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This page was generated on 2024-03-28 11:37:55 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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 1077/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
kebabs 1.37.1  (landing page)
Ulrich Bodenhofer
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/kebabs
git_branch: devel
git_last_commit: 4d20ee5
git_last_commit_date: 2024-02-15 09:41:16 -0400 (Thu, 15 Feb 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

BUILD BIN results for kebabs on palomino3


To the developers/maintainers of the kebabs package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/kebabs.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: kebabs
Version: 1.37.1
Command: rm -rf kebabs.buildbin-libdir && mkdir kebabs.buildbin-libdir && F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL --build --library=kebabs.buildbin-libdir kebabs_1.37.1.tar.gz
StartedAt: 2024-03-28 08:53:51 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 08:56:40 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 169.9 seconds
RetCode: 0
Status:   OK  
PackageFile: kebabs_1.37.1.zip
PackageFileSize: 3.945 MiB

Command output

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### Running command:
###
###   rm -rf kebabs.buildbin-libdir && mkdir kebabs.buildbin-libdir && F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL --build --library=kebabs.buildbin-libdir kebabs_1.37.1.tar.gz
###
##############################################################################
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* installing *source* package 'kebabs' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.19-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.19-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ByteStringVector.c -o ByteStringVector.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.19-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ExplicitRepC.cpp -o ExplicitRepC.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.19-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.19-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c GappyPairC.cpp -o GappyPairC.o
GappyPairC.cpp: In function 'SEXPREC* gappyPairKernelMatrixC(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
GappyPairC.cpp:3480:33: warning: 'y.ByteStringVector::nchar' may be used uninitialized [-Wmaybe-uninitialized]
 3480 |                 getKMStdAnnGappy(maxUIndex8, km, x, y, sizeX, sizeY, selX, selY, annCharset, annX, annY,
      |                 ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3481 |                                  k, m, normalized, symmetric, presence, reverseComplement,
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3482 |                                  maxSeqLength, dimFeatureSpace, &alphaInf);
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GappyPairC.cpp:3409:25: note: 'y.ByteStringVector::nchar' was declared here
 3409 |     ByteStringVector x, y, annX, annY, annCharset;
      |                         ^
GappyPairC.cpp:3480:33: warning: 'y.ByteStringVector::ptr' may be used uninitialized [-Wmaybe-uninitialized]
 3480 |                 getKMStdAnnGappy(maxUIndex8, km, x, y, sizeX, sizeY, selX, selY, annCharset, annX, annY,
      |                 ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3481 |                                  k, m, normalized, symmetric, presence, reverseComplement,
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3482 |                                  maxSeqLength, dimFeatureSpace, &alphaInf);
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GappyPairC.cpp:3409:25: note: 'y.ByteStringVector::ptr' was declared here
 3409 |     ByteStringVector x, y, annX, annY, annCharset;
      |                         ^
GappyPairC.cpp:3480:33: warning: 'annY.ByteStringVector::ptr' may be used uninitialized [-Wmaybe-uninitialized]
 3480 |                 getKMStdAnnGappy(maxUIndex8, km, x, y, sizeX, sizeY, selX, selY, annCharset, annX, annY,
      |                 ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3481 |                                  k, m, normalized, symmetric, presence, reverseComplement,
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3482 |                                  maxSeqLength, dimFeatureSpace, &alphaInf);
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GappyPairC.cpp:3409:34: note: 'annY.ByteStringVector::ptr' was declared here
 3409 |     ByteStringVector x, y, annX, annY, annCharset;
      |                                  ^~~~
GappyPairC.cpp:3480:33: warning: 'annX.ByteStringVector::ptr' may be used uninitialized [-Wmaybe-uninitialized]
 3480 |                 getKMStdAnnGappy(maxUIndex8, km, x, y, sizeX, sizeY, selX, selY, annCharset, annX, annY,
      |                 ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3481 |                                  k, m, normalized, symmetric, presence, reverseComplement,
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3482 |                                  maxSeqLength, dimFeatureSpace, &alphaInf);
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GappyPairC.cpp:3409:28: note: 'annX.ByteStringVector::ptr' was declared here
 3409 |     ByteStringVector x, y, annX, annY, annCharset;
      |                            ^~~~
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.19-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c IRanges_stubs.c -o IRanges_stubs.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.19-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c KernelUtils.cpp -o KernelUtils.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.19-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MismatchC.cpp -o MismatchC.o
MismatchC.cpp: In function 'SEXPREC* getMismatchKernelMatrix(Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, bool, int, bool, bool, int, int, bool, bool, int, alphaInfo*)':
MismatchC.cpp:432:41: warning: 'currValSqrt' may be used uninitialized [-Wmaybe-uninitialized]
  432 |                     km(i,j) = kernelVal / currValSqrt;
      |                               ~~~~~~~~~~^~~~~~~~~~~~~
MismatchC.cpp:368:32: note: 'currValSqrt' was declared here
