Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-20 12:08 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 2269/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wppi 1.14.0  (landing page)
Ana Galhoz
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/wppi
git_branch: RELEASE_3_20
git_last_commit: 240f65a
git_last_commit_date: 2024-10-29 10:58:10 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for wppi on kunpeng2

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.

raw results


Summary

Package: wppi
Version: 1.14.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings wppi_1.14.0.tar.gz
StartedAt: 2024-11-20 13:44:26 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 13:49:51 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 325.0 seconds
RetCode: 0
Status:   OK  
CheckDir: wppi.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings wppi_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/wppi.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    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 ‘1.14.0’
* 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
[2024-11-20 13:45:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 13:45:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 13:45:12] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 13:45:12] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-20 13:45:12] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 13:45:12] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-20 13:45:12] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-20 13:45:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 13:45:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 13:45:12] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 13:45:12] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-11-20 13:45:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-20 13:45:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 13:45:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-20 13:45:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 13:45:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-20 13:45:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 13:45:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-20 13:45:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 13:45:12] [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
[2024-11-20 13:45:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 13:45:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 13:45:33] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 13:45:33] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-20 13:45:33] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 13:45:33] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-20 13:45:33] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-20 13:45:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 13:45:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 13:45:33] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 13:45:33] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-11-20 13:45:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-20 13:45:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 13:45:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-20 13:45:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 13:45:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-20 13:45:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 13:45:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-20 13:45:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 13:45:34] [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                           41.746  0.156  42.001
score_candidate_genes_from_PPI 21.571  0.351  22.067
prioritization_genes           20.812  0.303  21.160
random_walk                    19.932  0.104  20.071
count_genes                    14.338  1.800  23.736
weighted_adj                   15.436  0.091  15.556
wppi_data                       8.904  0.064   8.977
filter_annot_with_network       8.658  0.164   8.842
common_neighbors                7.985  0.389  12.947
functional_annot                2.688  0.244  21.594
* 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-3.20-bioc/meat/wppi.Rcheck/00check.log’
for details.

Installation output

wppi.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL wppi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘wppi’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
[2024-11-19 21:05:03] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:05:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:05:03] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-19 21:05:03] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-19 21:05:03] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-19 21:05:03] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-19 21:05:03] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-19 21:05:03] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:05:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:05:03] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-19 21:05:03] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-11-19 21:05:03] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-19 21:05:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:05:03] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-19 21:05:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:05:03] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-19 21:05:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:05:03] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-19 21:05:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:05:03] [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
[2024-11-19 21:05:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:05:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:05:09] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-19 21:05:09] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-19 21:05:09] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-19 21:05:09] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-19 21:05:09] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-19 21:05:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:05:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:05:09] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-19 21:05:09] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-11-19 21:05:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-19 21:05:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:05:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-19 21:05:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:05:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-19 21:05:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:05:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-19 21:05:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:05:09] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-11-19 21:05:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:05:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:05:14] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-19 21:05:14] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-19 21:05:14] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-19 21:05:14] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-19 21:05:14] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-19 21:05:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-19 21:05:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:05:14] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-19 21:05:14] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-11-19 21:05:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-19 21:05:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:05:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-19 21:05:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:05:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-19 21:05:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:05:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-19 21:05:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-19 21:05:14] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (wppi)

Tests output


Example timings

wppi.Rcheck/wppi-Ex.timings

nameusersystemelapsed
common_neighbors 7.985 0.38912.947
count_genes14.338 1.80023.736
filter_annot_with_network8.6580.1648.842
functional_annot 2.688 0.24421.594
graph_from_op4.5940.0924.694
in_omnipath4.6080.0914.712
prioritization_genes20.812 0.30321.160
process_annot1.0040.0121.017
random_walk19.932 0.10420.071
score_candidate_genes_from_PPI21.571 0.35122.067
subgraph_op4.5250.0484.582
weighted_adj15.436 0.09115.556
wppi41.746 0.15642.001
wppi_data8.9040.0648.977
wppi_go_data3.6950.0043.703
wppi_hpo_data0.7390.0000.740
wppi_omnipath_data4.4420.0004.446