| Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:32:21 -0400 (Thu, 06 May 2021).
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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 1148/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MouseFM 1.0.0 (landing page) Matthias Munz
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
| Package: MouseFM |
| Version: 1.0.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MouseFM.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MouseFM_1.0.0.tar.gz |
| StartedAt: 2021-05-06 04:49:21 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 04:56:36 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 434.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: MouseFM.Rcheck |
| Warnings: NA |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MouseFM.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MouseFM_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/MouseFM.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.0.0'
* 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 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-3.12-bioc/meat/MouseFM.Rcheck/00check.log'
for details.
MouseFM.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/MouseFM_1.0.0.tar.gz && rm -rf MouseFM.buildbin-libdir && mkdir MouseFM.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MouseFM.buildbin-libdir MouseFM_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL MouseFM_1.0.0.zip && rm MouseFM_1.0.0.tar.gz MouseFM_1.0.0.zip
###
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% 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 18057 100 18057 0 0 512k 0 --:--:-- --:--:-- --:--:-- 534k
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_1.0.0.zip
* DONE (MouseFM)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'MouseFM' successfully unpacked and MD5 sums checked
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MouseFM.Rcheck/tests_i386/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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
84.10 0.64 89.56
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MouseFM.Rcheck/tests_x64/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-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
115.71 0.31 122.43
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MouseFM.Rcheck/examples_i386/MouseFM-Ex.timings
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MouseFM.Rcheck/examples_x64/MouseFM-Ex.timings
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