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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FastqCleaner.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings FastqCleaner_1.24.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/FastqCleaner.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'FastqCleaner/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'FastqCleaner' version '1.24.0'
* 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 ... NOTE
Found the following non-portable file paths:
  FastqCleaner/inst/application/www/help/docs/articles/Overview_files/figure-html/unnamed-chunk-11-1.png
  FastqCleaner/inst/application/www/help/docs/articles/Overview_files/figure-html/unnamed-chunk-12-1.png
  FastqCleaner/inst/application/www/help/docs/articles/Overview_files/figure-html/unnamed-chunk-13-1.png
  FastqCleaner/inst/application/www/help/docs/articles/Overview_files/figure-html/unnamed-chunk-14-1.png
  FastqCleaner/inst/application/www/help/docs/articles/Overview_files/figure-html/unnamed-chunk-7-1.png
  FastqCleaner/inst/application/www/help/docs/articles/Overview_files/figure-html/unnamed-chunk-8-1.png

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking whether package 'FastqCleaner' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    application   4.2Mb
* 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 code 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 ... 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 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 for x64 is not available
File 'F:/biocbuild/bbs-3.20-bioc/R/library/FastqCleaner/libs/x64/FastqCleaner.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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 ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/FastqCleaner.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL FastqCleaner
###
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* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'FastqCleaner' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
using C++11
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cpp_GC_content.cpp -o cpp_GC_content.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cpp_base_content.cpp -o cpp_base_content.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cpp_check_quality_threshold.cpp -o cpp_check_quality_threshold.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cpp_create_stringvec.cpp -o cpp_create_stringvec.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include/ -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cpp_which_true.cpp -o cpp_which_true.o
g++ -shared -s -static-libgcc -o FastqCleaner.dll tmp.def RcppExports.o cpp_GC_content.o cpp_base_content.o cpp_check_quality_threshold.o cpp_create_stringvec.o cpp_which_true.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-FastqCleaner/00new/FastqCleaner/libs/x64
** 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 (FastqCleaner)

R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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.

> library(testthat)
> library(FastqCleaner)
> 
> test_check("FastqCleaner")
[ FAIL 0 | WARN 0 | SKIP 10 | PASS 0 ]

══ Skipped tests (10) ══════════════════════════════════════════════════════════
• On CRAN (10): 'test-adapter_filter.R:2:1', 'test-complex_filter.R:2:1',
  'test-fixed_filter.R:2:1', 'test-length_filter.R:2:1', 'test-matching.R:2:1',
  'test-n_filter.R:2:1', 'test-qmean_filter.R:2:1', 'test-seq_filter.R:2:1',
  'test-trim3q_filter.R:2:1', 'test-unique_filter.R:2:1'

[ FAIL 0 | WARN 0 | SKIP 10 | PASS 0 ]
> 
> proc.time()
   user  system elapsed 
  10.45    0.56   11.56