##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Rfastp.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Rfastp_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/Rfastp.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rfastp/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rfastp’ version ‘1.0.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .github
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 ‘Rfastp’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 ... 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 shell scripts ... 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 ... NOTE
GNU make is a SystemRequirements.
* 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/Rfastp.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rfastp
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘Rfastp’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c main_fastp.cpp -o main_fastp.o
In file included from main_fastp.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
main_fastp.cpp:291:10: warning: unused variable 'supportEvaluation' [-Wunused-variable]
    bool supportEvaluation = true; 
         ^
main_fastp.cpp:366:12: warning: unused variable 't2' [-Wunused-variable]
    time_t t2 = time(NULL);
           ^
main_fastp.cpp:289:12: warning: unused variable 't1' [-Wunused-variable]
    time_t t1 = time(NULL);
           ^
4 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FASTP/adaptertrimmer.cpp -o FASTP/adaptertrimmer.o
In file included from FASTP/adaptertrimmer.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FASTP/basecorrector.cpp -o FASTP/basecorrector.o
In file included from FASTP/basecorrector.cpp:2:
In file included from FASTP/util.h:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FASTP/duplicate.cpp -o FASTP/duplicate.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FASTP/evaluator.cpp -o FASTP/evaluator.o
In file included from FASTP/evaluator.cpp:1:
In file included from FASTP/evaluator.h:8:
In file included from FASTP/util.h:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
FASTP/evaluator.cpp:479:21: warning: unused variable 'data' [-Wunused-variable]
        const char* data = r->mSeq.mStr.c_str();
                    ^
FASTP/evaluator.cpp:585:21: warning: unused variable 'data' [-Wunused-variable]
        const char* data = r->mSeq.mStr.c_str();
                    ^
FASTP/evaluator.cpp:601:21: warning: unused variable 'data' [-Wunused-variable]
        const char* data = r->mSeq.mStr.c_str();
                    ^
FASTP/evaluator.cpp:666:9: warning: unused variable 'rlen' [-Wunused-variable]
    int rlen = seq.length();
        ^
5 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FASTP/fastareader.cpp -o FASTP/fastareader.o
In file included from FASTP/fastareader.cpp:3:
In file included from FASTP/util.h:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FASTP/fastqreader.cpp -o FASTP/fastqreader.o
In file included from FASTP/fastqreader.cpp:2:
In file included from FASTP/util.h:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
FASTP/fastqreader.cpp:98:9: warning: unused variable 'copied' [-Wunused-variable]
    int copied = 0;
        ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FASTP/filter.cpp -o FASTP/filter.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FASTP/filterresult.cpp -o FASTP/filterresult.o
In file included from FASTP/filterresult.cpp:2:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FASTP/htmlreporter.cpp -o FASTP/htmlreporter.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FASTP/jsonreporter.cpp -o FASTP/jsonreporter.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FASTP/nucleotidetree.cpp -o FASTP/nucleotidetree.o
In file included from FASTP/nucleotidetree.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
FASTP/nucleotidetree.cpp:49:29: warning: array subscript is of type 'char' [-Wchar-subscripts]
        if(curNode->children[base] == NULL) {
                            ^~~~~
FASTP/nucleotidetree.cpp:50:30: warning: array subscript is of type 'char' [-Wchar-subscripts]
            curNode->children[base] = new NucleotideNode();
                             ^~~~~
FASTP/nucleotidetree.cpp:51:30: warning: array subscript is of type 'char' [-Wchar-subscripts]
            curNode->children[base]->base = seq[i];
                             ^~~~~
FASTP/nucleotidetree.cpp:53:26: warning: array subscript is of type 'char' [-Wchar-subscripts]
        curNode->children[base]->count++;
                         ^~~~~
FASTP/nucleotidetree.cpp:54:36: warning: array subscript is of type 'char' [-Wchar-subscripts]
        curNode = curNode->children[base];
                                   ^~~~~
6 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FASTP/options.cpp -o FASTP/options.o
In file included from FASTP/options.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FASTP/overlapanalysis.cpp -o FASTP/overlapanalysis.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FASTP/peprocessor.cpp -o FASTP/peprocessor.o
In file included from FASTP/peprocessor.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
FASTP/peprocessor.cpp:126:9: warning: unused variable 'cycle' [-Wunused-variable]
    int cycle = 151;
        ^
FASTP/peprocessor.cpp:228:13: warning: unused variable 'dupMeanTlen' [-Wunused-variable]
    double* dupMeanTlen = NULL;
            ^
FASTP/peprocessor.cpp:346:13: warning: unused variable 'nBaseNum1' [-Wunused-variable]
        int nBaseNum1 = 0;
            ^
FASTP/peprocessor.cpp:347:13: warning: unused variable 'lowQualNum2' [-Wunused-variable]
        int lowQualNum2 = 0;
            ^
FASTP/peprocessor.cpp:345:13: warning: unused variable 'lowQualNum1' [-Wunused-variable]
        int lowQualNum1 = 0;
            ^
FASTP/peprocessor.cpp:348:13: warning: unused variable 'nBaseNum2' [-Wunused-variable]
        int nBaseNum2 = 0;
            ^
FASTP/peprocessor.cpp:718:10: warning: unused variable 'splitSizeReEvaluated' [-Wunused-variable]
    bool splitSizeReEvaluated = false;
         ^