  368 |     double kernelVal, currVal, currValSqrt;
      |                                ^~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.19-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c MotifC.cpp -o MotifC.o
MotifC.cpp: In function 'void genPredProfileMotif(Rcpp::NumericMatrix, ByteStringVector, Rcpp::IntegerVector, int, ByteStringVector, ByteStringVector, int, bool, int, int, int, int, Rcpp::NumericMatrix, int, ByteStringVector, Rcpp::IntegerVector*, int, int, ByteStringVector, Rcpp::IntegerVector*, int, int, int, bool, bool, bool)':
MotifC.cpp:3677:18: warning: 'keyPool' may be used uninitialized [-Wmaybe-uninitialized]
 3677 |         pKeypool = keyPool;
      |         ~~~~~~~~~^~~~~~~~~
MotifC.cpp:3514:11: note: 'keyPool' was declared here
 3514 |     char *keyPool;
      |           ^~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.19-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c PredictionC.cpp -o PredictionC.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.19-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c PredictionProfileC.cpp -o PredictionProfileC.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.19-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_init_kebabs.cpp -o R_init_kebabs.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.19-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Rsvm.c -o Rsvm.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.19-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c SparseMatrixHash.cpp -o SparseMatrixHash.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.19-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c SpectrumC.cpp -o SpectrumC.o
In function 'void getKMStdAnnSpec(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, ByteStringVector, ByteStringVector, ByteStringVector, int, bool, bool, bool, bool, int, uint64_t, alphaInfo*) [with T = unsigned char]',
    inlined from 'SEXPREC* spectrumKernelMatrixC(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)' at SpectrumC.cpp:3228:32:
SpectrumC.cpp:832:38: warning: 'y.ByteStringVector::nchar' may be used uninitialized [-Wmaybe-uninitialized]
  832 |                 seqnchar = y.nchar[iY];
      |                            ~~~~~~~~~~^
SpectrumC.cpp: In function 'SEXPREC* spectrumKernelMatrixC(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
SpectrumC.cpp:3158:25: note: 'y.ByteStringVector::nchar' was declared here
 3158 |     ByteStringVector x, y, annX, annY, annCharset;
      |                         ^
In function 'void getKMStdAnnSpec(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, ByteStringVector, ByteStringVector, ByteStringVector, int, bool, bool, bool, bool, int, uint64_t, alphaInfo*) [with T = unsigned char]',
    inlined from 'SEXPREC* spectrumKernelMatrixC(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)' at SpectrumC.cpp:3228:32:
SpectrumC.cpp:831:34: warning: 'y.ByteStringVector::ptr' may be used uninitialized [-Wmaybe-uninitialized]
  831 |                 seqptr = y.ptr[iY];
      |                          ~~~~~~~~^
SpectrumC.cpp: In function 'SEXPREC* spectrumKernelMatrixC(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
SpectrumC.cpp:3158:25: note: 'y.ByteStringVector::ptr' was declared here
 3158 |     ByteStringVector x, y, annX, annY, annCharset;
      |                         ^
SpectrumC.cpp:3246:32: warning: 'annY.ByteStringVector::ptr' may be used uninitialized [-Wmaybe-uninitialized]
 3246 |                 getKMStdAnnSpec(maxUIndex16, km, x, y, sizeX, sizeY, selX, selY, annCharset, annX, annY,
      |                 ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3247 |                                 k, normalized, symmetric, presence, reverseComplement, maxSeqLength,
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3248 |                                 dimFeatureSpace, &alphaInf);
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
SpectrumC.cpp:3158:34: note: 'annY.ByteStringVector::ptr' was declared here
 3158 |     ByteStringVector x, y, annX, annY, annCharset;
      |                                  ^~~~
SpectrumC.cpp:3246:32: warning: 'annX.ByteStringVector::ptr' may be used uninitialized [-Wmaybe-uninitialized]
 3246 |                 getKMStdAnnSpec(maxUIndex16, km, x, y, sizeX, sizeY, selX, selY, annCharset, annX, annY,
      |                 ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3247 |                                 k, normalized, symmetric, presence, reverseComplement, maxSeqLength,
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3248 |                                 dimFeatureSpace, &alphaInf);
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
SpectrumC.cpp:3158:28: note: 'annX.ByteStringVector::ptr' was declared here
 3158 |     ByteStringVector x, y, annX, annY, annCharset;
      |                            ^~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.19-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c SymmetricPairC.cpp -o SymmetricPairC.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.19-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Utils.cpp -o Utils.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.19-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c XVector_stubs.c -o XVector_stubs.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'F:/biocbuild/bbs-3.19-bioc/R/library/IRanges/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/XVector/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Biostrings/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/S4Vectors/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c svm.cpp -o svm.o
g++ -std=gnu++17 -shared -s -static-libgcc -o kebabs.dll tmp.def Biostrings_stubs.o ByteStringVector.o ExplicitRepC.o FeatureWeightsPosDepC.o GappyPairC.o IRanges_stubs.o KernelUtils.o MismatchC.o MotifC.o PredictionC.o PredictionProfileC.o R_init_kebabs.o Rsvm.o SparseMatrixHash.o SpectrumC.o SymmetricPairC.o Utils.o XVector_stubs.o svm.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc/meat/kebabs.buildbin-libdir/00LOCK-kebabs/00new/kebabs/libs/x64
** R
** data
** 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
* MD5 sums
packaged installation of 'kebabs' as kebabs_1.37.1.zip
* DONE (kebabs)