This page was generated on 2019-04-09 11:51:32 -0400 (Tue, 09 Apr 2019).
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 | |
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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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