-08 13:09:37] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-05-08 13:09:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-08 13:09:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-08 13:09:37] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-08 13:09:37] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2024-05-08 13:09:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-08 13:09:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-08 13:09:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-08 13:09:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-08 13:09:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-08 13:09:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-08 13:09:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-08 13:09:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-08 13:09:37] [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
[2024-05-08 13:09:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-08 13:09:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-08 13:09:55] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-08 13:09:55] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-05-08 13:09:55] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-08 13:09:55] [TRACE] [OmnipathR] Contains 1 files.
[2024-05-08 13:09:55] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-05-08 13:09:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-08 13:09:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-08 13:09:55] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-08 13:09:55] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2024-05-08 13:09:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-08 13:09:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-08 13:09:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-08 13:09:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-08 13:09:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-08 13:09:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-08 13:09:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-08 13:09:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-05-08 13:09:55] [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 39.257 0.095 39.424
score_candidate_genes_from_PPI 20.651 0.056 20.767
prioritization_genes 19.980 0.119 20.178
random_walk 19.359 0.059 19.490
weighted_adj 14.498 0.048 14.574
count_genes 10.732 0.350 17.509
common_neighbors 8.463 0.472 15.310
filter_annot_with_network 8.159 0.075 8.269
wppi_data 8.092 0.060 8.166
in_omnipath 4.976 0.004 5.002
functional_annot 2.409 0.198 16.371
* 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
‘/home/biocbuild/bbs-3.19-bioc/meat/wppi.Rcheck/00check.log’
for details.
wppi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL wppi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’ * installing *source* package ‘wppi’ ... ** using staged installation ** R ** byte-compile and prepare package for lazy loading [2024-05-07 20:39:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-07 20:39:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 20:39:47] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-05-07 20:39:47] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-07 20:39:47] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-05-07 20:39:47] [TRACE] [OmnipathR] Contains 1 files. [2024-05-07 20:39:47] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-07 20:39:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-07 20:39:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 20:39:47] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-05-07 20:39:47] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2024-05-07 20:39:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-07 20:39:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 20:39:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-07 20:39:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 20:39:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-07 20:39:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 20:39:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-07 20:39:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 20:39:47] [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 [2024-05-07 20:39:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-07 20:39:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 20:39:51] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-05-07 20:39:51] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-07 20:39:51] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-05-07 20:39:51] [TRACE] [OmnipathR] Contains 1 files. [2024-05-07 20:39:51] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-07 20:39:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-07 20:39:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 20:39:51] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-05-07 20:39:51] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2024-05-07 20:39:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-07 20:39:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 20:39:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-07 20:39:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 20:39:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-07 20:39:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 20:39:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-07 20:39:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 20:39:52] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-05-07 20:39:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-07 20:39:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 20:39:55] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-05-07 20:39:55] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-07 20:39:55] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-05-07 20:39:55] [TRACE] [OmnipathR] Contains 1 files. [2024-05-07 20:39:55] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-07 20:39:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-07 20:39:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 20:39:55] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-05-07 20:39:55] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2024-05-07 20:39:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-07 20:39:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 20:39:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-07 20:39:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 20:39:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-07 20:39:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 20:39:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-07 20:39:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 20:39:55] [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 | 8.463 | 0.472 | 15.310 | |
| count_genes | 10.732 | 0.350 | 17.509 | |
| filter_annot_with_network | 8.159 | 0.075 | 8.269 | |
| functional_annot | 2.409 | 0.198 | 16.371 | |
| graph_from_op | 4.515 | 0.039 | 4.576 | |
| in_omnipath | 4.976 | 0.004 | 5.002 | |
| prioritization_genes | 19.980 | 0.119 | 20.178 | |
| process_annot | 1.092 | 0.008 | 1.104 | |
| random_walk | 19.359 | 0.059 | 19.490 | |
| score_candidate_genes_from_PPI | 20.651 | 0.056 | 20.767 | |
| subgraph_op | 4.782 | 0.008 | 4.800 | |
| weighted_adj | 14.498 | 0.048 | 14.574 | |
| wppi | 39.257 | 0.095 | 39.424 | |
| wppi_data | 8.092 | 0.060 | 8.166 | |
| wppi_go_data | 2.782 | 0.008 | 2.798 | |
| wppi_hpo_data | 1.004 | 0.000 | 1.005 | |
| wppi_omnipath_data | 4.549 | 0.008 | 4.565 | |