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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:qckitfastq.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings qckitfastq_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/qckitfastq.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘qckitfastq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘qckitfastq’ version ‘1.20.0’
* 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: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
run_all 11.27  1.602  16.466
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/qckitfastq.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL qckitfastq
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘qckitfastq’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++14
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RSeqAn/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RSeqAn/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c calc_adapter_content.cpp -o calc_adapter_content.o
In file included from calc_adapter_content.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RSeqAn/include/seqan/find.h:44:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RSeqAn/include/seqan/modifier.h:48:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RSeqAn/include/seqan/parallel.h:92:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RSeqAn/include/seqan/parallel/parallel_resource_pool.h:69:18: warning: variable 'count' set but not used [-Wunused-but-set-variable]
        unsigned count = 0;
                 ^
In file included from calc_adapter_content.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RSeqAn/include/seqan/find.h:45:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RSeqAn/include/seqan/score.h:48:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RSeqAn/include/seqan/score/score_matrix_io.h:125:19: warning: variable 'row' set but not used [-Wunused-but-set-variable]
    for (unsigned row = 0; !atEnd(reader); ++row)
                  ^
In file included from calc_adapter_content.cpp:7:
In file included from /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RSeqAn/include/seqan/find.h:73:
/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RSeqAn/include/seqan/find/find_wild_shiftand.h:160:11: warning: variable 'len' set but not used [-Wunused-but-set-variable]
    TWord len = nl;
          ^
3 warnings generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RSeqAn/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c gzstream.cpp -o gzstream.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RSeqAn/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c read_fastq.cpp -o read_fastq.o
read_fastq.cpp:30:32: warning: unused variable 'it' [-Wunused-variable]
    std::vector<int>::iterator it;
                               ^
read_fastq.cpp:158:36: warning: unused variable 'qual_by_col_it' [-Wunused-variable]
    std::vector<uint8_t>::iterator qual_by_col_it;
                                   ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o qckitfastq.so RcppExports.o calc_adapter_content.o gzstream.o read_fastq.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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) '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz'	done.
[fastq_Klocs] File ( 1/1) '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz' 	done.
[fastqq] File ( 1/1) '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz'	done.
[fastqq] File ( 1/1) '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz'	done.
2024-06-11 02:04:23.737 R[77436:38563831] XType: Using static font registry.
[fastq_Klocs] File ( 1/1) '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz' 	done.
[fastqq] File ( 1/1) '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/qckitfastq/extdata/10^5_reads_test.fq.gz'	done.
[fastq_Klocs] File ( 1/1) '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 
 18.118   2.275  28.265