Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1696/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Rfastp 1.15.0 (landing page) Thomas Carroll
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the Rfastp package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rfastp.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: Rfastp |
Version: 1.15.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Rfastp.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Rfastp_1.15.0.tar.gz |
StartedAt: 2024-06-10 08:14:19 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 08:19:01 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 282.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Rfastp.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Rfastp.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings Rfastp_1.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/Rfastp.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 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 'Rfastp/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'Rfastp' version '1.15.0' * 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 whether package 'Rfastp' can be installed ... OK * used C++ compiler: 'G__~1.EXE (GCC) 13.2.0' * 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 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 whether startup messages can be suppressed ... 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 for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/Rfastp/libs/x64/Rfastp.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: 3 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/Rfastp.Rcheck/00check.log' for details.
Rfastp.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL Rfastp ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'Rfastp' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/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++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c main_fastp.cpp -o main_fastp.o In file included from main_fastp.cpp:9: FASTP/util.h: In function 'std::string reverse(const std::string&)': FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 115 | for(int pos=0; pos<str.length(); pos++) { | ~~~^~~~~~~~~~~~~ main_fastp.cpp: In function 'int runFastp(std::string, std::string, std::string, std::string, std::string, bool, std::string, bool, bool, bool, bool, std::string, std::string, std::string, int, int, int, int, int, int, bool, bool, int, bool, int, bool, bool, bool, int, int, int, int, int, int, int, int, bool, int, int, int, int, bool, int, int, bool, int, std::string, std::string, int, bool, int, int, int, bool, bool, std::string, int, std::string, int, bool, int, int, int, int, bool)': main_fastp.cpp:289:12: warning: unused variable 't1' [-Wunused-variable] 289 | time_t t1 = time(NULL); | ^~ main_fastp.cpp:291:10: warning: unused variable 'supportEvaluation' [-Wunused-variable] 291 | bool supportEvaluation = true; | ^~~~~~~~~~~~~~~~~ main_fastp.cpp:366:12: warning: unused variable 't2' [-Wunused-variable] 366 | time_t t2 = time(NULL); | ^~ In file included from FASTP/fastqreader.h:12, from main_fastp.cpp:4: FASTP/common.h: At global scope: FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable] 57 | const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = { | ^~~~~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FASTP/adaptertrimmer.cpp -o FASTP/adaptertrimmer.o FASTP/adaptertrimmer.cpp: In static member function 'static bool AdapterTrimmer::trimByMultiSequences(Read*, FilterResult*, std::vector<std::__cxx11::basic_string<char> >&, bool, bool)': FASTP/adaptertrimmer.cpp:58:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 58 | for(int i=0; i<adapterList.size(); i++) { | ~^~~~~~~~~~~~~~~~~~~ FASTP/adaptertrimmer.cpp: In static member function 'static bool AdapterTrimmer::test()': FASTP/adaptertrimmer.cpp:145:10: warning: variable 'trimmed' set but not used [-Wunused-but-set-variable] 145 | bool trimmed = AdapterTrimmer::trimBySequence(&r, NULL, adapter); | ^~~~~~~ In file included from FASTP/overlapanalysis.h:9, from FASTP/adaptertrimmer.h:7, from FASTP/adaptertrimmer.cpp:1: FASTP/common.h: At global scope: FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable] 57 | const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = { | ^~~~~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FASTP/basecorrector.cpp -o FASTP/basecorrector.o In file included