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This page was generated on 2026-03-20 11:34 -0400 (Fri, 20 Mar 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" 4862
kjohnson3macOS 13.7.7 Venturaarm64R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences" 4064
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Package 1785/2368HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rfastp 1.21.3  (landing page)
Wei Wang
Snapshot Date: 2026-03-19 13:40 -0400 (Thu, 19 Mar 2026)
git_url: https://git.bioconductor.org/packages/Rfastp
git_branch: devel
git_last_commit: 8883e2a
git_last_commit_date: 2026-02-11 14:49:19 -0400 (Wed, 11 Feb 2026)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    WARNINGS    ERROR  
See other builds for Rfastp in R Universe.

INSTALL results for Rfastp on kjohnson3

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.

raw results


Summary

Package: Rfastp
Version: 1.21.3
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rfastp
StartedAt: 2026-03-19 15:03:55 -0400 (Thu, 19 Mar 2026)
EndedAt: 2026-03-19 15:04:23 -0400 (Thu, 19 Mar 2026)
EllapsedTime: 28.4 seconds
RetCode: 0
Status:   OK  

Command output

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘Rfastp’ ...
** this is package ‘Rfastp’ version ‘1.21.3’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 16.0.0 (clang-1600.0.26.6)’
using SDK: ‘MacOSX14.5.sdk’
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c main_fastp.cpp -o main_fastp.o
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);
      |            ^~
3 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FASTP/adaptertrimmer.cpp -o FASTP/adaptertrimmer.o
FASTP/adaptertrimmer.cpp:145:10: warning: variable 'trimmed' set but not used [-Wunused-but-set-variable]
  145 |     bool trimmed = AdapterTrimmer::trimBySequence(&r, NULL, adapter);
      |          ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FASTP/basecorrector.cpp -o FASTP/basecorrector.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FASTP/duplicate.cpp -o FASTP/duplicate.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FASTP/evaluator.cpp -o FASTP/evaluator.o
FASTP/evaluator.cpp:46:10: warning: variable 'reachedEOF' set but not used [-Wunused-but-set-variable]
   46 |     bool reachedEOF = false;
      |          ^
FASTP/evaluator.cpp:72:10: warning: variable 'records' set but not used [-Wunused-but-set-variable]
   72 |     long records = 0;
      |          ^
FASTP/evaluator.cpp:74:10: warning: variable 'reachedEOF' set but not used [-Wunused-but-set-variable]
   74 |     bool reachedEOF = false;
      |          ^
FASTP/evaluator.cpp:479:21: warning: unused variable 'data' [-Wunused-variable]
  479 |         const char* data = r->mSeq.mStr.c_str();
      |                     ^~~~
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:666:9: warning: unused variable 'rlen' [-Wunused-variable]
  666 |     int rlen = seq.length();
      |         ^~~~
7 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FASTP/fastareader.cpp -o FASTP/fastareader.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FASTP/fastqreader.cpp -o FASTP/fastqreader.o
FASTP/fastqreader.cpp:96:16: warning: variable 'c' set but not used [-Wunused-but-set-variable]
   96 |     static int c=0;
      |                ^
FASTP/fastqreader.cpp:98:9: warning: unused variable 'copied' [-Wunused-variable]
   98 |     int copied = 0;
      |         ^~~~~~
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FASTP/filter.cpp -o FASTP/filter.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FASTP/filterresult.cpp -o FASTP/filterresult.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FASTP/htmlreporter.cpp -o FASTP/htmlreporter.o
FASTP/htmlreporter.cpp:426:3: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
  426 |   sprintf(date, "%d-%02d-%02d      %02d:%02d:%02d",
      |   ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/stdio.h:180:1: note: 'sprintf' has been explicitly marked deprecated here
  180 | __deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
      | ^
/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro '__deprecated_msg'
  218 |         #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
      |                                                       ^
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FASTP/jsonreporter.cpp -o FASTP/jsonreporter.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FASTP/nucleotidetree.cpp -o FASTP/nucleotidetree.o
FASTP/nucleotidetree.cpp:49:29: warning: array subscript is of type 'char' [-Wchar-subscripts]
   49 |         if(curNode->children[base] == NULL) {
      |                             ^~~~~
FASTP/nucleotidetree.cpp:50:30: warning: array subscript is of type 'char' [-Wchar-subscripts]
   50 |             curNode->children[base] = new NucleotideNode();
      |                              ^~~~~
FASTP/nucleotidetree.cpp:51:30: warning: array subscript is of type 'char' [-Wchar-subscripts]
