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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:nanotatoR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings nanotatoR_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/nanotatoR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'nanotatoR/DESCRIPTION' ... OK
* this is package 'nanotatoR' version '1.11.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'nanotatoR' 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 ... NOTE
Namespace in Imports field not imported from: 'GenomicRanges'
  All declared Imports should be used.
* 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 ... OK
* 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: 2 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/nanotatoR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL nanotatoR
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'nanotatoR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'nanotatoR'
    finding HTML links ... done
    BNDBfrequency                           html  
    DGVfrequency                            html  
    Decipherfrequency                       html  
    FamilyInfoPrep                          html  
    OverlapRNAseq                           html  
    OverlapRNAseq_solo                      html  
    RNAseqcombine                           html  
    RNAseqcombine_solo                      html  
    SVexpression_duo_trio                   html  
    SVexpression_solo                       html  
    buildrunBNBedFiles                      html  
    clinvar_gene                            html  
    extract_clinvar_mod                     html  
    gene_extraction                         html  
    gene_list_generation                    html  
    gtr_gene                                html  
    internalFrequencyTrio_Duo               html  
    internalFrequency_solo                  html  
    makeInternalBNDatabase                  html  
    mergingSMAP_SE                          html  
    mergingSMAP_SVMerge                     html  
    merging_SE_SVMerge                      html  
    nanotatoR                               html  
    nanotatoR_Duo_SVmerge                   html  
    nanotatoR_SVmerge_Trio                  html  
    nanotatoR_main_Duo_SE                   html  
    nanotatoR_main_Solo_SE                  html  
    nanotatoR_main_Solo_SVmerge             html  
    nanotatoR_main_Trio_SE                  html  
    nonOverlapGenes                         html  
    nonOverlapRNAseq                        html  
    nonOverlapRNAseq_solo                   html  
    nonOverlappingDNGenes                   html  
    nonOverlappingUPGenes                   html  
    omim_gene                               html  
    overlapGenes                            html  
    overlapnearestgeneSearch                html  
    overlappingGenes                        html  
    phenoextractHPO_mod                     html  
    readBNBedFiles                          html  
    readSMap                                html  
    readSMap_DLE                            html  
    reading_GTR                             html  
    reading_mim2gene                        html  
    run_bionano_filter_SE_Trio              html  
    run_bionano_filter_SE_duo               html  
    run_bionano_filter_SE_solo              html  
    run_bionano_filter_SVMerge_Trio         html  
    run_bionano_filter_SVMerge_duo          html  
    run_bionano_filter_SVMerge_solo         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
* DONE (nanotatoR)
Making 'packages.html' ... done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
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(nanotatoR)

> 
> test_check("nanotatoR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
   4.64    0.32    4.95