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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PAST.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PAST_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/PAST.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PAST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PAST’ version ‘1.8.0’
* 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:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘PAST’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘S4Vectors::union’ by ‘dplyr::union’ when loading ‘PAST’
  Warning: replacing previous import ‘S4Vectors::intersect’ by ‘dplyr::intersect’ when loading ‘PAST’
  Warning: replacing previous import ‘S4Vectors::setdiff’ by ‘dplyr::setdiff’ when loading ‘PAST’
  Warning: replacing previous import ‘S4Vectors::first’ by ‘dplyr::first’ when loading ‘PAST’
  Warning: replacing previous import ‘S4Vectors::setequal’ by ‘dplyr::setequal’ when loading ‘PAST’
  Warning: replacing previous import ‘S4Vectors::rename’ by ‘dplyr::rename’ when loading ‘PAST’
  Warning: replacing previous import ‘S4Vectors::tail’ by ‘utils::tail’ when loading ‘PAST’
  Warning: replacing previous import ‘S4Vectors::stack’ by ‘utils::stack’ when loading ‘PAST’
  Warning: replacing previous import ‘S4Vectors::head’ by ‘utils::head’ when loading ‘PAST’
  Warning: replacing previous import ‘S4Vectors::complete.cases’ by ‘stats::complete.cases’ when loading ‘PAST’
  Warning: replacing previous import ‘S4Vectors::sd’ by ‘stats::sd’ when loading ‘PAST’
See ‘/Users/biocbuild/bbs-3.13-bioc/meat/PAST.Rcheck/00install.out’ for details.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
assign_SNPs_to_genes: no visible binding for global variable ‘position’
assign_SNPs_to_genes: no visible binding for global variable
  ‘Marker_original’
assign_SNPs_to_genes: no visible binding for global variable ‘effect’
assign_SNPs_to_genes: no visible binding for global variable ‘p.value’
assign_SNPs_to_genes: no visible binding for global variable
  ‘linked_snp_count’
assign_SNPs_to_genes: no visible binding for global variable ‘name’
assign_SNPs_to_genes: no visible binding for global variable ‘marker’
assign_chunk: no visible binding for global variable ‘chromosome’
assign_chunk: no visible global function definition for ‘IRanges’
assign_chunk: no visible binding for global variable ‘position’
assign_chunk: no visible binding for global variable ‘seqid’
assign_chunk: no visible binding for global variable ‘Name’
find_pathway_significance: no visible binding for global variable
  ‘gene_id’
plot_pathways: no visible binding for global variable
  ‘running_enrichment_score’
Undefined global functions or variables:
  IRanges Marker_original Name chromosome effect gene_id
  linked_snp_count marker name p.value position
  running_enrichment_score seqid
* 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 ... WARNING
Undocumented arguments in documentation object 'assign_SNPs_to_genes'
  ‘filter_type’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
plot_pathways             8.559  0.292 149.883
find_pathway_significance 7.883  0.302 142.911
assign_SNPs_to_genes      6.593  0.307  93.567
* 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 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/PAST.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL PAST
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘PAST’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘S4Vectors::union’ by ‘dplyr::union’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::intersect’ by ‘dplyr::intersect’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::setdiff’ by ‘dplyr::setdiff’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::first’ by ‘dplyr::first’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::setequal’ by ‘dplyr::setequal’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::rename’ by ‘dplyr::rename’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::tail’ by ‘utils::tail’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::stack’ by ‘utils::stack’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::head’ by ‘utils::head’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::complete.cases’ by ‘stats::complete.cases’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::sd’ by ‘stats::sd’ when loading ‘PAST’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘S4Vectors::union’ by ‘dplyr::union’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::intersect’ by ‘dplyr::intersect’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::setdiff’ by ‘dplyr::setdiff’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::first’ by ‘dplyr::first’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::setequal’ by ‘dplyr::setequal’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::rename’ by ‘dplyr::rename’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::tail’ by ‘utils::tail’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::stack’ by ‘utils::stack’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::head’ by ‘utils::head’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::complete.cases’ by ‘stats::complete.cases’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::sd’ by ‘stats::sd’ when loading ‘PAST’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘S4Vectors::union’ by ‘dplyr::union’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::intersect’ by ‘dplyr::intersect’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::setdiff’ by ‘dplyr::setdiff’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::first’ by ‘dplyr::first’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::setequal’ by ‘dplyr::setequal’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::rename’ by ‘dplyr::rename’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::tail’ by ‘utils::tail’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::stack’ by ‘utils::stack’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::head’ by ‘utils::head’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::complete.cases’ by ‘stats::complete.cases’ when loading ‘PAST’
Warning: replacing previous import ‘S4Vectors::sd’ by ‘stats::sd’ when loading ‘PAST’
** testing if installed package keeps a record of temporary installation path
* DONE (PAST)