Package: XCIR

Version: 1.0.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:XCIR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings XCIR_1.0.0.tar.gz

StartedAt: 2020-04-15 06:36:11 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:45:55 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 584.1 seconds

RetCode: 1

Status:  ERROR

CheckDir: XCIR.Rcheck

Warnings: NA

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:XCIR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings XCIR_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/XCIR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘XCIR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘XCIR’ version ‘1.0.0’
* 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 ‘XCIR’ 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 ‘XCIR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addAnno
> ### Title: Read annotation file
> ### Aliases: addAnno
> 
> ### ** Examples
> 
> # Example workflow for documentation
> 
> vcff <- system.file("extdata/AD_example.vcf", package = "XCIR")
> # Reading functions
> vcf <- readRNASNPs(vcff)
> vcf <- readVCF4(vcff)
> 
> # Annotation functions
> # Using seqminer (requires additional annotation files)
> # Using biomaRt
> anno <- annotateX(vcf)
Error in bmRequest(request = request, verbose = verbose) : 
  Gateway Timeout (HTTP 504).
Calls: annotateX ... listMarts -> .listMarts -> bmRequest -> stop_for_status
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-3.10-bioc/meat/XCIR.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL XCIR
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘XCIR’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (XCIR)

name	user	system	elapsed
BetaConversion	0.000	0.000	0.001