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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:gwascat.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings gwascat_2.32.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/gwascat.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘gwascat/DESCRIPTION’ ... OK
* this is package ‘gwascat’ version ‘2.32.0’
* 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 for sufficient/correct file permissions ... 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   15.7Mb
    obo       3.1Mb
    olddata   2.3Mb
    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 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 loading without being on the library search path ... OK
* checking 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 21.156  2.052  23.752
gwcat_snapshot    19.853  1.804  22.051
gwcex2gviz         9.512  0.676  10.189
gg17N              6.712  0.038   6.749
* 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 ...
  ‘gwascat.Rmd’ using ‘UTF-8’... OK
  ‘gwascatOnt.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/gwascat.Rcheck/00check.log’
for details.