   51 |             curNode->children[base]->base = seq[i];
      |                              ^~~~~
FASTP/nucleotidetree.cpp:53:26: warning: array subscript is of type 'char' [-Wchar-subscripts]
   53 |         curNode->children[base]->count++;
      |                          ^~~~~
FASTP/nucleotidetree.cpp:54:36: warning: array subscript is of type 'char' [-Wchar-subscripts]
   54 |         curNode = curNode->children[base];
      |                                    ^~~~~
5 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FASTP/options.cpp -o FASTP/options.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FASTP/overlapanalysis.cpp -o FASTP/overlapanalysis.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FASTP/peprocessor.cpp -o FASTP/peprocessor.o
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: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:716:9: warning: variable 'slept' set but not used [-Wunused-but-set-variable]
  716 |     int slept = 0;
      |         ^
FASTP/peprocessor.cpp:718:10: warning: unused variable 'splitSizeReEvaluated' [-Wunused-variable]
  718 |     bool splitSizeReEvaluated = false;
      |          ^~~~~~~~~~~~~~~~~~~~
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FASTP/polyx.cpp -o FASTP/polyx.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FASTP/processor.cpp -o FASTP/processor.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FASTP/read.cpp -o FASTP/read.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FASTP/seprocessor.cpp -o FASTP/seprocessor.o
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:386:9: warning: variable 'slept' set but not used [-Wunused-but-set-variable]
  386 |     int slept = 0;
      |         ^
FASTP/seprocessor.cpp:388:10: warning: unused variable 'splitSizeReEvaluated' [-Wunused-variable]
  388 |     bool splitSizeReEvaluated = false;
      |          ^~~~~~~~~~~~~~~~~~~~
4 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FASTP/sequence.cpp -o FASTP/sequence.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FASTP/stats.cpp -o FASTP/stats.o
FASTP/stats.cpp:187:34: warning: array subscript is of type 'char' [-Wchar-subscripts]
  187 |             if(mCycleBaseContents[b][c] == 0)
      |                                  ^~
FASTP/stats.cpp:190:54: warning: array subscript is of type 'char' [-Wchar-subscripts]
  190 |                 qualCurve[c] = (double)mCycleBaseQual[b][c] / (double)mCycleBaseContents[b][c];
      |                                                      ^~
FASTP/stats.cpp:190:89: warning: array subscript is of type 'char' [-Wchar-subscripts]
  190 |                 qualCurve[c] = (double)mCycleBaseQual[b][c] / (double)mCycleBaseContents[b][c];
      |                                                                                         ^~
FASTP/stats.cpp:191:57: warning: array subscript is of type 'char' [-Wchar-subscripts]
  191 |             contentCurve[c] = (double)mCycleBaseContents[b][c] / (double)mCycleTotalBase[c];
      |                                                         ^~
FASTP/stats.cpp:203:56: warning: array subscript is of type 'char' [-Wchar-subscripts]
  203 |         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]
  203 |         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]
  249 |             mCycleQ30Bases[b][i]++;
      |                           ^~
FASTP/stats.cpp:250:27: warning: array subscript is of type 'char' [-Wchar-subscripts]
  250 |             mCycleQ20Bases[b][i]++;
      |                           ^~
FASTP/stats.cpp:252:27: warning: array subscript is of type 'char' [-Wchar-subscripts]
  252 |             mCycleQ20Bases[b][i]++;
      |                           ^~
FASTP/stats.cpp:255:27: warning: array subscript is of type 'char' [-Wchar-subscripts]
  255 |         mCycleBaseContents[b][i]++;
      |                           ^~
FASTP/stats.cpp:256:23: warning: array subscript is of type 'char' [-Wchar-subscripts]
  256 |         mCycleBaseQual[b][i] += (qual-33);
      |                       ^~
FASTP/stats.cpp:551:9: warning: unused variable 'displayed' [-Wunused-variable]
  551 |     int displayed = 0;
      |         ^~~~~~~~~
FASTP/stats.cpp:850:34: warning: array subscript is of type 'char' [-Wchar-subscripts]
  850 |             count = mBaseContents[b];
      |                                  ^~
13 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FASTP/threadconfig.cpp -o FASTP/threadconfig.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FASTP/umiprocessor.cpp -o FASTP/umiprocessor.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FASTP/unittest.cpp -o FASTP/unittest.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FASTP/writer.cpp -o FASTP/writer.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c FASTP/writerthread.cpp -o FASTP/writerthread.o
clang++ -arch arm64 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/4.6/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6/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)