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This page was generated on 2023-10-20 09:37:58 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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baySeq 2.34.0  (landing page)
Thomas J. Hardcastle
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/baySeq
git_branch: RELEASE_3_17
git_last_commit: f4619cd
git_last_commit_date: 2023-04-25 09:49:38 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    ERROR  skippedskipped

BUILD results for baySeq on kjohnson2


To the developers/maintainers of the baySeq package:
- 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: baySeq
Version: 2.34.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data baySeq
StartedAt: 2023-10-15 21:24:44 -0400 (Sun, 15 Oct 2023)
EndedAt: 2023-10-15 21:31:41 -0400 (Sun, 15 Oct 2023)
EllapsedTime: 417.2 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data baySeq
###
##############################################################################
##############################################################################


* checking for file ‘baySeq/DESCRIPTION’ ... OK
* preparing ‘baySeq’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘baySeq.Rnw’ using Sweave
Loading required package: GenomicRanges
Loading required package: stats4
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

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
Loading required package: GenomeInfoDb
Loading required package: abind
Loading required package: parallel
Finding priors...done.
Length of priorReps:1000
Length of priorSubset:1000
Length of subset:1000
Length of postRows:1000
Finding priors...done.
Finding posterior likelihoods...Length of priorReps:0
Length of priorSubset:3000
Length of subset:3000
Length of postRows:3000
Analysing part 1 of 1
Preparing data...........................................................done.
Estimating likelihoods......done!
done.
Warning in summarisePosteriors(cD) :
  No orderings contained in countData object.
Finding priors...done.
Finding posterior likelihoods...Length of priorReps:0
Length of priorSubset:3000
Length of subset:3000
Length of postRows:3000
Analysing part 1 of 1
Preparing data.........................................................done.
Estimating likelihoods......done!
done.
--- finished re-building ‘baySeq.Rnw’

--- re-building ‘baySeq_generic.Rnw’ using Sweave
Finding priors...done.
Finding posterior likelihoods...Length of priorReps:0
Length of priorSubset:1000
Length of subset:1000
Length of postRows:1000
Analysing part 1 of 1
Preparing data..........................................................done.
Estimating likelihoods......done!
Warning in makeOrderings(listPosts[[cc]]) :
  No valid ordering function available.
done.
Finding priors...done.
Finding posterior likelihoods...Length of priorReps:0
Length of priorSubset:1000
Length of subset:1000
Length of postRows:1000
Analysing part 1 of 1
Preparing data....................................................done.
Estimating likelihoods......done!
Warning in makeOrderings(listPosts[[cc]]) :
  No valid ordering function available.
done.
Finding priors...done.
Finding posterior likelihoods...Length of priorReps:0
Length of priorSubset:1000
Length of subset:1000
Length of postRows:1000
Analysing part 1 of 1
Preparing data......................................................done.
Estimating likelihoods......done!
done.
Finding priors...done.
Finding posterior likelihoods...Length of priorReps:0
Length of priorSubset:1000
Length of subset:1000
Length of postRows:1000
Analysing part 1 of 1
Preparing data............................................................done.
Estimating likelihoods......done!
done.

Error: processing vignette 'baySeq_generic.Rnw' failed with diagnostics:
 chunk 20 
Error in pET %in% c("iteratively", "BIC") && (any(sapply(modelPriorValues,  : 
  'length = 2' in coercion to 'logical(1)'

--- failed re-building ‘baySeq_generic.Rnw’

SUMMARY: processing the following file failed:
  ‘baySeq_generic.Rnw’

Error: Vignette re-building failed.
Execution halted