Back to Multiple platform build/check report for BioC 3.11
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

CHECK report for MGFR on celaya2

This page was generated on 2020-01-16 13:45:38 -0500 (Thu, 16 Jan 2020).

Package 1033/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MGFR 1.13.0
Khadija El Amrani
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/MGFR
Branch: master
Last Commit: 6fe7715
Last Changed Date: 2019-10-29 13:41:47 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
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 [ ERROR ] OK 

Summary

Package: MGFR
Version: 1.13.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MGFR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MGFR_1.13.0.tar.gz
StartedAt: 2020-01-16 06:27:16 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 06:36:42 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 565.9 seconds
RetCode: 1
Status:  ERROR 
CheckDir: MGFR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MGFR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MGFR_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/MGFR.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MGFR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MGFR’ version ‘1.13.0’
* 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 ‘MGFR’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘MGFR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MGFR-package
> ### Title: Marker Gene Finder in RNA-seq data
> ### Aliases: MGFR-package MGFR
> ### Keywords: package
> 
> ### ** Examples
> 
> data(ref.mat)
> res.list <- getMarkerGenes.rnaseq(ref.mat, class.vec=colnames(ref.mat), samples2compare="all", annotate=TRUE, gene.ids.type="ensembl", score.cutoff=1)
Detecting marker genes...
Mapping gene IDs to gene symbols...
Error: biomaRt has encountered an unexpected server error.
Consider trying one of the Ensembl mirrors (for more details look at ?useEnsembl)
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
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/MGFR.Rcheck/00check.log’
for details.


Installation output

MGFR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MGFR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘MGFR’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘MGFR.Rnw’ using ‘UTF-8’ 
** 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 (MGFR)

Tests output


Example timings

MGFR.Rcheck/MGFR-Ex.timings

nameusersystemelapsed