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This page was generated on 2024-03-29 11:37:14 -0400 (Fri, 29 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4669
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4404
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4427
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 1801/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rRDP 1.36.0  (landing page)
Michael Hahsler
Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/rRDP
git_branch: RELEASE_3_18
git_last_commit: b269f9e
git_last_commit_date: 2023-10-24 10:38:42 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

BUILD results for rRDP on palomino4


To the developers/maintainers of the rRDP package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rRDP.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: rRDP
Version: 1.36.0
Command: chmod a+r rRDP -R && F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data rRDP
StartedAt: 2024-03-27 20:54:26 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 20:54:44 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 17.6 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r rRDP -R && F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data rRDP
###
##############################################################################
##############################################################################


* checking for file 'rRDP/DESCRIPTION' ... OK
* preparing 'rRDP':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'rRDP.Rnw' using Sweave
Loading required package: Biostrings
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm,
    append, as.data.frame, basename, cbind, colnames, dirname,
    do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Warning in system(exe, ignore.stdout = TRUE, ignore.stderr = TRUE, intern = FALSE) :
  '\bin\java.exe' not found

Error: processing vignette 'rRDP.Rnw' failed with diagnostics:
 chunk 8 (label = predict) 
Error in predict.RDPClassifier(rdp(), seq) : 
  Error executing: \bin\java.exe -Xmx1g -jar F:\biocbuild\bbs-3.18-bioc\tmpdir\Rtmpm6gwcw\Rinst336036e67b2f\rRDP\java\rdp_classifier.jar classify -t F:\biocbuild\bbs-3.18-bioc\R\library\rRDPData\extdata\16srrna\rRNAClassifier.properties -o F:\biocbuild\bbs-3.18-bioc\tmpdir\Rtmp6hoBly\file33bc7931326_tax_assignments.txt -c 0.8 -format fixrank  F:\biocbuild\bbs-3.18-bioc\tmpdir\Rtmp6hoBly\file33bc7931326.fasta

--- failed re-building 'rRDP.Rnw'

SUMMARY: processing the following file failed:
  'rRDP.Rnw'

Error: Vignette re-building failed.
Execution halted