Back to Multiple platform build/check report for BioC 3.12
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

CHECK report for MouseFM on malbec1

This page was generated on 2021-05-06 12:28:18 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the MouseFM package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1148/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MouseFM 1.0.0  (landing page)
Matthias Munz
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/MouseFM
Branch: RELEASE_3_12
Last Commit: b63d244
Last Changed Date: 2020-10-27 11:58:14 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    ERROR  
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: MouseFM
Version: 1.0.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:MouseFM.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings MouseFM_1.0.0.tar.gz
StartedAt: 2021-05-06 03:42:30 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 03:47:17 -0400 (Thu, 06 May 2021)
EllapsedTime: 286.2 seconds
RetCode: 1
Status:   ERROR  
CheckDir: MouseFM.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:MouseFM.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings MouseFM_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/MouseFM.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MouseFM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MouseFM’ version ‘1.0.0’
* package encoding: UTF-8
* 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 ‘MouseFM’ 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 ‘MouseFM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: annotate_mouse_genes
> ### Title: Annotate with genes
> ### Aliases: annotate_mouse_genes
> 
> ### ** Examples
> 
> geno = finemap("chr1",
+   start = 5000000, end = 6000000,
+   strain1 = c("C57BL_6J"), strain2 = c("AKR_J", "A_J", "BALB_cJ")
+ )
Query chr1:5,000,000-6,000,000
> 
> genes = annotate_mouse_genes(geno, 50000)
Error in annotate_mouse_genes(geno, 50000) : 
  Reference genome version of BiomaRt is different from the one used 
            in the R package. Contact maintainer.
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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-3.12-bioc/meat/MouseFM.Rcheck/00check.log’
for details.


Installation output

MouseFM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL MouseFM
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘MouseFM’ ...
** using staged installation
** R
** 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 (MouseFM)

Tests output

MouseFM.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(MouseFM)
> 
> test_check("MouseFM")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 9 ]
> 
> proc.time()
   user  system elapsed 
108.568   0.288 114.460 

Example timings

MouseFM.Rcheck/MouseFM-Ex.timings

nameusersystemelapsed
GRanges2df0.4760.0040.956
annotate_consequences0.7520.0003.365