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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:gwascat.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings gwascat_2.38.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/gwascat.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'gwascat/DESCRIPTION' ... OK
* this is package 'gwascat' version '2.38.0'
* 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 33.9Mb
  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 ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 whether startup messages can be suppressed ... 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
bindcadd_snv: no visible global function definition for 'TabixFile'
bindcadd_snv: no visible global function definition for 'findOverlaps'
chklocs: no visible binding for global variable 'gwrngs19'
chklocs: no visible global function definition for 'snpsBySeqname'
gwascat_from_AHub: no visible binding for global variable 'si.hs.38'
gwcat_snapshot: no visible binding for global variable 'si.hs.38'
lo38to19: no visible global function definition for 'liftOver'
lo38to19: no visible binding for global variable 'si.hs.37'
makeCurrentGwascat: no visible binding for global variable 'si.hs.38'
process_gwas_dataframe: no visible binding for global variable
  'si.hs.38'
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 findOverlaps getSNPlocs gwrngs gwrngs19
  liftOver phr si.hs.37 si.hs.38 snpsBySeqname
* checking Rd files ... NOTE
checkRd: (-1) gwcex2gviz.Rd:33: Escaped LaTeX specials: \_
checkRd: (-1) traitsManh.Rd:18: Escaped LaTeX specials: \_
* 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 52.15   0.97   55.42
gwcat_snapshot    51.44   0.89   53.04
gwcex2gviz        13.39   0.91   14.52
gg17N              9.83   0.21   10.04
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  'F:/biocbuild/bbs-3.20-bioc/meat/gwascat.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL gwascat
###
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* installing to library 'F:/biocbuild/bbs-3.20-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
** 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)

R version 4.4.3 (2025-02-28 ucrt) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
  15.00    0.81   15.81