from FASTP/basecorrector.cpp:2: FASTP/util.h: In function 'std::string reverse(const std::string&)': FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 115 | for(int pos=0; pos<str.length(); pos++) { | ~~~^~~~~~~~~~~~~ In file included from FASTP/overlapanalysis.h:9, from FASTP/basecorrector.h:7, from FASTP/basecorrector.cpp:1: FASTP/common.h: At global scope: FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable] 57 | const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = { | ^~~~~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FASTP/duplicate.cpp -o FASTP/duplicate.o In file included from FASTP/duplicate.h:9, from FASTP/duplicate.cpp:1: FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable] 57 | const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = { | ^~~~~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FASTP/evaluator.cpp -o FASTP/evaluator.o In file included from FASTP/evaluator.h:8, from FASTP/evaluator.cpp:1: FASTP/util.h: In function 'std::string reverse(const std::string&)': FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 115 | for(int pos=0; pos<str.length(); pos++) { | ~~~^~~~~~~~~~~~~ FASTP/evaluator.cpp: In member function 'int Evaluator::computeSeqLen(std::string)': FASTP/evaluator.cpp:46:10: warning: variable 'reachedEOF' set but not used [-Wunused-but-set-variable] 46 | bool reachedEOF = false; | ^~~~~~~~~~ FASTP/evaluator.cpp: In member function 'void Evaluator::computeOverRepSeq(std::string, std::map<std::__cxx11::basic_string<char>, long int>&, int)': FASTP/evaluator.cpp:108:25: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 108 | if(seq.length() >= seqlen-1) { | ~~~~~~~~~~~~~^~~~~~~~~~~ FASTP/evaluator.cpp:74:10: warning: variable 'reachedEOF' set but not used [-Wunused-but-set-variable] 74 | bool reachedEOF = false; | ^~~~~~~~~~ FASTP/evaluator.cpp: In member function 'std::string Evaluator::evalAdapterAndReadNumDepreciated(long int&)': FASTP/evaluator.cpp:304:22: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 304 | if(counts[i] >= repeatReq) { | ~~~~~~~~~~^~~~~~~~~~~~ FASTP/evaluator.cpp:308:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 308 | for(int s=0; s<seq.length() - 1; s++) { | ~^~~~~~~~~~~~~~~~~ FASTP/evaluator.cpp:336:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 336 | for(int i=0; i<needToDelete.size(); i++) { | ~^~~~~~~~~~~~~~~~~~~~ FASTP/evaluator.cpp:389:25: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 389 | if(iter->second > largest) { | ~~~~~~~~~~~~~^~~~~~~~~ FASTP/evaluator.cpp: In member function 'std::string Evaluator::evalAdapterAndReadNum(long int&, bool)': FASTP/evaluator.cpp:479:21: warning: unused variable 'data' [-Wunused-variable] 479 | const char* data = r->mSeq.mStr.c_str(); | ^~~~ FASTP/evaluator.cpp:549:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 549 | for(int s=0; s<seq.length() - 1; s++) { | ~^~~~~~~~~~~~~~~~~ FASTP/evaluator.cpp: In member function 'std::string Evaluator::getAdapterWithSeed(int, Read**, long int, int)': FASTP/evaluator.cpp:585:21: warning: unused variable 'data' [-Wunused-variable] 585 | const char* data = r->mSeq.mStr.c_str(); | ^~~~ FASTP/evaluator.cpp:601:21: warning: unused variable 'data' [-Wunused-variable] 601 | const char* data = r->mSeq.mStr.c_str(); | ^~~~ FASTP/evaluator.cpp: In static member function 'static std::string Evaluator::matchKnownAdapter(std::string)': FASTP/evaluator.cpp:643:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 643 | for(int i=0; i<adapter.length() && i<seq.length(); i++) { | ~^~~~~~~~~~~~~~~~~ FASTP/evaluator.cpp:643:45: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 643 | for(int i=0; i<adapter.length() && i<seq.length(); i++) { | ~^~~~~~~~~~~~~ FASTP/evaluator.cpp: In member function 'int Evaluator::seq2int(std::string&, int, int, int)': FASTP/evaluator.cpp:666:9: warning: unused variable 'rlen' [-Wunused-variable] 666 | int rlen = seq.length(); | ^~~~ In file included from FASTP/fastqreader.h:12, from FASTP/evaluator.cpp:3: FASTP/common.h: At global scope: FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable] 57 | const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = { | ^~~~~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FASTP/fastareader.cpp -o FASTP/fastareader.o In file included from FASTP/fastareader.cpp:3: FASTP/util.h: In function 'std::string reverse(const std::string&)': FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 115 | for(int pos=0; pos<str.length(); pos++) { | ~~~^~~~~~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FASTP/fastqreader.cpp -o FASTP/fastqreader.o In file included from FASTP/fastqreader.cpp:2: FASTP/util.h: In function 'std::string reverse(const std::string&)': FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 115 | for(int pos=0; pos<str.length(); pos++) { | ~~~^~~~~~~~~~~~~ FASTP/fastqreader.cpp: In member function 'std::string FastqReader::getLine()': FASTP/fastqreader.cpp:98:9: warning: unused variable 'copied' [-Wunused-variable] 98 | int copied = 0; | ^~~~~~ In file included from FASTP/fastqreader.h:12, from FASTP/fastqreader.cpp:1: FASTP/common.h: At global scope: FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable] 57 | const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = { | ^~~~~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FASTP/filter.cpp -o FASTP/filter.o FASTP/filter.cpp: In member function 'bool Filter::match(std::vector<std::__cxx11::basic_string<char> >&, std::string, int)': FASTP/filter.cpp:239:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 239 | for(int i=0; i<list.size(); i++) { | ~^~~~~~~~~~~~ In file included from FASTP/writer.h:11, from FASTP/threadconfig.h:9, from FASTP/peprocessor.h:13, from FASTP/filter.cpp:2: FASTP/common.h: At global scope: FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable] 57 | const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = { | ^~~~~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FASTP/filterresult.cpp -o FASTP/filterresult.o FASTP/filterresult.cpp: In static member function 'static FilterResult* FilterResult::merge(std::vector<FilterResult*>&)': FASTP/filterresult.cpp:43:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<FilterResult*>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 43 | for(int i=0; i<list.size(); i++) { | ~^~~~~~~~~~~~ FASTP/filterresult.cpp:75:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<FilterResult*>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 75 | for(int i=0; i<list.size(); i++) { | ~^~~~~~~~~~~~ In file included from FASTP/filterresult.h:9, from FASTP/filterresult.cpp:3: FASTP/common.h: At global scope: FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable] 57 | const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = { | ^~~~~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FASTP/htmlreporter.cpp -o FASTP/htmlreporter.o In file included from FASTP/filterresult.h:9, from FASTP/htmlreporter.h:10, from FASTP/htmlreporter.cpp:1: FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable] 57 | const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = { | ^~~~~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FASTP/jsonreporter.cpp -o FASTP/jsonreporter.o In file included from FASTP/filterresult.h:9, from FASTP/jsonreporter.h:10, from FASTP/jsonreporter.cpp:1: FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable] 57 | const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = { | ^~~~~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FASTP/nucleotidetree.cpp -o FASTP/nucleotidetree.o FASTP/nucleotidetree.cpp: In member function 'void NucleotideTree::addSeq(std::string)': FASTP/nucleotidetree.cpp:45:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 45 | for(int i=0; i<seq.length(); i++) { | ~^~~~~~~~~~~~~ FASTP/nucleotidetree.cpp:49:30: warning: array subscript has type 'char' [-Wchar-subscripts] 49 | if(curNode->children[base] == NULL) { | ^~~~ FASTP/nucleotidetree.cpp:50:31: warning: array subscript has type 'char' [-Wchar-subscripts] 50 | curNode->children[base] = new NucleotideNode(); | ^~~~ FASTP/nucleotidetree.cpp:51:31: warning: array subscript has type 'char' [-Wchar-subscripts] 51 | curNode->children[base]->base = seq[i]; | ^~~~ FASTP/nucleotidetree.cpp:53:27: warning: array subscript has type 'char' [-Wchar-subscripts] 53 | curNode->children[base]->count++; | ^~~~ FASTP/nucleotidetree.cpp:54:37: warning: array subscript has type 'char' [-Wchar-subscripts] 54 | curNode = curNode->children[base]; | ^~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FASTP/options.cpp -o FASTP/options.o In file included from FASTP/options.cpp:4: FASTP/util.h: In function 'std::string reverse(const std::string&)': FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 115 | for(int pos=0; pos<str.length(); pos++) { | ~~~^~~~~~~~~~~~~ FASTP/options.cpp: In member function 'bool