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This page was generated on 2024-05-30 12:36:31 -0400 (Thu, 30 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4669
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4404
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4431
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4384
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 2215/2233HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wppi 1.13.0  (landing page)
Ana Galhoz
Snapshot Date: 2024-05-29 11:04:14 -0400 (Wed, 29 May 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
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'OmnipathR' which is not available
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped

CHECK results for wppi on palomino4


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: 1.13.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:wppi.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings wppi_1.13.0.tar.gz
StartedAt: 2024-05-30 03:16:58 -0400 (Thu, 30 May 2024)
EndedAt: 2024-05-30 03:20:58 -0400 (Thu, 30 May 2024)
EllapsedTime: 240.6 seconds
RetCode: 0
Status:   OK  
CheckDir: wppi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:wppi.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings wppi_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/wppi.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 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 '1.13.0'
* 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 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
[2024-05-30 03:17:30] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 03:17:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:17:30] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-30 03:17:30] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-30 03:17:30] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-30 03:17:30] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-30 03:17:30] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-30 03:17:30] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 03:17:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:17:30] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-30 03:17:30] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-30 03:17:30] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-30 03:17:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:17:30] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-30 03:17:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:17:30] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-30 03:17:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:17:30] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-30 03:17:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:17:30] [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
[2024-05-30 03:17:49] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 03:17:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:17:49] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-30 03:17:49] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-30 03:17:49] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-30 03:17:49] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-30 03:17:49] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-30 03:17:49] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 03:17:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:17:49] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-30 03:17:49] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-30 03:17:49] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-30 03:17:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:17:49] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-30 03:17:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:17:49] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-30 03:17:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:17:49] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-30 03:17:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:17:49] [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                           31.93   0.68   32.64
score_candidate_genes_from_PPI 16.02   0.56   16.59
prioritization_genes           16.03   0.30   16.33
random_walk                    15.80   0.36   16.16
weighted_adj                   12.80   0.38   13.20
count_genes                    10.12   0.69    9.75
filter_annot_with_network       7.47   0.08    7.54
common_neighbors                7.28   0.22   10.14
wppi_data                       6.66   0.10    6.75
* 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
  'F:/biocbuild/bbs-3.20-bioc/meat/wppi.Rcheck/00check.log'
for details.


Installation output

wppi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL wppi
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'wppi' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
[2024-05-29 13:18:09] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 13:18:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 13:18:09] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-29 13:18:09] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-29 13:18:09] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-29 13:18:09] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-29 13:18:09] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-29 13:18:09] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 13:18:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 13:18:09] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-29 13:18:09] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-29 13:18:09] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-29 13:18:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 13:18:09] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-29 13:18:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 13:18:09] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-29 13:18:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 13:18:09] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-29 13:18:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 13:18:09] [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
[2024-05-29 13:18:14] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 13:18:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 13:18:14] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-29 13:18:14] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-29 13:18:14] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-29 13:18:14] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-29 13:18:14] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-29 13:18:14] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 13:18:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 13:18:14] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-29 13:18:15] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-29 13:18:15] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-29 13:18:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 13:18:15] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-29 13:18:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 13:18:15] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-29 13:18:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 13:18:15] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-29 13:18:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 13:18:15] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-05-29 13:18:18] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 13:18:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 13:18:18] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-29 13:18:18] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-29 13:18:18] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-29 13:18:18] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-29 13:18:18] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-29 13:18:18] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 13:18:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 13:18:18] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-29 13:18:19] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-29 13:18:19] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-29 13:18:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 13:18:19] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-29 13:18:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 13:18:19] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-29 13:18:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 13:18:19] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-29 13:18:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 13:18:19] [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 7.28 0.2210.14
count_genes10.12 0.69 9.75
filter_annot_with_network7.470.087.54
functional_annot2.260.202.67
graph_from_op3.520.093.61
in_omnipath3.780.053.83
prioritization_genes16.03 0.3016.33
process_annot0.670.030.70
random_walk15.80 0.3616.16
score_candidate_genes_from_PPI16.02 0.5616.59
subgraph_op3.950.064.02
weighted_adj12.80 0.3813.20
wppi31.93 0.6832.64
wppi_data6.660.106.75
wppi_go_data2.980.063.05
wppi_hpo_data0.720.030.75
wppi_omnipath_data4.130.054.17