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This page was generated on 2021-10-15 15:06:12 -0400 (Fri, 15 Oct 2021).

CHECK results for MouseFM on tokay2

To the developers/maintainers of the MouseFM package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MouseFM.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 1186/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MouseFM 1.2.0  (landing page)
Matthias Munz
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/MouseFM
git_branch: RELEASE_3_13
git_last_commit: b73aa9e
git_last_commit_date: 2021-05-19 12:53:20 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    ERROR  
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    ERROR    OK  
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: MouseFM
Version: 1.2.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MouseFM.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MouseFM_1.2.0.tar.gz
StartedAt: 2021-10-15 02:14:24 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 02:20:31 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 367.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: MouseFM.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MouseFM.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MouseFM_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/MouseFM.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MouseFM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MouseFM' version '1.2.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... 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
** running examples for arch 'x64' ... 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 tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 2 ERRORs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/MouseFM.Rcheck/00check.log'
for details.


Installation output

MouseFM.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/MouseFM_1.2.0.tar.gz && rm -rf MouseFM.buildbin-libdir && mkdir MouseFM.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MouseFM.buildbin-libdir MouseFM_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL MouseFM_1.2.0.zip && rm MouseFM_1.2.0.tar.gz MouseFM_1.2.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 17518  100 17518    0     0   147k      0 --:--:-- --:--:-- --:--:--  148k

install for i386

* installing *source* package 'MouseFM' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MouseFM'
    finding HTML links ... done
    GRanges2df                              html  
    annotate_consequences                   html  
    annotate_mouse_genes                    html  
    avail_chromosomes                       html  
    avail_consequences                      html  
    avail_strains                           html  
    backend_request                         html  
    comb                                    html  
    df2GRanges                              html  
    df_split                                html  
    ensembl_rest_vep                        html  
    fetch                                   html  
    finemap                                 html  
    finemap_query                           html  
    getURL                                  html  
    get_top                                 html  
    prio                                    html  
    reduction                               html  
    ref_genome                              html  
    setURL                                  html  
    vis_reduction_factors                   html  
** 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

install for x64

* installing *source* package 'MouseFM' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MouseFM' as MouseFM_1.2.0.zip
* DONE (MouseFM)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'MouseFM' successfully unpacked and MD5 sums checked

Tests output

MouseFM.Rcheck/tests_i386/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 
  93.39    0.78   98.25 

MouseFM.Rcheck/tests_x64/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
  79.92    0.59   85.12 

Example timings

MouseFM.Rcheck/examples_i386/MouseFM-Ex.timings

nameusersystemelapsed
GRanges2df0.460.001.00
annotate_consequences0.790.003.39

MouseFM.Rcheck/examples_x64/MouseFM-Ex.timings

nameusersystemelapsed
GRanges2df0.500.030.95
annotate_consequences1.070.003.19