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This page was generated on 2024-12-23 11:43 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4372
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 2254/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wppi 1.15.0  (landing page)
Ana Galhoz
Snapshot Date: 2024-12-22 13:40 -0500 (Sun, 22 Dec 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    ERROR  skippedskipped
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    OK    WARNINGS  

BUILD 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: chmod a+r wppi -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data wppi
StartedAt: 2024-12-22 21:53:29 -0500 (Sun, 22 Dec 2024)
EndedAt: 2024-12-22 21:53:53 -0500 (Sun, 22 Dec 2024)
EllapsedTime: 24.2 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r wppi -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data wppi
###
##############################################################################
##############################################################################


* checking for file 'wppi/DESCRIPTION' ... OK
* preparing 'wppi':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'wppi_workflow.Rmd' using rmarkdown
[2024-12-22 21:53:50] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-22 21:53:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-22 21:53:50] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-12-22 21:53:50] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-12-22 21:53:50] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-12-22 21:53:50] [TRACE]   [OmnipathR] Contains 1 files.
[2024-12-22 21:53:50] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-12-22 21:53:50] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-22 21:53:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-22 21:53:50] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-12-22 21:53:50] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-12-22 21:53:50] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-12-22 21:53:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-22 21:53:50] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-12-22 21:53:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-22 21:53:50] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-12-22 21:53:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-22 21:53:50] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-12-22 21:53:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-22 21:53:50] [TRACE]   [OmnipathR] Cache locked: FALSE
[2024-12-22 21:53:51] [INFO]    [wppi] Executing WPPI workflow.
[2024-12-22 21:53:51] [INFO]    [wppi] Collecting database knowledge.
[2024-12-22 21:53:51] [TRACE]   [OmnipathR] Looking up in cache: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2024-12-22 21:53:51] [INFO]    [OmnipathR] Cache record does not exist: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2024-12-22 21:53:51] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2024-12-22 21:53:51] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-22 21:53:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-22 21:53:51] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-22 21:53:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-22 21:53:51] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `unknown` to `started`.
[2024-12-22 21:53:51] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2024-12-22 21:53:51] [INFO]    [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2024-12-22 21:53:51] [TRACE]   [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`

Quitting from lines 80-102 [workflow] (wppi_workflow.Rmd)
Error: processing vignette 'wppi_workflow.Rmd' failed with diagnostics:
error writing to connection
--- failed re-building 'wppi_workflow.Rmd'

SUMMARY: processing the following file failed:
  'wppi_workflow.Rmd'

Error: Vignette re-building failed.
Execution halted