Thomas Carroll
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/Rfastp |
| git_branch: RELEASE_3_14 |
| git_last_commit: 81990f1 |
| git_last_commit_date: 2021-10-26 13:02:08 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:08:39 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 | ||||
|
To the developers/maintainers of the Rfastp package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1586/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rfastp 1.4.0 (landing page) Thomas Carroll
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: Rfastp |
| Version: 1.4.0 |
| Command: rm -rf Rfastp.buildbin-libdir && mkdir Rfastp.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rfastp_1.4.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Rfastp.buildbin-libdir |
| StartedAt: 2022-04-12 21:20:20 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 21:23:35 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 194.6 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: Rfastp_1.4.0.tgz |
| PackageFileSize: 2.784 MiB |
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###
### Running command:
###
### rm -rf Rfastp.buildbin-libdir && mkdir Rfastp.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rfastp_1.4.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Rfastp.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rfastp.buildbin-libdir Rfastp_1.4.0.tar.gz'
>>>>>>>
* installing *source* package ‘Rfastp’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -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:291:10: warning: unused variable 'supportEvaluation' [-Wunused-variable]
bool supportEvaluation = true;
^
main_fastp.cpp:366:12: warning: unused variable 't2' [-Wunused-variable]
time_t t2 = time(NULL);
^
3 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FASTP/adaptertrimmer.cpp -o FASTP/adaptertrimmer.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FASTP/basecorrector.cpp -o FASTP/basecorrector.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FASTP/duplicate.cpp -o FASTP/duplicate.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FASTP/evaluator.cpp -o FASTP/evaluator.o
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();
^
4 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FASTP/fastareader.cpp -o FASTP/fastareader.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -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++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FASTP/filter.cpp -o FASTP/filter.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FASTP/filterresult.cpp -o FASTP/filterresult.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FASTP/htmlreporter.cpp -o FASTP/htmlreporter.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FASTP/jsonreporter.cpp -o FASTP/jsonreporter.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -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++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FASTP/options.cpp -o FASTP/options.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FASTP/overlapanalysis.cpp -o FASTP/overlapanalysis.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -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:347:13: warning: unused variable 'lowQualNum2' [-Wunused-variable]
int lowQualNum2 = 0;
^
FASTP/peprocessor.cpp:345:13: warning: unused variable 'lowQualNum1' [-Wunused-variable]
int lowQualNum1 = 0;
^
FASTP/peprocessor.cpp:348:13: warning: unused variable 'nBaseNum2' [-Wunused-variable]
int nBaseNum2 = 0;
^
FASTP/peprocessor.cpp:346:13: warning: unused variable 'nBaseNum1' [-Wunused-variable]
int nBaseNum1 = 0;
^
FASTP/peprocessor.cpp:718:10: warning: unused variable 'splitSizeReEvaluated' [-Wunused-variable]
bool splitSizeReEvaluated = false;
^
7 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FASTP/polyx.cpp -o FASTP/polyx.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FASTP/processor.cpp -o FASTP/processor.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FASTP/read.cpp -o FASTP/read.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -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++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FASTP/sequence.cpp -o FASTP/sequence.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -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++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FASTP/threadconfig.cpp -o FASTP/threadconfig.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FASTP/umiprocessor.cpp -o FASTP/umiprocessor.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FASTP/unittest.cpp -o FASTP/unittest.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -Wall -g -O2 -c FASTP/writer.cpp -o FASTP/writer.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I. -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/zlibbioc/include' -I/usr/local/include -fPIC -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++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Rfastp.so ./RcppExports.o ./main_fastp.o ./FASTP/adaptertrimmer.o ./FASTP/basecorrector.o ./FASTP/duplicate.o ./FASTP/evaluator.o ./FASTP/fastareader.o ./FASTP/fastqreader.o ./FASTP/filter.o ./FASTP/filterresult.o ./FASTP/htmlreporter.o ./FASTP/jsonreporter.o ./FASTP/nucleotidetree.o ./FASTP/options.o ./FASTP/overlapanalysis.o ./FASTP/peprocessor.o ./FASTP/polyx.o ./FASTP/processor.o ./FASTP/read.o ./FASTP/seprocessor.o ./FASTP/sequence.o ./FASTP/stats.o ./FASTP/threadconfig.o ./FASTP/umiprocessor.o ./FASTP/unittest.o ./FASTP/writer.o ./FASTP/writerthread.o /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.14-bioc/meat/Rfastp.buildbin-libdir/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)
>>>>>>>
>>>>>>> FIXING LINKS FOR Rfastp.buildbin-libdir/Rfastp/libs/Rfastp.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgcc_s.1.dylib" "Rfastp.buildbin-libdir/Rfastp/libs/Rfastp.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgfortran.5.dylib" "Rfastp.buildbin-libdir/Rfastp/libs/Rfastp.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libquadmath.0.dylib" "Rfastp.buildbin-libdir/Rfastp/libs/Rfastp.so"