##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:qckitfastq.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings qckitfastq_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/qckitfastq.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘qckitfastq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘qckitfastq’ version ‘1.21.0’
* 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 ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘qckitfastq’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking C++ specification ... NOTE
  Specified C++14: please drop specification unless essential
* 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 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 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 ... 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
run_all 8.402  0.132   8.497
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/qckitfastq.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL qckitfastq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘qckitfastq’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++14
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RSeqAn/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RSeqAn/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c calc_adapter_content.cpp -o calc_adapter_content.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RSeqAn/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c gzstream.cpp -o gzstream.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RSeqAn/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c read_fastq.cpp -o read_fastq.o
read_fastq.cpp: In function ‘Rcpp::List qual_score_per_read(std::string)’:
read_fastq.cpp:181:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map<int, std::vector<unsigned char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  181 |                 if (pos_counter <= qual_score_matrix.size()) {
      |                     ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o qckitfastq.so RcppExports.o calc_adapter_content.o gzstream.o read_fastq.o -lz -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-qckitfastq/00new/qckitfastq/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (qckitfastq)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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(qckitfastq)
> 
> test_check("qckitfastq")
[fastqq] File ( 1/1) '/home/biocbuild/bbs-3.20-bioc/R/site-library/qckitfastq/extdata/10^5_reads_test.fq.gz'	done.
[fastq_Klocs] File ( 1/1) '/home/biocbuild/bbs-3.20-bioc/R/site-library/qckitfastq/extdata/10^5_reads_test.fq.gz' 	done.
[fastqq] File ( 1/1) '/home/biocbuild/bbs-3.20-bioc/R/site-library/qckitfastq/extdata/10^5_reads_test.fq.gz'	done.
[fastqq] File ( 1/1) '/home/biocbuild/bbs-3.20-bioc/R/site-library/qckitfastq/extdata/10^5_reads_test.fq.gz'	done.
[fastq_Klocs] File ( 1/1) '/home/biocbuild/bbs-3.20-bioc/R/site-library/qckitfastq/extdata/10^5_reads_test.fq.gz' 	done.
[fastqq] File ( 1/1) '/home/biocbuild/bbs-3.20-bioc/R/site-library/qckitfastq/extdata/10^5_reads_test.fq.gz'	done.
[fastq_Klocs] File ( 1/1) '/home/biocbuild/bbs-3.20-bioc/R/site-library/qckitfastq/extdata/10^5_reads_test.fq.gz' 	done.
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 37 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 37 ]
> 
> proc.time()
   user  system elapsed 
 13.919   0.343  14.223