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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:systemPipeRdata.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings systemPipeRdata_1.22.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-data-experiment/meat/systemPipeRdata.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘systemPipeRdata/DESCRIPTION’ ... OK
* this is package ‘systemPipeRdata’ version ‘1.22.3’
* 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:
  inst/extdata/param/.batchtools.conf.R
  inst/extdata/param/.batchtools.conf.R.sge
  inst/extdata/param/.batchtools.conf.R.torque
  inst/extdata/workflows/new/.batchtools.conf.R
  inst/rmarkdown/templates/systemPipeR_new/skeleton/.batchtools.conf.R
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 ‘systemPipeRdata’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 294.5Mb
  sub-directories of 1Mb or more:
    extdata  294.2Mb
* 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
.subsetAnno: no visible global function definition for ‘%within%’
.subsetAnno: no visible global function definition for ‘reduce’
.subsetAnno: no visible global function definition for ‘mcols’
.subsetAnno: no visible global function definition for ‘seqnames’
.subsetAnno: no visible global function definition for ‘shift’
.subsetRef: no visible global function definition for ‘getSeq’
.subsetRef: no visible global function definition for ‘FaFile’
.subsetRef: no visible global function definition for ‘DNAStringSet’
.subsetRef: no visible global function definition for ‘writeXStringSet’
getSubsetReads: no visible binding for global variable ‘anno’
Undefined global functions or variables:
  %within% DNAStringSet FaFile anno getSeq mcols reduce seqnames shift
  writeXStringSet
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-data-experiment/meat/systemPipeRdata.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL systemPipeRdata
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘systemPipeRdata’ ...
** using staged installation
** R
** 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 (systemPipeRdata)

R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.

> BiocGenerics:::testPackage("systemPipeRdata")


RUNIT TEST PROTOCOL -- Wed Apr 13 11:51:50 2022 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
systemPipeRdata RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  0.274   0.039   0.295