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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:seqTools.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings seqTools_1.33.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/seqTools.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
    GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘seqTools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqTools’ version ‘1.33.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘seqTools’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’
* 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 loading without being on the library search path ... 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 ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.17-bioc/R/site-library/seqTools/libs/seqTools.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:
  Warning: working directory was changed to ‘/home/biocbuild/bbs-3.17-bioc/R/site-library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/home/biocbuild/bbs-3.17-bioc/R/site-library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/home/biocbuild/bbs-3.17-bioc/R/site-library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/home/biocbuild/bbs-3.17-bioc/R/site-library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/home/biocbuild/bbs-3.17-bioc/R/site-library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/home/biocbuild/bbs-3.17-bioc/R/site-library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/home/biocbuild/bbs-3.17-bioc/R/site-library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/home/biocbuild/bbs-3.17-bioc/R/site-library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/home/biocbuild/bbs-3.17-bioc/R/site-library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/home/biocbuild/bbs-3.17-bioc/R/site-library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/home/biocbuild/bbs-3.17-bioc/R/site-library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/home/biocbuild/bbs-3.17-bioc/R/site-library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/home/biocbuild/bbs-3.17-bioc/R/site-library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/home/biocbuild/bbs-3.17-bioc/R/site-library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/home/biocbuild/bbs-3.17-bioc/R/site-library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/home/biocbuild/bbs-3.17-bioc/R/site-library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/home/biocbuild/bbs-3.17-bioc/R/site-library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/home/biocbuild/bbs-3.17-bioc/R/site-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 ...
  ‘seqTools.Rnw’ using ‘UTF-8’... OK
  ‘seqTools_qual_report.Rnw’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/seqTools.Rcheck/00check.log’
for details.