Package: alpineData

Version: 1.6.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:alpineData.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings alpineData_1.6.0.tar.gz

StartedAt: 2018-10-16 10:37:05 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 10:38:18 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 72.8 seconds

RetCode: 1

Status:  ERROR

CheckDir: alpineData.Rcheck

Warnings: NA

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:alpineData.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings alpineData_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-data-experiment/meat/alpineData.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘alpineData/DESCRIPTION’ ... OK
* this is package ‘alpineData’ version ‘1.6.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘alpineData’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘alpineData-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: alpineData
> ### Title: GAlignmentPairs for four samples from the GEUVADIS project
> ### Aliases: alpineData alpineData-package ERR188297 ERR188088 ERR188204
> ###   ERR188317
> ### Keywords: datasets
> 
> ### ** Examples
> 
>   ERR188297()
snapshotDate(): 2018-04-27
see ?alpineData and browseVignettes('alpineData') for documentation
downloading 0 resources
loading from cache 
    ‘/home/biocbuild//.ExperimentHub/166’
Loading required package: GenomicAlignments
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

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

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
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")'.


Attaching package: ‘Biobase’

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

    cache

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

    cache

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: ‘matrixStats’

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

    anyMissing, rowMedians

Loading required package: BiocParallel
Error: package or namespace load failed for ‘DelayedArray’:
 .onLoad failed in loadNamespace() for 'DelayedArray', details:
  call: initialize(value, ...)
  error: attempt to apply non-function
Failed with error:  ‘package ‘DelayedArray’ could not be loaded’
Error in .requirePackage(package) : 
  unable to find required package ‘GenomicAlignments’
Calls: <Anonymous> ... getClass -> getClassDef -> .classEnv -> .requirePackage
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.7-data-experiment/meat/alpineData.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL alpineData
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘alpineData’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (alpineData)

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