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BUILD report for appreci8R on malbec2

This page was generated on 2019-04-09 11:51:32 -0400 (Tue, 09 Apr 2019).

Package 70/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
appreci8R 1.1.0
Sarah Sandmann
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/appreci8R
Branch: master
Last Commit: 240c997
Last Changed Date: 2018-10-30 11:54:39 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK [ ERROR ] skipped 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: appreci8R
Version: 1.1.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data appreci8R
StartedAt: 2019-04-08 22:11:12 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 22:14:19 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 187.0 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data appreci8R
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* checking for file ‘appreci8R/DESCRIPTION’ ... OK
* preparing ‘appreci8R’:
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
* saving partial Rd database
* creating vignettes ... ERROR
--- re-building ‘appreci8R.Rnw’ using Sweave


Registered S3 method overwritten by 'crul':
  method                 from
  as.character.form_file httr
0. Reading input
1. Target filtration
2. Normalize
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap,
    parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from ‘package:appreci8R’:

    normalize

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, append, as.data.frame, basename,
    cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply, setdiff,
    sort, table, tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite
    Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: GenomicFeatures
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

3. Annotate
'select()' returned 1:1 mapping between keys and columns
Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 11 out-of-bound ranges located on sequences 10808, 10809, 10810,
  and 18309. Note that ranges located on a sequence whose length is unknown (NA) or on a
  circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to
  get the lengths and circularity flags of the underlying sequences). You can use trim() to
  trim these ranges. See ?`trim,GenomicRanges-method` for more information.
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 11 out-of-bound ranges located on sequences 10808, 10809, 10810,
  and 18309. Note that ranges located on a sequence whose length is unknown (NA) or on a
  circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to
  get the lengths and circularity flags of the underlying sequences). You can use trim() to
  trim these ranges. See ?`trim,GenomicRanges-method` for more information.
4. Combine Output
5. Evaluate Coverage and BQ
6. Determine Extended Set of Characteristics (databases)
-> Downloading databases 

Error: processing vignette 'appreci8R.Rnw' failed with diagnostics:
 chunk 9 (label = 9) 
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Error in the HTTP2 framing layer

--- failed re-building ‘appreci8R.Rnw’

SUMMARY: processing the following file failed:
  ‘appreci8R.Rnw’

Error: Vignette re-building failed.
Execution halted