Options::validate()': FASTP/options.cpp:360:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 360 | for(int i=0; i<adapter.sequence.length(); i++) { | ~^~~~~~~~~~~~~~~~~~~~~~~~~~ FASTP/options.cpp:376:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 376 | for(int i=0; i<adapter.sequenceR2.length(); i++) { | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ FASTP/options.cpp:406:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 406 | for(int i=0; i<umi.prefix.length(); i++) { | ~^~~~~~~~~~~~~~~~~~~~ FASTP/options.cpp:417:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 417 | for(int i=0; i<umi.separator.length(); i++) { | ~^~~~~~~~~~~~~~~~~~~~~~~ FASTP/options.cpp: In member function 'std::vector<std::__cxx11::basic_string<char> > Options::makeListFromFileByLine(std::string)': FASTP/options.cpp:486:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 486 | for(int i=0; i<linestr.length(); i++) { | ~^~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FASTP/overlapanalysis.cpp -o FASTP/overlapanalysis.o In file included from FASTP/overlapanalysis.h:9, from FASTP/overlapanalysis.cpp:1: FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable] 57 | const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = { | ^~~~~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FASTP/peprocessor.cpp -o FASTP/peprocessor.o In file included from FASTP/peprocessor.cpp:9: FASTP/util.h: In function 'std::string reverse(const std::string&)': FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 115 | for(int pos=0; pos<str.length(); pos++) { | ~~~^~~~~~~~~~~~~ FASTP/peprocessor.cpp: In member function 'bool PairEndProcessor::process()': FASTP/peprocessor.cpp:126:9: warning: unused variable 'cycle' [-Wunused-variable] 126 | int cycle = 151; | ^~~~~ FASTP/peprocessor.cpp:228:13: warning: unused variable 'dupMeanTlen' [-Wunused-variable] 228 | double* dupMeanTlen = NULL; | ^~~~~~~~~~~ FASTP/peprocessor.cpp: In member function 'bool PairEndProcessor::processPairEnd(ReadPairPack*, ThreadConfig*)': FASTP/peprocessor.cpp:345:13: warning: unused variable 'lowQualNum1' [-Wunused-variable] 345 | int lowQualNum1 = 0; | ^~~~~~~~~~~ FASTP/peprocessor.cpp:346:13: warning: unused variable 'nBaseNum1' [-Wunused-variable] 346 | int nBaseNum1 = 0; | ^~~~~~~~~ FASTP/peprocessor.cpp:347:13: warning: unused variable 'lowQualNum2' [-Wunused-variable] 347 | int lowQualNum2 = 0; | ^~~~~~~~~~~ FASTP/peprocessor.cpp:348:13: warning: unused variable 'nBaseNum2' [-Wunused-variable] 348 | int nBaseNum2 = 0; | ^~~~~~~~~ FASTP/peprocessor.cpp: In member function 'void PairEndProcessor::producerTask()': FASTP/peprocessor.cpp:718:10: warning: unused variable 'splitSizeReEvaluated' [-Wunused-variable] 718 | bool splitSizeReEvaluated = false; | ^~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FASTP/polyx.cpp -o FASTP/polyx.o In file included from FASTP/overlapanalysis.h:9, from FASTP/polyx.h:7, from FASTP/polyx.cpp:1: FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable] 57 | const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = { | ^~~~~~~~~~~~ FASTP/polyx.cpp: In static member function 'static void PolyX::trimPolyX(Read*, FilterResult*, int)': FASTP/polyx.cpp:108:14: warning: 'poly' may be used uninitialized [-Wmaybe-uninitialized] 108 | char polyBase = ATCG_BASES[poly]; | ^~~~~~~~ FASTP/polyx.cpp:100:13: note: 'poly' was declared here 100 | int poly; | ^~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FASTP/processor.cpp -o FASTP/processor.o In file included from FASTP/writer.h:11, from FASTP/threadconfig.h:9, from FASTP/peprocessor.h:13, from FASTP/processor.cpp:2: FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable] 57 | const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = { | ^~~~~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FASTP/read.cpp -o FASTP/read.o In file included from FASTP/read.cpp:4: FASTP/util.h: In function 'std::string reverse(const std::string&)': FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 115 | for(int pos=0; pos<str.length(); pos++) { | ~~~^~~~~~~~~~~~~ FASTP/read.cpp: In member function 'void Read::convertPhred64To33()': FASTP/read.cpp:41:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 41 | for(int i=0; i<mQuality.length(); i++) { | ~^~~~~~~~~~~~~~~~~~ FASTP/read.cpp: In member function 'int Read::lowQualCount(int)': FASTP/read.cpp:120:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 120 | for(int q=0;q<mQuality.size();q++){ | ~^~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FASTP/seprocessor.cpp -o FASTP/seprocessor.o In file included from FASTP/seprocessor.cpp:9: FASTP/util.h: In function 'std::string reverse(const std::string&)': FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 115 | for(int pos=0; pos<str.length(); pos++) { | ~~~^~~~~~~~~~~~~ FASTP/seprocessor.cpp: In member function 'bool SingleEndProcessor::process()': FASTP/seprocessor.cpp:76:9: warning: unused variable 'cycle' [-Wunused-variable] 76 | int cycle = 151; | ^~~~~ FASTP/seprocessor.cpp:142:13: warning: unused variable 'dupMeanTlen' [-Wunused-variable] 142 | double* dupMeanTlen = NULL; | ^~~~~~~~~~~ FASTP/seprocessor.cpp: In member function 'void SingleEndProcessor::producerTask()': FASTP/seprocessor.cpp:388:10: warning: unused variable 'splitSizeReEvaluated' [-Wunused-variable] 388 | bool splitSizeReEvaluated = false; | ^~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FASTP/sequence.cpp -o FASTP/sequence.o FASTP/sequence.cpp: In member function 'Sequence Sequence::reverseComplement()': FASTP/sequence.cpp:21:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 21 | for(int c=0;c<mStr.length();c++){ | ~^~~~~~~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FASTP/stats.cpp -o FASTP/stats.o In file included from FASTP/stats.cpp:5: FASTP/util.h: In function 'std::string reverse(const std::string&)': FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 115 | for(int pos=0; pos<str.length(); pos++) { | ~~~^~~~~~~~~~~~~ FASTP/stats.cpp: In member function 'void Stats::summarize(bool)': FASTP/stats.cpp:187:35: warning: array subscript has type 'char' [-Wchar-subscripts] 187 | if(mCycleBaseContents[b][c] == 0) | ^ FASTP/stats.cpp:190:55: warning: array subscript has type 'char' [-Wchar-subscripts] 190 | qualCurve[c] = (double)mCycleBaseQual[b][c] / (double)mCycleBaseContents[b][c]; | ^ FASTP/stats.cpp:190:90: warning: array subscript has type 'char' [-Wchar-subscripts] 190 | qualCurve[c] = (double)mCycleBaseQual[b][c] / (double)mCycleBaseContents[b][c]; | ^ FASTP/stats.cpp:191:58: warning: array subscript has type 'char' [-Wchar-subscripts] 191 | contentCurve[c] = (double)mCycleBaseContents[b][c] / (double)mCycleTotalBase[c]; | ^ FASTP/stats.cpp:203:57: warning: array subscript has type 'char' [-Wchar-subscripts] 203 | gcContentCurve[c] = (double)(mCycleBaseContents[gBase][c] + mCycleBaseContents[cBase][c]) / (double)mCycleTotalBase[c]; | ^~~~~ FASTP/stats.cpp:203:88: warning: array subscript has type 'char' [-Wchar-subscripts] 203 | gcContentCurve[c] = (double)(mCycleBaseContents[gBase][c] + mCycleBaseContents[cBase][c]) / (double)mCycleTotalBase[c]; | ^~~~~ FASTP/stats.cpp: In member function 'void Stats::statRead(Read*)': FASTP/stats.cpp:249:28: warning: array subscript has type 'char' [-Wchar-subscripts] 249 | mCycleQ30Bases[b][i]++; | ^ FASTP/stats.cpp:250:28: warning: array subscript has type 'char' [-Wchar-subscripts] 250 | mCycleQ20Bases[b][i]++; | ^ FASTP/stats.cpp:252:28: warning: array subscript has type 'char' [-Wchar-subscripts] 252 | mCycleQ20Bases[b][i]++; | ^ FASTP/stats.cpp:255:28: warning: array subscript has type 'char' [-Wchar-subscripts] 255 | mCycleBaseContents[b][i]++; | ^ FASTP/stats.cpp:256:24: warning: array subscript has type 'char' [-Wchar-subscripts] 256 | mCycleBaseQual[b][i] += (qual-33); | ^ FASTP/stats.cpp:313:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 313 | for(int p = i; p < seq.length() + i && p < mEvaluatedSeqLen; p++) { | ~~^~~~~~~~~~~~~~~~~~ FASTP/stats.cpp: In member function 'void Stats::reportHtmlORA(std::ofstream&, std::string, std::string)': FASTP/stats.cpp:551:9: warning: unused variable 'displayed' [-Wunused-variable] 551 | int displayed = 0; | ^~~~~~~~~ FASTP/stats.cpp: In member function 'void Stats::reportHtmlContents(std::ofstream&, std::string, std::string)': FASTP/stats.cpp:850:35: warning: array subscript has type 'char' [-Wchar-subscripts] 850 | count = mBaseContents[b]; | ^ FASTP/stats.cpp: In static member function 'static Stats* Stats::merge(std::vector<Stats*>&)': FASTP/stats.cpp:888:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Stats*>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 888 | for(int t=0; t<list.size(); t++) { | ~^~~~~~~~~~~~ FASTP/stats.cpp:898:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Stats*>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 898 | for(int