baySeq.build

[martin-g]

biocbuild@kunpeng1 ~/git> 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 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

[martin-g]

Fails the same way on x86_64 - https://bioconductor.org/checkResults/3.17/bioc-LATEST/baySeq/nebbiolo1-buildsrc.html

[martin-g]

https://bioconductor.org/checkResults/3.18/bioc-LATEST/baySeq/kunpeng2-checksrc.html builds fine now! It has only warnings in check