8 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FASTP/polyx.cpp -o FASTP/polyx.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FASTP/processor.cpp -o FASTP/processor.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FASTP/read.cpp -o FASTP/read.o
In file included from FASTP/read.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FASTP/seprocessor.cpp -o FASTP/seprocessor.o
In file included from FASTP/seprocessor.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
FASTP/seprocessor.cpp:142:13: warning: unused variable 'dupMeanTlen' [-Wunused-variable]
    double* dupMeanTlen = NULL;
            ^
FASTP/seprocessor.cpp:76:9: warning: unused variable 'cycle' [-Wunused-variable]
    int cycle = 151;
        ^
FASTP/seprocessor.cpp:388:10: warning: unused variable 'splitSizeReEvaluated' [-Wunused-variable]
    bool splitSizeReEvaluated = false;
         ^
4 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FASTP/sequence.cpp -o FASTP/sequence.o
In file included from FASTP/sequence.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FASTP/stats.cpp -o FASTP/stats.o
In file included from FASTP/stats.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
FASTP/stats.cpp:187:34: warning: array subscript is of type 'char' [-Wchar-subscripts]
            if(mCycleBaseContents[b][c] == 0)
                                 ^~
FASTP/stats.cpp:190:54: warning: array subscript is of type 'char' [-Wchar-subscripts]
                qualCurve[c] = (double)mCycleBaseQual[b][c] / (double)mCycleBaseContents[b][c];
                                                     ^~
FASTP/stats.cpp:190:89: warning: array subscript is of type 'char' [-Wchar-subscripts]
                qualCurve[c] = (double)mCycleBaseQual[b][c] / (double)mCycleBaseContents[b][c];
                                                                                        ^~
FASTP/stats.cpp:191:57: warning: array subscript is of type 'char' [-Wchar-subscripts]
            contentCurve[c] = (double)mCycleBaseContents[b][c] / (double)mCycleTotalBase[c];
                                                        ^~
FASTP/stats.cpp:203:56: warning: array subscript is of type 'char' [-Wchar-subscripts]
        gcContentCurve[c] = (double)(mCycleBaseContents[gBase][c] + mCycleBaseContents[cBase][c]) / (double)mCycleTotalBase[c];
                                                       ^~~~~~
FASTP/stats.cpp:203:87: warning: array subscript is of type 'char' [-Wchar-subscripts]
        gcContentCurve[c] = (double)(mCycleBaseContents[gBase][c] + mCycleBaseContents[cBase][c]) / (double)mCycleTotalBase[c];
                                                                                      ^~~~~~
FASTP/stats.cpp:249:27: warning: array subscript is of type 'char' [-Wchar-subscripts]
            mCycleQ30Bases[b][i]++;
                          ^~
FASTP/stats.cpp:250:27: warning: array subscript is of type 'char' [-Wchar-subscripts]
            mCycleQ20Bases[b][i]++;
                          ^~
FASTP/stats.cpp:252:27: warning: array subscript is of type 'char' [-Wchar-subscripts]
            mCycleQ20Bases[b][i]++;
                          ^~
FASTP/stats.cpp:255:27: warning: array subscript is of type 'char' [-Wchar-subscripts]
        mCycleBaseContents[b][i]++;
                          ^~
FASTP/stats.cpp:256:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
        mCycleBaseQual[b][i] += (qual-33);
                      ^~
FASTP/stats.cpp:551:9: warning: unused variable 'displayed' [-Wunused-variable]
    int displayed = 0;
        ^
FASTP/stats.cpp:850:34: warning: array subscript is of type 'char' [-Wchar-subscripts]
            count = mBaseContents[b];
                                 ^~
14 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FASTP/threadconfig.cpp -o FASTP/threadconfig.o
In file included from FASTP/threadconfig.cpp:2:
In file included from FASTP/util.h:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FASTP/umiprocessor.cpp -o FASTP/umiprocessor.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FASTP/unittest.cpp -o FASTP/unittest.o
In file included from FASTP/unittest.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FASTP/writer.cpp -o FASTP/writer.o
In file included from FASTP/writer.cpp:2:
In file included from FASTP/util.h:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c FASTP/writerthread.cpp -o FASTP/writerthread.o
In file included from FASTP/writerthread.cpp:2:
In file included from FASTP/util.h:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
/bin/sh:  /Library/Frameworks/R.framework/Resources/bin/R: No such file or directory
/bin/sh:  /Library/Frameworks/R.framework/Resources/bin/R: No such file or directory
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Rfastp.so ./RcppExports.o ./main_fastp.o ./FASTP/adaptertrimmer.o ./FASTP/basecorrector.o ./FASTP/duplicate.o ./FASTP/evaluator.o ./FASTP/fastareader.o ./FASTP/fastqreader.o ./FASTP/filter.o ./FASTP/filterresult.o ./FASTP/htmlreporter.o ./FASTP/jsonreporter.o ./FASTP/nucleotidetree.o ./FASTP/options.o ./FASTP/overlapanalysis.o ./FASTP/peprocessor.o ./FASTP/polyx.o ./FASTP/processor.o ./FASTP/read.o ./FASTP/seprocessor.o ./FASTP/sequence.o ./FASTP/stats.o ./FASTP/threadconfig.o ./FASTP/umiprocessor.o ./FASTP/unittest.o ./FASTP/writer.o ./FASTP/writerthread.o /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-Rfastp/00new/Rfastp/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 (Rfastp)

R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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Type 'license()' or 'licence()' for distribution details.

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> library(testthat)
> library(Rfastp)
Rfastp is a wrapper of fastp project: https://github.com/OpenGene/fastp

Please cite fastp in your publication:
Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu; fastp: an ultra-fast all-in-one 
    FASTQ preprocessor, Bioinformatics, Volume 34, Issue 17, 1 September 2018,
    Pages i884-i890, https://doi.org/10.1093/bioinformatics/bty560
> 
> test_check("Rfastp")
Detecting adapter sequence for read1...
No adapter detected for read1

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
  2.241   0.354   2.509