t=0; t<list.size(); t++) { | ~^~~~~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FASTP/threadconfig.cpp -o FASTP/threadconfig.o In file included from FASTP/threadconfig.cpp:2: FASTP/util.h: In function 'std::string reverse(const std::string&)': FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 115 | for(int pos=0; pos<str.length(); pos++) { | ~~~^~~~~~~~~~~~~ FASTP/threadconfig.cpp: In member function 'void ThreadConfig::initWriterForSplit()': FASTP/threadconfig.cpp:96:26: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 96 | while(num.size() < mOptions->split.digits) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from FASTP/writer.h:11, from FASTP/threadconfig.h:9, from FASTP/threadconfig.cpp:1: FASTP/common.h: At global scope: FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable] 57 | const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = { | ^~~~~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FASTP/umiprocessor.cpp -o FASTP/umiprocessor.o FASTP/umiprocessor.cpp: In member function 'void UmiProcessor::addUmiToName(Read*, std::string)': FASTP/umiprocessor.cpp:70:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 70 | for(int i=0; i<r->mName.length(); i++) { | ~^~~~~~~~~~~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FASTP/unittest.cpp -o FASTP/unittest.o In file included from FASTP/evaluator.h:8, from FASTP/unittest.cpp:12: FASTP/util.h: In function 'std::string reverse(const std::string&)': FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 115 | for(int pos=0; pos<str.length(); pos++) { | ~~~^~~~~~~~~~~~~ In file included from FASTP/fastqreader.h:12, from FASTP/unittest.cpp:4: FASTP/common.h: At global scope: FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable] 57 | const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = { | ^~~~~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FASTP/writer.cpp -o FASTP/writer.o In file included from FASTP/writer.cpp:2: FASTP/util.h: In function 'std::string reverse(const std::string&)': FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 115 | for(int pos=0; pos<str.length(); pos++) { | ~~~^~~~~~~~~~~~~ In file included from FASTP/writer.h:11, from FASTP/writer.cpp:1: FASTP/common.h: At global scope: FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable] 57 | const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = { | ^~~~~~~~~~~~ g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -fpermissive -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/zlibbioc/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FASTP/writerthread.cpp -o FASTP/writerthread.o In file included from FASTP/writerthread.cpp:2: FASTP/util.h: In function 'std::string reverse(const std::string&)': FASTP/util.h:115:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long long unsigned int'} [-Wsign-compare] 115 | for(int pos=0; pos<str.length(); pos++) { | ~~~^~~~~~~~~~~~~ In file included from FASTP/writer.h:11, from FASTP/writerthread.h:8, from FASTP/writerthread.cpp:1: FASTP/common.h: At global scope: FASTP/common.h:57:20: warning: 'FAILED_TYPES' defined but not used [-Wunused-variable] 57 | const static char* FAILED_TYPES[FILTER_RESULT_TYPES] = { | ^~~~~~~~~~~~ /bin/sh: line 1: F:/biocbuild/bbs-3.20-bioc/R/bin/R: No such file or directory /bin/sh: line 1: F:/biocbuild/bbs-3.20-bioc/R/bin/R: No such file or directory /bin/sh: line 1: F:/biocbuild/bbs-3.20-bioc/R/bin/R: No such file or directory /bin/sh: line 1: F:/biocbuild/bbs-3.20-bioc/R/bin/R: No such file or directory g++ -std=gnu++17 -shared -s -static-libgcc -o Rfastp.dll tmp.def ./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 F:/biocbuild/bbs-3.20-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lm -lbz2 -llzma -lcurl -lpsl -lbrotlidec -lbrotlicommon -lbcrypt -lidn2 -lunistring -liconv -lssl -lcrypto -lz -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -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-Rfastp/00new/Rfastp/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 (Rfastp)
Rfastp.Rcheck/tests/testthat.Rout
R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 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(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 1.65 7.12 8.57
Rfastp.Rcheck/Rfastp-Ex.timings
name | user | system | elapsed | |
catfastq | 0.00 | 0.05 | 0.06 | |
curvePlot | 0.74 | 0.20 | 0.92 | |
qcSummary | 0.31 | 0.17 | 0.44 | |
rfastp | 1.14 | 0.67 | 1.60 | |
trimSummary | 0.34 | 0.14 | 0.42 | |