##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:seqTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings seqTools_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/seqTools.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 ‘seqTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqTools’ version ‘1.26.0’
* 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 ‘seqTools’ can be installed ... OK
* 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘kmerSvd’
Undocumented S4 methods:
  generic 'kmerSvd' and siglist 'Fastqq'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/seqTools/extdata’, resetting
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
  Running ‘test_seqTools.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: 2 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/seqTools.Rcheck/00check.log’
for details.