##############################################################################
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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:gwascat.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings gwascat_2.27.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/gwascat.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 'gwascat/DESCRIPTION' ... OK
* this is package 'gwascat' version '2.27.0'
* 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 'gwascat' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 34.1Mb
  sub-directories of 1Mb or more:
    data     10.1Mb
    legacy   15.6Mb
    obo       3.0Mb
    olddata   2.2Mb
    tab       1.1Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'IRanges'
A package should be listed in only one of these fields.
* 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 ... NOTE
addSeqlengths: no visible global function definition for 'seqlengths'
addSeqlengths: no visible global function definition for 'seqlengths<-'
bindcadd_snv: no visible global function definition for 'TabixFile'
bindcadd_snv: no visible global function definition for 'findOverlaps'
buildq: no visible global function definition for 'read.delim'
chklocs: no visible binding for global variable 'gwrngs19'
chklocs: no visible global function definition for 'snpsBySeqname'
gwascat_from_AHub: no visible global function definition for 'data'
gwascat_from_AHub: no visible binding for global variable 'si.hs.38'
gwascat_from_AHub: no visible global function definition for
  'sessionInfo'
gwcat_snapshot: no visible global function definition for 'data'
gwcat_snapshot: no visible binding for global variable 'si.hs.38'
gwcat_snapshot: no visible global function definition for 'sessionInfo'
lo38to19: no visible global function definition for 'liftOver'
lo38to19: no visible global function definition for 'sessionInfo'
lo38to19: no visible global function definition for 'data'
lo38to19: no visible binding for global variable 'si.hs.37'
makeCurrentGwascat: no visible global function definition for
  'download.file'
makeCurrentGwascat: no visible global function definition for 'data'
makeCurrentGwascat: no visible binding for global variable 'si.hs.38'
makeCurrentGwascat: no visible global function definition for
  'sessionInfo'
process_gwas_dataframe: no visible global function definition for
  'data'
process_gwas_dataframe: no visible binding for global variable
  'si.hs.38'
process_gwas_dataframe: no visible global function definition for
  'sessionInfo'
snpGenos: no visible global function definition for 'getSNPlocs'
tfilt: no visible binding for global variable 'phr'
tpad: no visible binding for global variable 'phr'
traitsManh: no visible global function definition for 'aes'
traitsManh: no visible binding for global variable 'PVALUE_MLOG'
variantProps: no visible binding for global variable 'gwrngs'
Undefined global functions or variables:
  PVALUE_MLOG TabixFile aes data download.file findOverlaps getSNPlocs
  gwrngs gwrngs19 liftOver phr read.delim seqlengths seqlengths<-
  sessionInfo si.hs.37 si.hs.38 snpsBySeqname
Consider adding
  importFrom("utils", "data", "download.file", "read.delim",
             "sessionInfo")
to your NAMESPACE file.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... NOTE
  Note: found 2077 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
gwascat_from_AHub 36.47   0.91   39.03
gwcat_snapshot    34.25   0.73   35.70
gwcex2gviz         7.73   0.42    8.16
gg17N              5.14   0.08    5.22
* 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: 4 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/gwascat.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL gwascat
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'gwascat' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'gwascat'
    finding HTML links ... done
    bindcadd_snv                            html  
    chklocs                                 html  
    ebicat_2020_04_30                       html  
    g17SM                                   html  
    getRsids-gwaswloc-method                html  
    getRsids                                html  
    getTraits-gwaswloc-method               html  
    getTraits                               html  
    get_cached_gwascat                      html  
    gg17N                                   html  
    gr6.0_hg38                              html  
    gw6.rs_17                               html  
    gwascat_from_AHub                       html  
    gwastagger                              html  
    gwaswloc-class                          html  
    gwcat_snapshot                          html  
    gwcex2gviz                              html  
    ldtagr                                  html  
    locon6                                  html  
    locs4trait                              html  
    low17                                   html  
    makeCurrentGwascat                      html  
    obo2graphNEL                            html  
    process_gwas_dataframe                  html  
    riskyAlleleCount                        html  
    si.hs.37                                html  
    si.hs.38                                html  
    sub-gwaswloc-ANY-ANY-ANY-method         html  
    subsetByChromosome-gwaswloc-method      html  
    subsetByChromosome                      html  
    subsetByTraits-gwaswloc-method          html  
    subsetByTraits                          html  
    topTraits                               html  
    traitsManh                              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 (gwascat)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'iCNV' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'Ularcirc' is missing or broken
 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)
> 
> test_check("gwascat")
Loading required package: gwascat
gwascat loaded.  Use makeCurrentGwascat() to extract current image.
 from EBI.  The data folder of this package has some legacy extracts.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
> 
> 
> proc.time()
   user  system elapsed 
  10.68    0.84   11.59