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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MouseFM.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MouseFM_1.4.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MouseFM.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.4.2'
* 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 ... NOTE
File 'MouseFM/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("\n  ---------\n  \n  For example usage please run: vignette('MouseFM')\n  \n  Github Repo: https://github.com/matmu/MouseFM\n  MouseFM Backend: https://github.com/matmu/MouseFM-Backend  \n\n  Citation appreciated:\n  Munz M, Khodaygani M, Aherrahrou Z, Busch H, Wohlers I (2021) In silico candidate variant and gene identification using inbred mouse strains. PeerJ. doi:10.7717/peerj.11017\n                        \n  ---------",     domain = NULL, appendLF = TRUE)

See section 'Good practice' in '?.onAttach'.
* 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' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
vis_reduction_factors 50.69   1.12   52.76
prio                  23.22   0.38   24.11
get_top               22.64   0.42   23.44
annotate_mouse_genes   9.35   0.03   12.91
fetch                  2.75   0.20    5.06
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
vis_reduction_factors 51.88   0.67   53.47
prio                  22.17   0.38   23.03
get_top               21.06   0.32   21.75
annotate_mouse_genes   6.78   0.03   10.37
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/MouseFM.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/MouseFM_1.4.2.tar.gz && rm -rf MouseFM.buildbin-libdir && mkdir MouseFM.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MouseFM.buildbin-libdir MouseFM_1.4.2.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MouseFM_1.4.2.zip && rm MouseFM_1.4.2.tar.gz MouseFM_1.4.2.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 18530  100 18530    0     0  39877      0 --:--:-- --:--:-- --:--:-- 39849
100 18530  100 18530    0     0  39854      0 --:--:-- --:--:-- --:--:-- 39849

install for i386

* installing *source* package 'MouseFM' ...
** using staged installation
** R
** inst
** 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_1.4.2.zip
* DONE (MouseFM)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'MouseFM' successfully unpacked and MD5 sums checked