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This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 1073/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
kebabs 1.41.0  (landing page)
Ulrich Bodenhofer
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/kebabs
git_branch: devel
git_last_commit: 56e9334
git_last_commit_date: 2024-10-29 09:56:18 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows 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
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

INSTALL results for kebabs on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: kebabs
Version: 1.41.0
Command: /home/biocbuild/R/R/bin/R CMD INSTALL kebabs
StartedAt: 2024-12-23 19:36:32 -0000 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 19:39:04 -0000 (Mon, 23 Dec 2024)
EllapsedTime: 152.2 seconds
RetCode: 0
Status:   OK  

Command output

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL kebabs
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘kebabs’ ...
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c Biostrings_stubs.c -o Biostrings_stubs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c ByteStringVector.c -o ByteStringVector.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c ExplicitRepC.cpp -o ExplicitRepC.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c GappyPairC.cpp -o GappyPairC.o
In function ‘void getKMStdAnnGappy(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, ByteStringVector, ByteStringVector, ByteStringVector, int, int, bool, bool, bool, bool, int, uint64_t, alphaInfo*) [with T = unsigned char]’,
    inlined from ‘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)’ at GappyPairC.cpp:3480:33:
GappyPairC.cpp:1157:38: warning: ‘y.ByteStringVector::nchar’ may be used uninitialized [-Wmaybe-uninitialized]
 1157 |                 seqnchar = y.nchar[iY];
      |                            ~~~~~~~~~~^
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:3409:25: note: ‘y.ByteStringVector::nchar’ was declared here
 3409 |     ByteStringVector x, y, annX, annY, annCharset;
      |                         ^
In function ‘void getKMStdAnnGappy(T, Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, ByteStringVector, ByteStringVector, ByteStringVector, int, int, bool, bool, bool, bool, int, uint64_t, alphaInfo*) [with T = unsigned char]’,
    inlined from ‘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)’ at GappyPairC.cpp:3480:33:
GappyPairC.cpp:1156:34: warning: ‘y.ByteStringVector::ptr’ may be used uninitialized [-Wmaybe-uninitialized]
 1156 |                 seqptr = y.ptr[iY];
      |                          ~~~~~~~~^
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:3409:25: note: ‘y.ByteStringVector::ptr’ was declared here
 3409 |     ByteStringVector x, y, annX, annY, annCharset;
      |                         ^
GappyPairC.cpp:3535:33: warning: ‘annY.ByteStringVector::ptr’ may be used uninitialized [-Wmaybe-uninitialized]
 3535 |                 getKMStdAnnGappy(maxUIndex64, km, x, y, sizeX, sizeY, selX, selY, annCharset, annX, annY,
      |                 ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3536 |                                  k, m, normalized, symmetric, presence, reverseComplement,
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3537 |                                  maxSeqLength, dimFeatureSpace, &alphaInf);
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GappyPairC.cpp:3409:34: note: ‘annY.ByteStringVector::ptr’ was declared here
 3409 |     ByteStringVector x, y, annX, annY, annCharset;
      |                                  ^~~~
GappyPairC.cpp:3535:33: warning: ‘annX.ByteStringVector::ptr’ may be used uninitialized [-Wmaybe-uninitialized]
 3535 |                 getKMStdAnnGappy(maxUIndex64, km, x, y, sizeX, sizeY, selX, selY, annCharset, annX, annY,
      |                 ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3536 |                                  k, m, normalized, symmetric, presence, reverseComplement,
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3537 |                                  maxSeqLength, dimFeatureSpace, &alphaInf);
      |                                  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GappyPairC.cpp:3409:28: note: ‘annX.ByteStringVector::ptr’ was declared here
 3409 |     ByteStringVector x, y, annX, annY, annCharset;
      |                            ^~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c IRanges_stubs.c -o IRanges_stubs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c KernelUtils.cpp -o KernelUtils.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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;
      |                                ^~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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;
      |           ^~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c PredictionC.cpp -o PredictionC.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c PredictionProfileC.cpp -o PredictionProfileC.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c R_init_kebabs.cpp -o R_init_kebabs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c Rsvm.c -o Rsvm.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c SparseMatrixHash.cpp -o SparseMatrixHash.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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:3283:32: warning: ‘annY.ByteStringVector::ptr’ may be used uninitialized [-Wmaybe-uninitialized]
 3283 |                 getKMStdAnnSpec(maxUIndex64, km, x, y, sizeX, sizeY, selX, selY, annCharset, annX, annY,
      |                 ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3284 |                                 k, normalized, symmetric, presence, reverseComplement, maxSeqLength,
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3285 |                                 dimFeatureSpace, &alphaInf);
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
SpectrumC.cpp:3158:34: note: ‘annY.ByteStringVector::ptr’ was declared here
 3158 |     ByteStringVector x, y, annX, annY, annCharset;
      |                                  ^~~~
SpectrumC.cpp:3283:32: warning: ‘annX.ByteStringVector::ptr’ may be used uninitialized [-Wmaybe-uninitialized]
 3283 |                 getKMStdAnnSpec(maxUIndex64, km, x, y, sizeX, sizeY, selX, selY, annCharset, annX, annY,
      |                 ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3284 |                                 k, normalized, symmetric, presence, reverseComplement, maxSeqLength,
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 3285 |                                 dimFeatureSpace, &alphaInf);
      |                                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
SpectrumC.cpp:3158:28: note: ‘annX.ByteStringVector::ptr’ was declared here
 3158 |     ByteStringVector x, y, annX, annY, annCharset;
      |                            ^~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c SymmetricPairC.cpp -o SymmetricPairC.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c Utils.cpp -o Utils.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c XVector_stubs.c -o XVector_stubs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -DSTRICT_R_HEADERS -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/IRanges/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/XVector/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Biostrings/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/S4Vectors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c svm.cpp -o svm.o
svm.cpp: In function ‘svm_model* svm_train(const svm_problem*, const svm_parameter*)’:
svm.cpp:42:38: warning: argument 1 range [18446744056529682432, 18446744073709551608] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
   42 | #define Malloc(type,n) (type *)malloc((n)*sizeof(type))
      |                                ~~~~~~^~~~~~~~~~~~~~~~~~
svm.cpp:2382:34: note: in expansion of macro ‘Malloc’
 2382 |                 model->sv_coef = Malloc(double *,nr_class-1);
      |                                  ^~~~~~
In file included from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/cstdlib:79,
                 from /home/biocbuild/R/R/include/R.h:39,
                 from svm.cpp:1:
/usr/include/stdlib.h:672:14: note: in a call to allocation function ‘void* malloc(size_t)’ declared here
  672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__
      |              ^~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o kebabs.so 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 -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-kebabs/00new/kebabs/libs
** 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
** 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 (kebabs)