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This page was generated on 2022-01-19 13:05:06 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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

BUILD results for appreci8R on nebbiolo2


To the developers/maintainers of the appreci8R package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/appreci8R.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 76/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
appreci8R 1.12.0  (landing page)
Sarah Sandmann
Snapshot Date: 2022-01-18 01:55:07 -0500 (Tue, 18 Jan 2022)
git_url: https://git.bioconductor.org/packages/appreci8R
git_branch: RELEASE_3_14
git_last_commit: a9fde70
git_last_commit_date: 2021-10-26 12:45:40 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    ERROR  skipped
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: appreci8R
Version: 1.12.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data appreci8R
StartedAt: 2022-01-18 03:44:14 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 03:46:23 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 129.8 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data appreci8R
###
##############################################################################
##############################################################################


* 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


0. Reading input
1. Target filtration
2. Normalize
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

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, 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: 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) : 
  Timeout was reached: [eutils.ncbi.nlm.nih.gov] Operation timed out after 10001 milliseconds with 0 out of 0 bytes received

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

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

Error: Vignette re-building failed.
Execution halted