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This page was generated on 2024-11-28 12:15 -0500 (Thu, 28 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4748
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4459
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4398
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 2252/2272HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wppi 1.15.0  (landing page)
Ana Galhoz
Snapshot Date: 2024-11-27 13:40 -0500 (Wed, 27 Nov 2024)
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

CHECK results for wppi on nebbiolo1

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: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings wppi_1.15.0.tar.gz
StartedAt: 2024-11-28 08:02:08 -0500 (Thu, 28 Nov 2024)
EndedAt: 2024-11-28 08:10:55 -0500 (Thu, 28 Nov 2024)
EllapsedTime: 527.3 seconds
RetCode: 0
Status:   OK  
CheckDir: wppi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings wppi_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/wppi.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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
[2024-11-28 08:06:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-28 08:06:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 08:06:20] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-28 08:06:20] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-28 08:06:20] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-28 08:06:20] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-28 08:06:20] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-28 08:06:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-28 08:06:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 08:06:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-28 08:06:20] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-11-28 08:06:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-28 08:06:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 08:06:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-28 08:06:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 08:06:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-28 08:06:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 08:06:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-28 08:06:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 08:06:20] [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
[2024-11-28 08:06:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-28 08:06:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 08:06:34] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-28 08:06:34] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-28 08:06:34] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-28 08:06:34] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-28 08:06:34] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-28 08:06:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-28 08:06:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 08:06:34] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-28 08:06:34] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-11-28 08:06:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-28 08:06:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 08:06:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-28 08:06:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 08:06:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-28 08:06:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 08:06:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-28 08:06:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 08:06:34] [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                           39.123  0.066  39.191
score_candidate_genes_from_PPI 20.325  0.111  20.436
prioritization_genes           20.063  0.261  20.325
random_walk                    19.260  0.107  19.385
weighted_adj                   16.098  0.112  16.222
common_neighbors               10.633  0.462  15.766
count_genes                     9.228  0.561   9.625
wppi_data                       6.773  0.021   6.796
filter_annot_with_network       6.450  0.120   6.570
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/wppi.Rcheck/00check.log’
for details.

Installation output

wppi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL wppi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘wppi’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
[2024-11-27 15:32:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-27 15:32:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-27 15:32:26] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-27 15:32:26] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-27 15:32:26] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-27 15:32:26] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-27 15:32:26] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-27 15:32:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-27 15:32:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-27 15:32:26] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-27 15:32:26] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-11-27 15:32:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-27 15:32:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-27 15:32:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-27 15:32:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-27 15:32:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-27 15:32:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-27 15:32:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-27 15:32:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-27 15:32:26] [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
[2024-11-27 15:32:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-27 15:32:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-27 15:32:30] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-27 15:32:30] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-27 15:32:30] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-27 15:32:30] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-27 15:32:30] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-27 15:32:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-27 15:32:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-27 15:32:30] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-27 15:32:30] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-11-27 15:32:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-27 15:32:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-27 15:32:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-27 15:32:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-27 15:32:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-27 15:32:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-27 15:32:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-27 15:32:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-27 15:32:30] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-11-27 15:32:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-27 15:32:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-27 15:32:33] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-27 15:32:33] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-27 15:32:33] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-27 15:32:33] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-27 15:32:33] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-27 15:32:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-27 15:32:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-27 15:32:33] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-27 15:32:33] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2024-11-27 15:32:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-27 15:32:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-27 15:32:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-27 15:32:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-27 15:32:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-27 15:32:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-27 15:32:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-27 15:32:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-27 15:32:33] [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_neighbors10.633 0.46215.766
count_genes9.2280.5619.625
filter_annot_with_network6.450.126.57
functional_annot1.7730.1352.428
graph_from_op2.8950.0922.987
in_omnipath2.9920.0283.019
prioritization_genes20.063 0.26120.325
process_annot0.8960.0180.914
random_walk19.260 0.10719.385
score_candidate_genes_from_PPI20.325 0.11120.436
subgraph_op2.8860.0192.905
weighted_adj16.098 0.11216.222
wppi39.123 0.06639.191
wppi_data6.7730.0216.796
wppi_go_data2.8280.0032.831
wppi_hpo_data0.7620.0030.766
wppi_omnipath_data3.1940.0063.201