Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2023-10-13 11:40:57 -0400 (Fri, 13 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4679
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4414
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4433
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4419
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 2226/2244HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wppi 1.9.0  (landing page)
Ana Galhoz
Snapshot Date: 2023-10-12 14:05:06 -0400 (Thu, 12 Oct 2023)
git_url: https://git.bioconductor.org/packages/wppi
git_branch: devel
git_last_commit: 64a68df
git_last_commit_date: 2023-04-25 11:28:27 -0400 (Tue, 25 Apr 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.3.1 Ventura / arm64see weekly results here
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: 1.9.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings wppi_1.9.0.tar.gz
StartedAt: 2023-10-13 14:04:51 -0000 (Fri, 13 Oct 2023)
EndedAt: 2023-10-13 14:11:04 -0000 (Fri, 13 Oct 2023)
EllapsedTime: 373.6 seconds
RetCode: 0
Status:   OK  
CheckDir: wppi.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings wppi_1.9.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/wppi.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* 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
* checking for file ‘wppi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wppi’ version ‘1.9.0’
* 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... NOTE
[2023-10-13 14:05:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-13 14:05:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-13 14:05:23] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-10-13 14:05:23] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-10-13 14:05:23] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-10-13 14:05:23] [TRACE]   [OmnipathR] Contains 1 files.
[2023-10-13 14:05:23] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-10-13 14:05:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-13 14:05:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-13 14:05:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-10-13 14:05:23] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2023-10-13 14:05:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-10-13 14:05:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-13 14:05:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-10-13 14:05:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-13 14:05:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-10-13 14:05:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-13 14:05:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-10-13 14:05:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-13 14:05:23] [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
[2023-10-13 14:05:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-13 14:05:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-13 14:05:40] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-10-13 14:05:40] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-10-13 14:05:40] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-10-13 14:05:40] [TRACE]   [OmnipathR] Contains 1 files.
[2023-10-13 14:05:40] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-10-13 14:05:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-13 14:05:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-13 14:05:40] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-10-13 14:05:40] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2023-10-13 14:05:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-10-13 14:05:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-13 14:05:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-10-13 14:05:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-13 14:05:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-10-13 14:05:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-13 14:05:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-10-13 14:05:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-13 14:05:40] [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                           42.595  0.099  42.774
score_candidate_genes_from_PPI 21.949  0.154  22.149
prioritization_genes           21.701  0.257  22.001
random_walk                    21.521  0.214  21.779
weighted_adj                   16.101  0.103  16.238
count_genes                    10.514  0.806  17.691
wppi_data                       8.546  0.060   8.620
filter_annot_with_network       7.666  0.126   7.804
common_neighbors                7.470  0.321   9.175
functional_annot                2.366  0.182  18.532
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘wppi_workflow.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/wppi.Rcheck/00check.log’
for details.

Installation output

wppi.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL wppi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘wppi’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
[2023-10-12 19:41:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-12 19:41:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-12 19:41:44] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-10-12 19:41:44] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-10-12 19:41:44] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-10-12 19:41:44] [TRACE]   [OmnipathR] Contains 1 files.
[2023-10-12 19:41:44] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-10-12 19:41:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-12 19:41:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-12 19:41:44] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-10-12 19:41:44] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2023-10-12 19:41:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-10-12 19:41:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-12 19:41:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-10-12 19:41:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-12 19:41:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-10-12 19:41:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-12 19:41:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-10-12 19:41:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-12 19:41:44] [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
[2023-10-12 19:41:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-12 19:41:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-12 19:41:49] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-10-12 19:41:49] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-10-12 19:41:49] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-10-12 19:41:49] [TRACE]   [OmnipathR] Contains 1 files.
[2023-10-12 19:41:49] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-10-12 19:41:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-12 19:41:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-12 19:41:49] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-10-12 19:41:49] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2023-10-12 19:41:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-10-12 19:41:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-12 19:41:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-10-12 19:41:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-12 19:41:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-10-12 19:41:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-12 19:41:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-10-12 19:41:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-12 19:41:49] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2023-10-12 19:41:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-12 19:41:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-12 19:41:52] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-10-12 19:41:52] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-10-12 19:41:52] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-10-12 19:41:52] [TRACE]   [OmnipathR] Contains 1 files.
[2023-10-12 19:41:52] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-10-12 19:41:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-12 19:41:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-12 19:41:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-10-12 19:41:52] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2023-10-12 19:41:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-10-12 19:41:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-12 19:41:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-10-12 19:41:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-12 19:41:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-10-12 19:41:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-12 19:41:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-10-12 19:41:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-10-12 19:41:52] [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_neighbors7.4700.3219.175
count_genes10.514 0.80617.691
filter_annot_with_network7.6660.1267.804
functional_annot 2.366 0.18218.532
graph_from_op4.4650.2124.687
in_omnipath4.4340.1154.558
prioritization_genes21.701 0.25722.001
process_annot1.0420.0001.043
random_walk21.521 0.21421.779
score_candidate_genes_from_PPI21.949 0.15422.149
subgraph_op4.4450.0084.463
weighted_adj16.101 0.10316.238
wppi42.595 0.09942.774
wppi_data8.5460.0608.620
wppi_go_data2.5240.0042.531
wppi_hpo_data0.9060.0040.912
wppi_omnipath_data4.3650.0044.377