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This page was generated on 2025-01-11 11:42 -0500 (Sat, 11 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4760
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4479
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4443
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4398
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4391
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 2257/2277HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wppi 1.15.0  (landing page)
Ana Galhoz
Snapshot Date: 2025-01-10 13:40 -0500 (Fri, 10 Jan 2025)
git_url: https://git.bioconductor.org/packages/wppi
git_branch: devel
git_last_commit: 321e17d
git_last_commit_date: 2024-10-29 10:58:10 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows 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
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    ERROR  skipped

CHECK results for wppi on palomino7

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.

raw results


Summary

Package: wppi
Version: 1.15.0
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:wppi.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings wppi_1.15.0.tar.gz
StartedAt: 2025-01-11 06:40:58 -0500 (Sat, 11 Jan 2025)
EndedAt: 2025-01-11 06:46:29 -0500 (Sat, 11 Jan 2025)
EllapsedTime: 330.5 seconds
RetCode: 0
Status:   OK  
CheckDir: wppi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:wppi.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings wppi_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/wppi.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'wppi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'wppi' version '1.15.0'
* 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 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
[2025-01-11 06:41:36] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-11 06:41:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-11 06:41:36] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-11 06:41:36] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-11 06:41:36] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-11 06:41:36] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-11 06:41:36] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-11 06:41:36] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-11 06:41:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-11 06:41:36] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-11 06:41:36] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-11 06:41:36] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-11 06:41:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-11 06:41:36] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-11 06:41:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-11 06:41:36] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-11 06:41:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-11 06:41:36] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-11 06:41:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-11 06:41:36] [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
[2025-01-11 06:41:57] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-11 06:41:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-11 06:41:57] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-11 06:41:57] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-11 06:41:57] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-11 06:41:57] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-11 06:41:57] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-11 06:41:57] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-11 06:41:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-11 06:41:57] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-11 06:41:57] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-11 06:41:57] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-11 06:41:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-11 06:41:57] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-11 06:41:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-11 06:41:57] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-11 06:41:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-11 06:41:58] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-11 06:41:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-11 06:41:58] [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                           53.39   0.84   54.28
score_candidate_genes_from_PPI 27.17   0.61   27.84
random_walk                    24.83   0.62   25.45
prioritization_genes           24.75   0.48   25.25
weighted_adj                   21.11   0.43   21.53
common_neighbors               14.52   0.44   17.23
count_genes                    12.52   0.78   11.80
wppi_data                       8.68   0.22    8.91
filter_annot_with_network       7.79   0.26    8.07
* 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
  'E:/biocbuild/bbs-3.21-bioc/meat/wppi.Rcheck/00check.log'
for details.

Installation output

wppi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL wppi
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'wppi' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
[2025-01-10 15:54:09] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-10 15:54:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:54:09] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-10 15:54:09] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-10 15:54:09] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-10 15:54:09] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-10 15:54:09] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-10 15:54:09] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-10 15:54:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:54:09] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-10 15:54:09] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-10 15:54:09] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-10 15:54:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:54:09] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-10 15:54:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:54:09] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-10 15:54:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:54:09] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-10 15:54:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:54:09] [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
[2025-01-10 15:54:18] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-10 15:54:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:54:18] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-10 15:54:18] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-10 15:54:18] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-10 15:54:18] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-10 15:54:18] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-10 15:54:18] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-10 15:54:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:54:18] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-10 15:54:18] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-10 15:54:18] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-10 15:54:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:54:18] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-10 15:54:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:54:18] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-10 15:54:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:54:18] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-10 15:54:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:54:18] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-01-10 15:54:22] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-10 15:54:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:54:22] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-10 15:54:22] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-10 15:54:22] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-10 15:54:22] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-10 15:54:22] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-10 15:54:22] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-10 15:54:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:54:22] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-10 15:54:22] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-10 15:54:22] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-10 15:54:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:54:22] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-10 15:54:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:54:22] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-10 15:54:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:54:22] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-10 15:54:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:54:22] [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_neighbors14.52 0.4417.23
count_genes12.52 0.7811.80
filter_annot_with_network7.790.268.07
functional_annot2.130.192.51
graph_from_op4.110.034.14
in_omnipath4.330.024.35
prioritization_genes24.75 0.4825.25
process_annot1.010.051.06
random_walk24.83 0.6225.45
score_candidate_genes_from_PPI27.17 0.6127.84
subgraph_op3.520.033.55
weighted_adj21.11 0.4321.53
wppi53.39 0.8454.28
wppi_data8.680.228.91
wppi_go_data3.910.144.05
wppi_hpo_data0.860.050.90
wppi_omnipath_data4.080.034.11