Thomas Carroll
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/Rfastp |
| git_branch: RELEASE_3_17 |
| git_last_commit: 90045b6 |
| git_last_commit_date: 2023-04-25 11:22:10 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:10 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 1696/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rfastp 1.10.0 (landing page) Thomas Carroll
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the Rfastp package: - 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: 1.10.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rfastp.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rfastp_1.10.0.tar.gz |
| StartedAt: 2023-10-18 18:38:07 -0400 (Wed, 18 Oct 2023) |
| EndedAt: 2023-10-18 18:39:16 -0400 (Wed, 18 Oct 2023) |
| EllapsedTime: 68.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Rfastp.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rfastp.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rfastp_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/Rfastp.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rfastp/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rfastp’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rfastp’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 ... WARNING
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rfastp/libs/Rfastp.so’:
Found ‘_sprintf’, possibly from ‘sprintf’ (C)
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 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: 1 WARNING, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/Rfastp.Rcheck/00check.log’
for details.
Rfastp.Rcheck/00install.out
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###
### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rfastp
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘Rfastp’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/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]
time_t t1 = time(NULL);
^
main_fastp.cpp:366:12: warning: unused variable 't2' [-Wunused-variable]
time_t t2 = time(NULL);
^
main_fastp.cpp:291:10: warning: unused variable 'supportEvaluation' [-Wunused-variable]
bool supportEvaluation = true;
^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/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]
bool trimmed = AdapterTrimmer::trimBySequence(&r, NULL, adapter);
^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/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++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/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++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/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]
bool reachedEOF = false;
^
FASTP/evaluator.cpp:74:10: warning: variable 'reachedEOF' set but not used [-Wunused-but-set-variable]
bool reachedEOF = false;
^
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();
^
6 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/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++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FASTP/fastqreader.cpp -o FASTP/fastqreader.o
FASTP/fastqreader.cpp:98:9: warning: unused variable 'copied' [-Wunused-variable]
int copied = 0;
^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/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++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/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++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FASTP/htmlreporter.cpp -o FASTP/htmlreporter.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/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++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/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]
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];
^~~~~
5 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/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++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/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++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FASTP/peprocessor.cpp -o FASTP/peprocessor.o
FASTP/peprocessor.cpp:228:13: warning: unused variable 'dupMeanTlen' [-Wunused-variable]
double* dupMeanTlen = NULL;
^
FASTP/peprocessor.cpp:126:9: warning: unused variable 'cycle' [-Wunused-variable]
int cycle = 151;
^
FASTP/peprocessor.cpp:348:13: warning: unused variable 'nBaseNum2' [-Wunused-variable]
int nBaseNum2 = 0;
^
FASTP/peprocessor.cpp:347:13: warning: unused variable 'lowQualNum2' [-Wunused-variable]
int lowQualNum2 = 0;
^
FASTP/peprocessor.cpp:346:13: warning: unused variable 'nBaseNum1' [-Wunused-variable]
int nBaseNum1 = 0;
^
FASTP/peprocessor.cpp:345:13: warning: unused variable 'lowQualNum1' [-Wunused-variable]
int lowQualNum1 = 0;
^
FASTP/peprocessor.cpp:718:10: warning: unused variable 'splitSizeReEvaluated' [-Wunused-variable]
bool splitSizeReEvaluated = false;
^
7 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/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++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/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++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/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++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FASTP/seprocessor.cpp -o FASTP/seprocessor.o
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;
^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/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++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/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]
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];
^~
13 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/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++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/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++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/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++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/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++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FASTP/writerthread.cpp -o FASTP/writerthread.o
/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++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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/4.3-arm64/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/4.3-arm64/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)
Rfastp.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)
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
1.757 0.270 2.668
Rfastp.Rcheck/Rfastp-Ex.timings
| name | user | system | elapsed | |
| catfastq | 0.011 | 0.024 | 0.044 | |
| curvePlot | 0.948 | 0.114 | 1.356 | |
| qcSummary | 0.391 | 0.073 | 0.565 | |
| rfastp | 0.682 | 0.260 | 1.146 | |
| trimSummary | 0.178 | 0.054 | 0.255 | |