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This page was generated on 2024-07-06 11:45 -0400 (Sat, 06 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4643
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4414
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4442
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4391
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 3833
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 2224/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wppi 1.13.0  (landing page)
Ana Galhoz
Snapshot Date: 2024-07-05 14:00 -0400 (Fri, 05 Jul 2024)
git_url: https://git.bioconductor.org/packages/wppi
git_branch: devel
git_last_commit: 65eba9a
git_last_commit_date: 2024-04-30 11:33:03 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  NO, package depends on 'OmnipathR' which is not available
palomino6Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'OmnipathR' which is not available
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'OmnipathR' which is not available
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: 1.13.0
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_1.13.0.tar.gz
StartedAt: 2024-07-06 09:30:27 -0000 (Sat, 06 Jul 2024)
EndedAt: 2024-07-06 09:35:24 -0000 (Sat, 06 Jul 2024)
EllapsedTime: 297.1 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_1.13.0.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 ‘1.13.0’
* 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
[2024-07-06 09:31:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-06 09:31:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-06 09:31:02] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-07-06 09:31:02] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-06 09:31:02] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-07-06 09:31:02] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-06 09:31:02] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-06 09:31:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-06 09:31:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-06 09:31:02] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-07-06 09:31:02] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-07-06 09:31:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-06 09:31:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-06 09:31:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-06 09:31:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-06 09:31:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-06 09:31:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-06 09:31:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-06 09:31:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-06 09:31:02] [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
[2024-07-06 09:31:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-06 09:31:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-06 09:31:20] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-07-06 09:31:20] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-06 09:31:20] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-07-06 09:31:20] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-06 09:31:20] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-06 09:31:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-06 09:31:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-06 09:31:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-07-06 09:31:20] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-07-06 09:31:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-06 09:31:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-06 09:31:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-06 09:31:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-06 09:31:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-06 09:31:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-06 09:31:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-06 09:31:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-06 09:31:20] [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                           40.033  0.131  40.250
score_candidate_genes_from_PPI 21.201  0.075  21.329
prioritization_genes           20.645  0.289  20.990
random_walk                    20.163  0.178  20.395
weighted_adj                   15.034  0.075  15.144
count_genes                    12.167  0.831  21.402
wppi_data                       8.869  0.060   8.946
common_neighbors                8.487  0.355  13.389
filter_annot_with_network       8.281  0.142   8.437
functional_annot                2.476  0.240  19.748
* 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
[2024-07-05 20:38:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-05 20:38:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-05 20:38:00] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-07-05 20:38:00] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-05 20:38:00] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-07-05 20:38:00] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-05 20:38:00] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-05 20:38:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-05 20:38:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-05 20:38:00] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-07-05 20:38:00] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-07-05 20:38:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-05 20:38:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-05 20:38:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-05 20:38:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-05 20:38:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-05 20:38:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-05 20:38:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-05 20:38:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-05 20:38:00] [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
[2024-07-05 20:38:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-05 20:38:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-05 20:38:04] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-07-05 20:38:04] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-05 20:38:04] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-07-05 20:38:04] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-05 20:38:04] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-05 20:38:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-05 20:38:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-05 20:38:04] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-07-05 20:38:04] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-07-05 20:38:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-05 20:38:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-05 20:38:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-05 20:38:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-05 20:38:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-05 20:38:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-05 20:38:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-05 20:38:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-05 20:38:04] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-07-05 20:38:08] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-05 20:38:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-05 20:38:08] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-07-05 20:38:08] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-05 20:38:08] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-07-05 20:38:08] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-05 20:38:08] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-05 20:38:08] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-05 20:38:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-05 20:38:08] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-07-05 20:38:08] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-07-05 20:38:08] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-05 20:38:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-05 20:38:08] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-05 20:38:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-05 20:38:08] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-05 20:38:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-05 20:38:08] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-05 20:38:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-05 20:38:08] [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 8.487 0.35513.389
count_genes12.167 0.83121.402
filter_annot_with_network8.2810.1428.437
functional_annot 2.476 0.24019.748
graph_from_op4.5020.1684.682
in_omnipath4.6960.0714.778
prioritization_genes20.645 0.28920.990
process_annot1.1350.0201.158
random_walk20.163 0.17820.395
score_candidate_genes_from_PPI21.201 0.07521.329
subgraph_op4.5860.0124.610
weighted_adj15.034 0.07515.144
wppi40.033 0.13140.250
wppi_data8.8690.0608.946
wppi_go_data3.2020.0243.231
wppi_hpo_data0.7900.0080.799
wppi_omnipath_data4.4480.0004.457